Updated samtools to 0.1.19
authorBo Li <bli@cs.wisc.edu>
Thu, 9 Jan 2014 00:26:18 +0000 (18:26 -0600)
committerBo Li <bli@cs.wisc.edu>
Thu, 9 Jan 2014 00:26:18 +0000 (18:26 -0600)
221 files changed:
EBSeq/BiocInstaller/DESCRIPTION [new file with mode: 0644]
EBSeq/BiocInstaller/INDEX [new file with mode: 0644]
EBSeq/BiocInstaller/Meta/Rd.rds [new file with mode: 0644]
EBSeq/BiocInstaller/Meta/hsearch.rds [new file with mode: 0644]
EBSeq/BiocInstaller/Meta/links.rds [new file with mode: 0644]
EBSeq/BiocInstaller/Meta/nsInfo.rds [new file with mode: 0644]
EBSeq/BiocInstaller/Meta/package.rds [new file with mode: 0644]
EBSeq/BiocInstaller/NAMESPACE [new file with mode: 0644]
EBSeq/BiocInstaller/NEWS [new file with mode: 0644]
EBSeq/BiocInstaller/R/BiocInstaller [new file with mode: 0644]
EBSeq/BiocInstaller/R/BiocInstaller.rdb [new file with mode: 0644]
EBSeq/BiocInstaller/R/BiocInstaller.rdx [new file with mode: 0644]
EBSeq/BiocInstaller/help/AnIndex [new file with mode: 0644]
EBSeq/BiocInstaller/help/BiocInstaller.rdb [new file with mode: 0644]
EBSeq/BiocInstaller/help/BiocInstaller.rdx [new file with mode: 0644]
EBSeq/BiocInstaller/help/aliases.rds [new file with mode: 0644]
EBSeq/BiocInstaller/help/paths.rds [new file with mode: 0644]
EBSeq/BiocInstaller/html/00Index.html [new file with mode: 0644]
EBSeq/BiocInstaller/html/R.css [new file with mode: 0644]
EBSeq/BiocInstaller/scripts/biocLite.R [new file with mode: 0644]
EBSeq/BiocInstaller/unitTests/test_BiocUpgrade.R [new file with mode: 0644]
EBSeq/BiocInstaller/unitTests/test_biocinstallRepos.R [new file with mode: 0644]
EBSeq/calcClusteringInfo.cpp
README.md
ReadReader.h
Refs.h
extractRef.cpp
makefile
sam/.DS_Store [new file with mode: 0644]
sam/._.DS_Store [new file with mode: 0644]
sam/._.gitignore [new file with mode: 0644]
sam/._AUTHORS [new file with mode: 0644]
sam/._COPYING [new file with mode: 0644]
sam/._ChangeLog.old [new file with mode: 0644]
sam/._INSTALL [new file with mode: 0644]
sam/._Makefile.mingw [new file with mode: 0644]
sam/._NEWS [new file with mode: 0644]
sam/._bam.c [new file with mode: 0644]
sam/._bam.h [new file with mode: 0644]
sam/._bam2bcf.c [new file with mode: 0644]
sam/._bam2bcf.h [new file with mode: 0644]
sam/._bam2bcf_indel.c [new file with mode: 0644]
sam/._bam2depth.c [new file with mode: 0644]
sam/._bam_aux.c [new file with mode: 0644]
sam/._bam_cat.c [new file with mode: 0644]
sam/._bam_color.c [new file with mode: 0644]
sam/._bam_endian.h [new file with mode: 0644]
sam/._bam_import.c [new file with mode: 0644]
sam/._bam_index.c [new file with mode: 0644]
sam/._bam_lpileup.c [new file with mode: 0644]
sam/._bam_mate.c [new file with mode: 0644]
sam/._bam_md.c [new file with mode: 0644]
sam/._bam_pileup.c [new file with mode: 0644]
sam/._bam_plcmd.c [new file with mode: 0644]
sam/._bam_reheader.c [new file with mode: 0644]
sam/._bam_rmdup.c [new file with mode: 0644]
sam/._bam_rmdupse.c [new file with mode: 0644]
sam/._bam_sort.c [new file with mode: 0644]
sam/._bam_stat.c [new file with mode: 0644]
sam/._bam_tview.c [new file with mode: 0644]
sam/._bam_tview.h [new file with mode: 0644]
sam/._bam_tview_curses.c [new file with mode: 0644]
sam/._bam_tview_html.c [new file with mode: 0644]
sam/._bamshuf.c [new file with mode: 0644]
sam/._bamtk.c [new file with mode: 0644]
sam/._bcftools [new file with mode: 0755]
sam/._bedcov.c [new file with mode: 0644]
sam/._bedidx.c [new file with mode: 0644]
sam/._bgzf.c [new file with mode: 0644]
sam/._bgzf.h [new file with mode: 0644]
sam/._bgzip.c [new file with mode: 0644]
sam/._cut_target.c [new file with mode: 0644]
sam/._errmod.c [new file with mode: 0644]
sam/._errmod.h [new file with mode: 0644]
sam/._examples [new file with mode: 0755]
sam/._faidx.c [new file with mode: 0644]
sam/._faidx.h [new file with mode: 0644]
sam/._kaln.c [new file with mode: 0644]
sam/._kaln.h [new file with mode: 0644]
sam/._khash.h [new file with mode: 0644]
sam/._klist.h [new file with mode: 0644]
sam/._knetfile.c [new file with mode: 0644]
sam/._knetfile.h [new file with mode: 0644]
sam/._kprobaln.c [new file with mode: 0644]
sam/._kprobaln.h [new file with mode: 0644]
sam/._kseq.h [new file with mode: 0644]
sam/._ksort.h [new file with mode: 0644]
sam/._kstring.c [new file with mode: 0644]
sam/._kstring.h [new file with mode: 0644]
sam/._misc [new file with mode: 0755]
sam/._padding.c [new file with mode: 0644]
sam/._phase.c [new file with mode: 0644]
sam/._razf.c [new file with mode: 0644]
sam/._razf.h [new file with mode: 0644]
sam/._razip.c [new file with mode: 0644]
sam/._sam.c [new file with mode: 0644]
sam/._sam.h [new file with mode: 0644]
sam/._sam_header.c [new file with mode: 0644]
sam/._sam_header.h [new file with mode: 0644]
sam/._sam_view.c [new file with mode: 0644]
sam/._sample.c [new file with mode: 0644]
sam/._sample.h [new file with mode: 0644]
sam/._samtools.1 [new file with mode: 0644]
sam/._win32 [new file with mode: 0755]
sam/ChangeLog [deleted file]
sam/ChangeLog.old [new file with mode: 0644]
sam/Makefile
sam/NEWS
sam/bam.c
sam/bam.h
sam/bam2bcf.c
sam/bam2bcf.h
sam/bam2bcf_indel.c
sam/bam2depth.c
sam/bam_aux.c
sam/bam_cat.c
sam/bam_color.c
sam/bam_import.c
sam/bam_index.c
sam/bam_mate.c
sam/bam_md.c
sam/bam_plcmd.c
sam/bam_reheader.c
sam/bam_sort.c
sam/bam_tview.c
sam/bam_tview.h [new file with mode: 0644]
sam/bam_tview_curses.c [new file with mode: 0644]
sam/bam_tview_html.c [new file with mode: 0644]
sam/bamshuf.c [new file with mode: 0644]
sam/bamtk.c
sam/bcftools/._Makefile [new file with mode: 0644]
sam/bcftools/._README [new file with mode: 0644]
sam/bcftools/._bcf.c [new file with mode: 0644]
sam/bcftools/._bcf.h [new file with mode: 0644]
sam/bcftools/._bcf.tex [new file with mode: 0644]
sam/bcftools/._bcf2qcall.c [new file with mode: 0644]
sam/bcftools/._bcfutils.c [new file with mode: 0644]
sam/bcftools/._call1.c [new file with mode: 0644]
sam/bcftools/._em.c [new file with mode: 0644]
sam/bcftools/._fet.c [new file with mode: 0644]
sam/bcftools/._index.c [new file with mode: 0644]
sam/bcftools/._kfunc.c [new file with mode: 0644]
sam/bcftools/._kmin.c [new file with mode: 0644]
sam/bcftools/._kmin.h [new file with mode: 0644]
sam/bcftools/._main.c [new file with mode: 0644]
sam/bcftools/._mut.c [new file with mode: 0644]
sam/bcftools/._prob1.c [new file with mode: 0644]
sam/bcftools/._prob1.h [new file with mode: 0644]
sam/bcftools/._vcf.c [new file with mode: 0644]
sam/bcftools/._vcfutils.pl [new file with mode: 0755]
sam/bcftools/Makefile
sam/bcftools/bcf.c
sam/bcftools/bcf.h
sam/bcftools/bcfutils.c
sam/bcftools/call1.c
sam/bcftools/index.c
sam/bcftools/main.c
sam/bcftools/prob1.c
sam/bcftools/prob1.h
sam/bcftools/vcf.c
sam/bedcov.c [new file with mode: 0644]
sam/bgzf.c
sam/bgzf.h
sam/examples/._00README.txt [new file with mode: 0644]
sam/examples/._Makefile [new file with mode: 0644]
sam/examples/._bam2bed.c [new file with mode: 0644]
sam/examples/._calDepth.c [new file with mode: 0644]
sam/examples/._chk_indel.c [new file with mode: 0644]
sam/examples/._ex1.fa [new file with mode: 0644]
sam/examples/._ex1.sam.gz [new file with mode: 0644]
sam/examples/._toy.fa [new file with mode: 0644]
sam/examples/._toy.sam [new file with mode: 0644]
sam/examples/chk_indel.c [new file with mode: 0644]
sam/faidx.c
sam/kprobaln.c
sam/kseq.h
sam/ksort.h
sam/kstring.c
sam/kstring.h
sam/misc/._HmmGlocal.java [new file with mode: 0644]
sam/misc/._Makefile [new file with mode: 0644]
sam/misc/._ace2sam.c [new file with mode: 0644]
sam/misc/._bamcheck.c [new file with mode: 0644]
sam/misc/._blast2sam.pl [new file with mode: 0755]
sam/misc/._bowtie2sam.pl [new file with mode: 0755]
sam/misc/._export2sam.pl [new file with mode: 0755]
sam/misc/._interpolate_sam.pl [new file with mode: 0755]
sam/misc/._maq2sam.c [new file with mode: 0644]
sam/misc/._md5.c [new file with mode: 0644]
sam/misc/._md5.h [new file with mode: 0644]
sam/misc/._md5fa.c [new file with mode: 0644]
sam/misc/._novo2sam.pl [new file with mode: 0755]
sam/misc/._plot-bamcheck [new file with mode: 0755]
sam/misc/._psl2sam.pl [new file with mode: 0755]
sam/misc/._r2plot.lua [new file with mode: 0755]
sam/misc/._sam2vcf.pl [new file with mode: 0755]
sam/misc/._samtools.pl [new file with mode: 0755]
sam/misc/._soap2sam.pl [new file with mode: 0755]
sam/misc/._varfilter.py [new file with mode: 0755]
sam/misc/._vcfutils.lua [new file with mode: 0755]
sam/misc/._wgsim.c [new file with mode: 0644]
sam/misc/._wgsim_eval.pl [new file with mode: 0755]
sam/misc/._zoom2sam.pl [new file with mode: 0755]
sam/misc/Makefile
sam/misc/ace2sam.c [new file with mode: 0644]
sam/misc/bamcheck.c [new file with mode: 0644]
sam/misc/plot-bamcheck [new file with mode: 0755]
sam/misc/r2plot.lua [new file with mode: 0755]
sam/misc/seqtk.c [deleted file]
sam/misc/vcfutils.lua [new file with mode: 0755]
sam/padding.c [new file with mode: 0644]
sam/sam.c
sam/sam.h
sam/sam_header.c
sam/sam_header.h
sam/sam_view.c
sam/samtools.1
sam/win32/._xcurses.h [new file with mode: 0644]
sam/win32/._zconf.h [new file with mode: 0644]
sam/win32/._zlib.h [new file with mode: 0644]
synthesisRef.cpp

diff --git a/EBSeq/BiocInstaller/DESCRIPTION b/EBSeq/BiocInstaller/DESCRIPTION
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--- /dev/null
@@ -0,0 +1,13 @@
+Package: BiocInstaller
+Title: Install/Update Bioconductor and CRAN Packages
+Description: Installs/updates Bioconductor and CRAN packages
+Version: 1.12.0
+Author: Dan Tenenbaum and Biocore Team
+Maintainer: Bioconductor Package Maintainer
+        <maintainer@bioconductor.org>
+biocViews: Software
+Depends: R (>= 3.0.0)
+Suggests: RUnit, BiocGenerics
+License: Artistic-2.0
+Packaged: 2013-10-15 04:03:53 UTC; biocbuild
+Built: R 3.0.2; ; 2013-10-15 11:47:50 UTC; unix
diff --git a/EBSeq/BiocInstaller/INDEX b/EBSeq/BiocInstaller/INDEX
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index 0000000..ec33cf3
--- /dev/null
@@ -0,0 +1,13 @@
+BiocUpgrade             Upgrade Bioconductor to the latest version
+                        available for this version of R
+biocLite                Install or update Bioconductor and CRAN
+                        packages
+biocValid               Validate installed package versions against
+                        biocLite versions.
+biocVersion             Bioconductor version
+biocases_group          Convenience functions to return package names
+                        associated with Bioconductor publications.
+biocinstallRepos        Display current Bioconductor and CRAN
+                        repositories.
+useDevel                Get the 'devel' version of the BiocInstaller
+                        package.
diff --git a/EBSeq/BiocInstaller/Meta/Rd.rds b/EBSeq/BiocInstaller/Meta/Rd.rds
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index 0000000..e07c822
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diff --git a/EBSeq/BiocInstaller/Meta/hsearch.rds b/EBSeq/BiocInstaller/Meta/hsearch.rds
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index 0000000..e320f87
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diff --git a/EBSeq/BiocInstaller/Meta/links.rds b/EBSeq/BiocInstaller/Meta/links.rds
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index 0000000..cc993be
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diff --git a/EBSeq/BiocInstaller/Meta/nsInfo.rds b/EBSeq/BiocInstaller/Meta/nsInfo.rds
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index 0000000..f32ede4
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diff --git a/EBSeq/BiocInstaller/Meta/package.rds b/EBSeq/BiocInstaller/Meta/package.rds
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index 0000000..8dee4bd
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diff --git a/EBSeq/BiocInstaller/NAMESPACE b/EBSeq/BiocInstaller/NAMESPACE
new file mode 100644 (file)
index 0000000..2415823
--- /dev/null
@@ -0,0 +1,4 @@
+import("utils")
+
+export(biocLite, biocVersion, biocinstallRepos, useDevel, biocValid,
+    monograph_group, RBioinf_group, biocases_group, all_group)
diff --git a/EBSeq/BiocInstaller/NEWS b/EBSeq/BiocInstaller/NEWS
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index 0000000..67c3189
--- /dev/null
@@ -0,0 +1,16 @@
+CHANGES IN VERSION 1.10.0
+-------------------------
+
+NEW FEATURES
+
+    o biocValid() checks that installed packages are consistent with
+    those available via biocLite().
+
+    o biocVersion() returns the version of Bioconductor expected with
+    this version of the BiocInstaller package.
+
+USER-VISIBLE CHANGES
+
+    o biocLite() invoked with no arguments updates currently installed
+    packages to their most-recent version.
+
diff --git a/EBSeq/BiocInstaller/R/BiocInstaller b/EBSeq/BiocInstaller/R/BiocInstaller
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--- /dev/null
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+#  File share/R/nspackloader.R
+#  Part of the R package, http://www.R-project.org
+#
+#  Copyright (C) 1995-2012 The R Core Team
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  A copy of the GNU General Public License is available at
+#  http://www.r-project.org/Licenses/
+
+local({
+    info <- loadingNamespaceInfo()
+    pkg <- info$pkgname
+    ns <- .getNamespace(as.name(pkg))
+    if (is.null(ns))
+        stop("cannot find namespace environment for ", pkg, domain = NA);
+    dbbase <- file.path(info$libname, pkg, "R", pkg)
+    lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})
diff --git a/EBSeq/BiocInstaller/R/BiocInstaller.rdb b/EBSeq/BiocInstaller/R/BiocInstaller.rdb
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diff --git a/EBSeq/BiocInstaller/R/BiocInstaller.rdx b/EBSeq/BiocInstaller/R/BiocInstaller.rdx
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diff --git a/EBSeq/BiocInstaller/help/AnIndex b/EBSeq/BiocInstaller/help/AnIndex
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--- /dev/null
@@ -0,0 +1,10 @@
+all_group      packageGroups
+biocases_group packageGroups
+biocinstallRepos       biocinstallRepos
+biocLite       biocLite
+BiocUpgrade    BiocUpgrade
+biocValid      biocValid
+biocVersion    biocVersion
+monograph_group        packageGroups
+RBioinf_group  packageGroups
+useDevel       useDevel
diff --git a/EBSeq/BiocInstaller/help/BiocInstaller.rdb b/EBSeq/BiocInstaller/help/BiocInstaller.rdb
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diff --git a/EBSeq/BiocInstaller/help/BiocInstaller.rdx b/EBSeq/BiocInstaller/help/BiocInstaller.rdx
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diff --git a/EBSeq/BiocInstaller/help/aliases.rds b/EBSeq/BiocInstaller/help/aliases.rds
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diff --git a/EBSeq/BiocInstaller/help/paths.rds b/EBSeq/BiocInstaller/help/paths.rds
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diff --git a/EBSeq/BiocInstaller/html/00Index.html b/EBSeq/BiocInstaller/html/00Index.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Install/Update Bioconductor and CRAN Packages</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Install/Update Bioconductor and CRAN Packages
+<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package &lsquo;BiocInstaller&rsquo; version 1.12.0</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../NEWS">Package NEWS</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="packageGroups.html">all_group</a></td>
+<td>Convenience functions to return package names associated with Bioconductor publications.</td></tr>
+<tr><td width="25%"><a href="packageGroups.html">biocases_group</a></td>
+<td>Convenience functions to return package names associated with Bioconductor publications.</td></tr>
+<tr><td width="25%"><a href="biocinstallRepos.html">biocinstallRepos</a></td>
+<td>Display current Bioconductor and CRAN repositories.</td></tr>
+<tr><td width="25%"><a href="biocLite.html">biocLite</a></td>
+<td>Install or update Bioconductor and CRAN packages</td></tr>
+<tr><td width="25%"><a href="BiocUpgrade.html">BiocUpgrade</a></td>
+<td>Upgrade Bioconductor to the latest version available for this version of R</td></tr>
+<tr><td width="25%"><a href="biocValid.html">biocValid</a></td>
+<td>Validate installed package versions against biocLite versions.</td></tr>
+<tr><td width="25%"><a href="biocVersion.html">biocVersion</a></td>
+<td>Bioconductor version</td></tr>
+<tr><td width="25%"><a href="packageGroups.html">monograph_group</a></td>
+<td>Convenience functions to return package names associated with Bioconductor publications.</td></tr>
+<tr><td width="25%"><a href="packageGroups.html">RBioinf_group</a></td>
+<td>Convenience functions to return package names associated with Bioconductor publications.</td></tr>
+<tr><td width="25%"><a href="useDevel.html">useDevel</a></td>
+<td>Get the 'devel' version of the BiocInstaller package.</td></tr>
+</table>
+</body></html>
diff --git a/EBSeq/BiocInstaller/html/R.css b/EBSeq/BiocInstaller/html/R.css
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+BODY{          background: white;
+               color: black }
+
+A:link{         background: white;
+                color: blue }
+A:visited{     background: white;
+               color: rgb(50%, 0%, 50%) }
+
+H1{            background: white;
+               color: rgb(55%, 55%, 55%);
+               font-family: monospace;
+               font-size: x-large;
+               text-align: center }
+
+H2{            background: white;
+               color: rgb(40%, 40%, 40%);
+               font-family: monospace;
+               font-size: large;
+               text-align: center }
+
+H3{            background: white;
+               color: rgb(40%, 40%, 40%);
+               font-family: monospace;
+               font-size: large }
+
+H4{            background: white;
+               color: rgb(40%, 40%, 40%);
+               font-family: monospace;
+               font-style: italic;
+               font-size: large }
+
+H5{            background: white;
+               color: rgb(40%, 40%, 40%);
+               font-family: monospace }
+
+H6{            background: white;
+               color: rgb(40%, 40%, 40%);
+               font-family: monospace;
+               font-style: italic }
+               
+IMG.toplogo{   vertical-align: middle }
+
+IMG.arrow{     width: 30px;
+               height: 30px;
+               border: 0 }
+
+span.acronym{font-size: small}
+span.env{font-family: monospace}
+span.file{font-family: monospace}
+span.option{font-family: monospace}
+span.pkg{font-weight: bold}
+span.samp{font-family: monospace}
+
+div.vignettes a:hover {
+  background: rgb(85%, 85%, 85%);
+}
+
diff --git a/EBSeq/BiocInstaller/scripts/biocLite.R b/EBSeq/BiocInstaller/scripts/biocLite.R
new file mode 100644 (file)
index 0000000..9940cfb
--- /dev/null
@@ -0,0 +1,86 @@
+## Mirrors: uncomment the following and change to your favorite CRAN mirror
+## if you don't want to use the default (cran.fhcrc.org, Seattle, USA).
+## options("repos" = c(CRAN="http://cran.fhcrc.org"))
+
+## Mirrors: uncomment the following and change to your favorite Bioconductor
+## mirror, if you don't want to use the default (www.bioconductor.org,
+## Seattle, USA)
+## options("BioC_mirror" = "http://www.bioconductor.org")
+
+local({
+    currBiocVers <- 
+        package_version(readLines("http://bioconductor.org/bioc-version",
+        warn=FALSE))
+    vers <- getRversion()
+    biocVers <- tryCatch({
+        BiocInstaller::biocVersion() # recent BiocInstaller
+    }, error=function(...) {         # no / older BiocInstaller
+        tools:::.BioC_version_associated_with_R_version
+    })
+
+    if (biocVers < currBiocVers) {
+        txt <- strwrap(sprintf("Your Bioconductor is out-of-date, upgrade
+            to version %s by following instructions at
+            http://bioconductor.org/install.", currBiocVers))
+        message(paste(txt, collapse="\n"))
+    }
+
+    if (vers > "2.13" && biocVers > "2.8") {
+
+        if (exists("biocLite", .GlobalEnv, inherits=FALSE)) {
+            txt <- strwrap("There is an outdated biocLite() function in the
+                global environment; run 'rm(biocLite)' and try again.")
+            stop("\n", paste(txt, collapse="\n"))
+        }
+          
+        if (!suppressWarnings(require("BiocInstaller", quietly=TRUE))) {
+            a <- NULL
+            p <- file.path(Sys.getenv("HOME"), ".R", "repositories")
+            if (file.exists(p)) {
+                a <- tools:::.read_repositories(p)
+                if (!"BioCsoft" %in% rownames(a)) 
+                    a <- NULL
+            }
+            if (is.null(a)) {
+                p <- file.path(R.home("etc"), "repositories")
+                a <- tools:::.read_repositories(p)
+            }
+            if (!"package:utils" %in% search()) {
+                url <- "http://bioconductor.org/biocLite.R"
+                txt <- sprintf("use 'source(\"%s\")' to update 'BiocInstaller'
+                                after 'utils' package is attached",
+                               url)
+                message(paste(strwrap(txt), collapse="\n  "))
+            } else {
+                ## add a conditional for Bioc releases occuring WITHIN
+                ## a single R minor version
+                if (vers >= "2.15" && vers < "2.16") {
+                    a["BioCsoft", "URL"] <- sub(as.character(biocVers), "2.11",
+                      a["BioCsoft", "URL"])
+                    biocVers <- numeric_version("2.11")
+                }
+                install.packages("BiocInstaller", repos=a["BioCsoft", "URL"])
+                if (!suppressWarnings(require("BiocInstaller",
+                                              quietly=TRUE))) {
+                    url0 <- "http://www.bioconductor.org/packages"
+                    url <- sprintf("%s/%s/bioc",
+                                   url0, as.character(biocVers))
+                    txt0 <- "'biocLite.R' failed to install 'BiocInstaller',
+                            use 'install.packages(\"%s\", repos=\"%s\")'"
+                    txt <- sprintf(txt0, "BiocInstaller", url)
+                    message(paste(strwrap(txt), collapse="\n  "))
+                }
+            }
+        }
+    } else {
+        source("http://bioconductor.org/getBioC.R")
+        biocLite <<-
+            function(pkgs, groupName="lite", ...)
+            {
+                if (missing(pkgs))
+                    biocinstall(groupName=groupName, ...)
+                else
+                    biocinstall(pkgs=pkgs, groupName=groupName, ...)
+            }
+    }
+})
diff --git a/EBSeq/BiocInstaller/unitTests/test_BiocUpgrade.R b/EBSeq/BiocInstaller/unitTests/test_BiocUpgrade.R
new file mode 100644 (file)
index 0000000..d4cb4e7
--- /dev/null
@@ -0,0 +1,29 @@
+test_useDevel <- function()
+{
+    if (!BiocInstaller:::IS_END_OF_LIFE) {
+        checkException(useDevel(), silent=TRUE)
+    } else if (!BiocInstaller:::IS_DOWNGRADEABLE) {
+        checkException(useDevel(FALSE), silent=TRUE)
+    }
+    if (!BiocInstaller:::IS_UPGRADEABLE) {
+        checkException(useDevel(), silent=TRUE)
+        opts <- options(warn=2); on.exit(options(opts))
+        checkException(biocLite("BiocUpgrade"))
+    }
+}
+
+test_getContribUrl_exist <- function()
+{
+    fun <- BiocInstaller:::.getContribUrl
+    
+    vers <- BiocInstaller:::BIOC_VERSION
+    checkTrue(grepl(vers, fun(vers)))
+    if (BiocInstaller:::IS_UPGRADEABLE) {
+        vers <- BiocInstaller:::UPGRADE_VERSION
+        checkTrue(grepl(vers, fun(vers)))
+    }
+    if (BiocInstaller:::IS_DOWNGRADEABLE) {
+        vers <- BiocInstaller:::DOWNGRADE_VERSION
+        checkTrue(grepl(vers, fun(vers)))
+    }
+}
diff --git a/EBSeq/BiocInstaller/unitTests/test_biocinstallRepos.R b/EBSeq/BiocInstaller/unitTests/test_biocinstallRepos.R
new file mode 100644 (file)
index 0000000..e6fb520
--- /dev/null
@@ -0,0 +1,27 @@
+repos <- biocinstallRepos()
+
+test_biocinstallRepos_named_repositories <- function()
+{
+
+    allOS <- c("BioCsoft", "CRAN", "BioCann", "BioCexp", "BioCextra")
+    windowsOnly <- "CRANextra"
+
+    checkTrue(all(allOS %in% names(repos)))
+    if (.Platform$OS.type == "windows")
+    {
+        checkTrue(windowsOnly %in% names(repos))
+    } else {
+        checkTrue(!windowsOnly %in% names(repos))
+    }
+   
+}
+
+test_biocinstallRepos_noNA_repositories <- function()
+{
+    checkTrue(!any(is.na(repos)))
+}
+
+test_biocinstallRepos_order <- function()
+{
+    checkIdentical("BioCsoft", names(repos)[[1]])
+}
index 2103f61..c1d64bb 100644 (file)
@@ -65,18 +65,17 @@ string convert(const string& rawseq) {
 void loadRef(char* inpF) {
   ifstream fin(inpF);
   string tag, line, rawseq;
-  void *pt;
 
   assert(fin.is_open());
 
   names.clear(); names.push_back("");
   seqs.clear(); seqs.push_back("");
   
-  pt = getline(fin, line);
-  while (pt != 0 && line[0] == '>') {
+  getline(fin, line);
+  while ((fin) && (line[0] == '>')) {
     tag = line.substr(1);
     rawseq = "";
-    while((pt = getline(fin, line)) && line[0] != '>') {
+    while((getline(fin, line)) && (line[0] != '>')) {
       rawseq += line;
     }
     if (rawseq.size() <= 0) {
index 5c6943b..e3e890c 100644 (file)
--- a/README.md
+++ b/README.md
@@ -46,6 +46,13 @@ To compile RSEM, simply run
    
     make
 
+For cygwin users, please uncomment the 3rd and 7th line in
+'sam/Makefile' before you run 'make'.
+
+To compile EBSeq, which is included in the RSEM package, run
+
+    make ebseq
+
 To install, simply put the rsem directory in your environment's PATH
 variable.
 
@@ -111,7 +118,7 @@ using an alternative aligner, you may also want to provide the
 indices are not built.
 
 RSEM requires all alignments of the same read group together. For
-paired-end reads, RSEM also requires the two mates of any alignment be
+vpaired-end reads, RSEM also requires the two mates of any alignment be
 adjacent. To check if your SAM/BAM file satisfy the requirements,
 please run
 
@@ -181,7 +188,7 @@ Usage:
 
 sorted_bam_input        : Input BAM format file, must be sorted  
 wig_output              : Output wiggle file's name, e.g. output.wig  
-wiggle_name             : The name of this wiggle plot  
+wiggle_name             : the name of this wiggle plot  
 --no-fractional-weight  : If this is set, RSEM will not look for "ZW" tag and each alignment appeared in the BAM file has weight 1. Set this if your BAM file is not generated by RSEM. Please note that this option must be at the end of the command line
 
 #### c) Loading a BAM and/or Wiggle file into the UCSC Genome Browser or Integrative Genomics Viewer(IGV)
@@ -243,7 +250,7 @@ Histogram of reads with different number of alignments: x-axis is the number of
 ## <a name="example"></a> Example
 
 Suppose we download the mouse genome from UCSC Genome Browser.  We
-will use a reference_name of 'mouse_125'.  We have a FASTQ-formatted file,
+will use a reference_name of 'mm9'.  We have a FASTQ-formatted file,
 'mmliver.fq', containing single-end reads from one sample, which we
 call 'mmliver_single_quals'.  We want to estimate expression values by
 using the single-end model with a fragment length distribution. We
@@ -259,69 +266,36 @@ list is 'gene_ids.txt'. We will visualize the models learned in
 
 The commands for this scenario are as follows:
 
-    rsem-prepare-reference --gtf mm9.gtf --mapping knownIsoforms.txt --bowtie-path /sw/bowtie /data/mm9 /ref/mouse_125
-    rsem-calculate-expression --bowtie-path /sw/bowtie --phred64-quals --fragment-length-mean 150.0 --fragment-length-sd 35.0 -p 8 --output-genome-bam --calc-ci --memory-allocate 1024 /data/mmliver.fq /ref/mouse_125 mmliver_single_quals
+    rsem-prepare-reference --gtf mm9.gtf --mapping knownIsoforms.txt --bowtie-path /sw/bowtie /data/mm9 /ref/mm9
+    rsem-calculate-expression --bowtie-path /sw/bowtie --phred64-quals --fragment-length-mean 150.0 --fragment-length-sd 35.0 -p 8 --output-genome-bam --calc-ci --memory-allocate 1024 /data/mmliver.fq /ref/mm9 mmliver_single_quals
     rsem-bam2wig mmliver_single_quals.sorted.bam mmliver_single_quals.sorted.wig mmliver_single_quals
     rsem-plot-transcript-wiggles --gene-list --show-unique mmliver_single_quals gene_ids.txt output.pdf 
     rsem-plot-model mmliver_single_quals mmliver_single_quals.models.pdf
 
 ## <a name="simulation"></a> Simulation
 
-RSEM provides users the 'rsem-simulate-reads' program to simulate RNA-Seq data based on parameters learned from real data sets. Run
-
-    rsem-simulate-reads
-
-to get usage information or read the following subsections.
 ### Usage: 
 
     rsem-simulate-reads reference_name estimated_model_file estimated_isoform_results theta0 N output_name [-q]
 
-__reference_name:__ The name of RSEM references, which should be already generated by 'rsem-prepare-reference'              
-
-__estimated_model_file:__ This file describes how the RNA-Seq reads will be sequenced given the expression levels. It determines what kind of reads will be simulated (single-end/paired-end, w/o quality score) and includes parameters for fragment length distribution, read start position distribution, sequencing error models, etc. Normally, this file should be learned from real data using 'rsem-calculate-expression'. The file can be found under the 'sample_name.stat' folder with the name of 'sample_name.model'    
-
-__estimated_isoform_results:__ This file contains expression levels for all isoforms recorded in the reference. It can be learned using 'rsem-calculate-expression' from real data. The corresponding file users want to use is 'sample_name.isoforms.results'. If simulating from user-designed expression profile is desired, start from a learned 'sample_name.isoforms.results' file and only modify the 'TPM' column. The simulator only reads the TPM column. But keeping the file format the same is required.   
-
-__theta0:__ This parameter determines the fraction of reads that are coming from background "noise" (instead of from a transcript). It can also be estimated using 'rsem-calculate-expression' from real data. Users can find it as the first value of the third line of the file 'sample_name.stat/sample_name.theta'.   
-
-__N:__ The total number of reads to be simulated. If 'rsem-calculate-expression' is executed on a real data set, the total number of reads can be found as the 4th number of the first line of the file 'sample_name.stat/sample_name.cnt'.   
-
-__output_name:__ Prefix for all output files.   
-
-__-q:__ Set it will stop outputting intermediate information.   
+estimated_model_file:  file containing model parameters.  Generated by
+rsem-calculate-expression.   
+estimated_isoform_results: file containing isoform expression levels.
+Generated by rsem-calculate-expression.   
+theta0: fraction of reads that are "noise" (not derived from a transcript).   
+N: number of reads to simulate.   
+output_name: prefix for all output files.   
+[-q] : set it will stop outputting intermediate information.   
 
 ### Outputs:
 
-output_name.sim.isoforms.results, output_name.sim.genes.results: Expression levels estimated by counting where each simulated read comes from.
-
 output_name.fa if single-end without quality score;   
 output_name.fq if single-end with quality score;   
 output_name_1.fa & output_name_2.fa if paired-end without quality
 score;   
 output_name_1.fq & output_name_2.fq if paired-end with quality score.   
 
-**Format of the header line**: Each simulated read's header line encodes where it comes from. The header line has the format:
-
-    {>/@}_rid_dir_sid_pos[_insertL]
-
-__{>/@}:__ Either '>' or '@' must appear. '>' appears if FASTA files are generated and '@' appears if FASTQ files are generated
-
-__rid:__ Simulated read's index, numbered from 0   
-
-__dir:__ The direction of the simulated read. 0 refers to forward strand ('+') and 1 refers to reverse strand ('-')   
-
-__sid:__ Represent which transcript this read is simulated from. It ranges between 0 and M, where M is the total number of transcripts. If sid=0, the read is simulated from the background noise. Otherwise, the read is simulated from a transcript with index sid. Transcript sid's transcript name can be found in the 'transcript_id' column of the 'sample_name.isoforms.results' file (at line sid + 1, line 1 is for column names)   
-
-__pos:__ The start position of the simulated read in strand dir of transcript sid. It is numbered from 0   
-
-__insertL:__ Only appear for paired-end reads. It gives the insert length of the simulated read.   
-
-### Example:
-
-Suppose we want to simulate 50 millon single-end reads with quality scores and use the parameters learned from [Example](#example). In addition, we set theta0 as 0.2 and output_name as 'simulated_reads'. The command is:
-
-    rsem-simulate-reads /ref/mouse_125 mmliver_single_quals.stat/mmliver_single_quals.model mmliver_single_quals.isoforms.results 0.2 50000000 simulated_reads
+output_name.sim.isoforms.results, output_name.sim.genes.results : Results estimated based on sample values.
 
 ## <a name="gen_trinity"></a> Generate Transcript-to-Gene-Map from Trinity Output
 
index 9cd88e9..141585a 100644 (file)
@@ -7,6 +7,7 @@
 #include<iostream>
 #include<cassert>
 #include<fstream>
+#include<vector>
 
 #include "utils.h"
 #include "SingleRead.h"
@@ -94,7 +95,7 @@ bool ReadReader<ReadType>::locate(READ_INT_TYPE rid) {
 
        if (crid < rid) return false;
 
-       std::streampos tmp[s];
+       std::vector<std::streampos> tmp(s);
        for (int i = 0; i < s; i++) { tmp[i] = arr[i]->tellg(); }
 
        if (!read.read(s, (std::istream**)arr, 0)) return false;
diff --git a/Refs.h b/Refs.h
index 008d275..711f64b 100644 (file)
--- a/Refs.h
+++ b/Refs.h
@@ -84,7 +84,6 @@ void Refs::makeRefs(char *inpF, RefSeqPolicy& policy, PolyARules& rules) {
   //read standard fasta format here
   std::ifstream fin;
   std::string tag, line, rawseq;
-  void* pt; // istream& is indeed a pointer, that's why I can use void* here
 
   seqs.clear();
   seqs.push_back(RefSeq()); // noise isoform
@@ -94,11 +93,11 @@ void Refs::makeRefs(char *inpF, RefSeqPolicy& policy, PolyARules& rules) {
 
   fin.open(inpF);
   if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", inpF); exit(-1); }
-  pt = getline(fin, line);
-  while (pt != 0 && line[0] == '>') {
+  getline(fin, line);
+  while ((fin) && (line[0] == '>')) {
     tag = line.substr(1);
     rawseq = "";
-    while((pt = getline(fin, line)) && line[0] != '>') {
+    while((getline(fin, line)) && (line[0] != '>')) {
       rawseq += line;
     }
     if (rawseq.size() <= 0) {
index 2d2b17c..fb7d3ec 100644 (file)
@@ -260,7 +260,6 @@ int main(int argc, char* argv[]) {
 
        ifstream fin;
        string line, gseq, seqname;
-       void* pt;
 
        chrvec.clear();
 
@@ -270,31 +269,31 @@ int main(int argc, char* argv[]) {
        for (int i = start; i < argc; i++) {
                fin.open(argv[i]);
                if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", argv[i]); exit(-1); }
-               pt = getline(fin, line);
-               while (pt != 0 && line[0] == '>') {
+               getline(fin, line);
+               while ((fin) && (line[0] == '>')) {
                        istringstream strin(line.substr(1));
                        strin>>seqname;
 
                        gseq = "";
-                   while((pt = getline(fin, line)) && line[0] != '>') {
-                       gseq += line;
-                   }
-
-                   size_t len = gseq.length();
-                   assert(len > 0);
-                   for (size_t j = 0; j < len; j++) gseq[j] = check(gseq[j]);
-
-                   iter = sn2tr.find(seqname);
-                   if (iter == sn2tr.end()) continue;
-
-                   chrvec.push_back(ChrInfo(seqname, len));
-
-                   vector<int>& vec = iter->second;
-                   int s = vec.size();
-                   for (int j = 0; j < s; j++) {
-                       assert(vec[j] > 0 && vec[j] <= M);
-                       transcripts.getTranscriptAt(vec[j]).extractSeq(gseq, seqs[vec[j]]);
-                   }
+                       while((getline(fin, line)) && (line[0] != '>')) {
+                         gseq += line;
+                       }
+
+                       size_t len = gseq.length();
+                       assert(len > 0);
+                       for (size_t j = 0; j < len; j++) gseq[j] = check(gseq[j]);
+                       
+                       iter = sn2tr.find(seqname);
+                       if (iter == sn2tr.end()) continue;
+                       
+                       chrvec.push_back(ChrInfo(seqname, len));
+                       
+                       vector<int>& vec = iter->second;
+                       int s = vec.size();
+                       for (int j = 0; j < s; j++) {
+                         assert(vec[j] > 0 && vec[j] <= M);
+                         transcripts.getTranscriptAt(vec[j]).extractSeq(gseq, seqs[vec[j]]);
+                       }
                }
                fin.close();
 
@@ -304,8 +303,8 @@ int main(int argc, char* argv[]) {
        for (int i = 1; i <= M; i++) {
                if (seqs[i] == "") {
                        const Transcript& transcript = transcripts.getTranscriptAt(i);
-                       fprintf(stderr, "Cannot extract transcript %s's sequence from chromosome %s! Loading chromosome %s's sequence is failed. Please check if 1) the chromosome directory is set correctly; 2) the list of chromosome files is complete; 3) the FASTA files containing chromosome sequences are not truncated or having wrong format.\n", \
-                               transcript.getTranscriptID().c_str(), transcript.getSeqName().c_str(), transcript.getSeqName().c_str());
+                       fprintf(stderr, "Cannot extract transcript %s's sequence from chromosome %s, whose information might not be provided! Please check if the chromosome directory is set correctly or the list of chromosome files is complete.\n", \
+                                       transcript.getTranscriptID().c_str(), transcript.getSeqName().c_str());
                        exit(-1);
                }
        }
index d706f55..3c48e69 100644 (file)
--- a/makefile
+++ b/makefile
@@ -135,6 +135,8 @@ rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam
 rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
        $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -o $@
 
+.PHONY: ebseq
+
 ebseq :
        cd EBSeq ; ${MAKE} all
 
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new file mode 100644 (file)
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diff --git a/sam/._.gitignore b/sam/._.gitignore
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diff --git a/sam/._COPYING b/sam/._COPYING
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diff --git a/sam/._ChangeLog.old b/sam/._ChangeLog.old
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diff --git a/sam/._bam_color.c b/sam/._bam_color.c
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diff --git a/sam/._bam_import.c b/sam/._bam_import.c
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diff --git a/sam/._bcftools b/sam/._bcftools
new file mode 100755 (executable)
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index 0000000..94286bb
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diff --git a/sam/._padding.c b/sam/._padding.c
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index 0000000..94286bb
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index 0000000..94286bb
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index 0000000..94286bb
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index 0000000..94286bb
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diff --git a/sam/._sam_header.c b/sam/._sam_header.c
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index 0000000..94286bb
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diff --git a/sam/._sam_header.h b/sam/._sam_header.h
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index 0000000..94286bb
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diff --git a/sam/._sam_view.c b/sam/._sam_view.c
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index 0000000..94286bb
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diff --git a/sam/._sample.c b/sam/._sample.c
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index 0000000..94286bb
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diff --git a/sam/._sample.h b/sam/._sample.h
new file mode 100644 (file)
index 0000000..94286bb
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diff --git a/sam/._samtools.1 b/sam/._samtools.1
new file mode 100644 (file)
index 0000000..94286bb
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diff --git a/sam/._win32 b/sam/._win32
new file mode 100755 (executable)
index 0000000..94286bb
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diff --git a/sam/ChangeLog b/sam/ChangeLog
deleted file mode 100644 (file)
index a471838..0000000
+++ /dev/null
@@ -1,5948 +0,0 @@
-------------------------------------------------------------------------
-r925 | lh3lh3 | 2011-02-28 15:45:17 -0500 (Mon, 28 Feb 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/phase.c
-
-minor changes to a heuristic rule
-
-------------------------------------------------------------------------
-r924 | lh3lh3 | 2011-02-28 15:24:04 -0500 (Mon, 28 Feb 2011) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bcftools/vcfutils.pl
-   M /trunk/samtools/phase.c
-
- * 0.1.12-r924:126
- * fixed a bug in phase (due to recent changes)
- * fixed a bug in vcf2fq
-
-------------------------------------------------------------------------
-r923 | lh3lh3 | 2011-02-28 12:57:39 -0500 (Mon, 28 Feb 2011) | 5 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/phase.c
-
- * put version number in bam.h
- * write version to BCF
- * in phase, change the default -q to 37
- * output a little more information during phasing
-
-------------------------------------------------------------------------
-r922 | lh3lh3 | 2011-02-25 16:40:09 -0500 (Fri, 25 Feb 2011) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.tex
-   M /trunk/samtools/bcftools/bcf2qcall.c
-   M /trunk/samtools/bcftools/bcfutils.c
-   M /trunk/samtools/bcftools/ld.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/vcf.c
-   M /trunk/samtools/cut_target.c
-
- * change the order of PL/GL according to the latest VCF spec
- * change the type of SP to int32_t
-
-------------------------------------------------------------------------
-r921 | lh3lh3 | 2011-02-25 14:40:56 -0500 (Fri, 25 Feb 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.tex
-
-update the BCF spec
-
-------------------------------------------------------------------------
-r920 | lh3lh3 | 2011-02-25 00:59:27 -0500 (Fri, 25 Feb 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-   A /trunk/samtools/cut_target.c
-   M /trunk/samtools/errmod.h
-   M /trunk/samtools/faidx.c
-   M /trunk/samtools/khash.h
-   M /trunk/samtools/kstring.c
-   M /trunk/samtools/kstring.h
-   A /trunk/samtools/phase.c
-   M /trunk/samtools/samtools.1
-
-added the phase command
-
-------------------------------------------------------------------------
-r918 | lh3lh3 | 2011-02-24 10:05:54 -0500 (Thu, 24 Feb 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/prob1.h
-
-added "const" to bcf_p1_cal()
-
-------------------------------------------------------------------------
-r917 | lh3lh3 | 2011-02-24 09:36:30 -0500 (Thu, 24 Feb 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-
-more meaningful BAM truncation message
-
-------------------------------------------------------------------------
-r916 | lh3lh3 | 2011-02-24 09:35:06 -0500 (Thu, 24 Feb 2011) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/vcf.c
-
- * automatically fix errors in GL
- * output unrecognized FORMAT as "."
-
-------------------------------------------------------------------------
-r913 | lh3lh3 | 2011-02-10 22:59:47 -0500 (Thu, 10 Feb 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/vcf.c
-
-finished VCF->BCF conversion
-
-------------------------------------------------------------------------
-r910 | petulda | 2011-02-03 03:13:48 -0500 (Thu, 03 Feb 2011) | 1 line
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-Prevent division by zero
-------------------------------------------------------------------------
-r909 | lh3lh3 | 2011-02-02 11:29:20 -0500 (Wed, 02 Feb 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-
-fixed a typo in the VCF header
-
-------------------------------------------------------------------------
-r908 | lh3lh3 | 2011-02-02 11:28:24 -0500 (Wed, 02 Feb 2011) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam_index.c
-
- * fixed an out-of-boundary bug
- * improved sorting order checking in index
-
-------------------------------------------------------------------------
-r907 | lh3lh3 | 2011-01-29 22:59:20 -0500 (Sat, 29 Jan 2011) | 4 lines
-Changed paths:
-   M /trunk/samtools/INSTALL
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/knetfile.c
-
- * avoid a segfault when network connect fails
- * update INSTALL
- * fixed a bug in tview on big-endian by Nathan Weeks
-
-------------------------------------------------------------------------
-r903 | lh3lh3 | 2011-01-27 14:50:02 -0500 (Thu, 27 Jan 2011) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_md.c
-
- * fixed a rare memory issue in bam_md.c
- * fixed a bug in indel calling related to unmapped and refskip reads
-
-------------------------------------------------------------------------
-r902 | lh3lh3 | 2011-01-23 21:46:18 -0500 (Sun, 23 Jan 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/fet.c
-
-fixed two minor bugs in Fisher's exact test
-
-------------------------------------------------------------------------
-r899 | petulda | 2011-01-19 09:28:02 -0500 (Wed, 19 Jan 2011) | 1 line
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-Skip sites with unknown ref
-------------------------------------------------------------------------
-r898 | lh3lh3 | 2011-01-15 12:56:05 -0500 (Sat, 15 Jan 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_md.c
-
-move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
-
-------------------------------------------------------------------------
-r896 | lh3lh3 | 2011-01-06 10:52:15 -0500 (Thu, 06 Jan 2011) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/bcfutils.c
-   M /trunk/samtools/bcftools/call1.c
-
- * samtools-0.1.12-10 (r896)
- * allow to exclude read groups in mpileup
-
-------------------------------------------------------------------------
-r895 | lh3lh3 | 2011-01-04 11:31:29 -0500 (Tue, 04 Jan 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.tex
-
-sorry. It is SP not ST
-
-------------------------------------------------------------------------
-r894 | lh3lh3 | 2011-01-04 11:29:06 -0500 (Tue, 04 Jan 2011) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.tex
-
-added ST
-
-------------------------------------------------------------------------
-r893 | petulda | 2011-01-04 06:55:56 -0500 (Tue, 04 Jan 2011) | 1 line
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-
-Fixed a typo in read_samples
-------------------------------------------------------------------------
-r892 | jmarshall | 2010-12-28 08:06:49 -0500 (Tue, 28 Dec 2010) | 9 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bcftools/Makefile
-   M /trunk/samtools/examples/Makefile
-
-System libraries go *after* user libraries in link commands, because
-the user libraries may themselves have dependencies that are satisfied
-by the system libraries.  It's not rocket science!
-
-This makes a difference with some linkers; or with -static or --as-needed.
-
-The examples/Makefile fix is from Charles Plessy.
-See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004
-
-------------------------------------------------------------------------
-r891 | lh3lh3 | 2010-12-21 12:16:33 -0500 (Tue, 21 Dec 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/bcfutils.c
-   M /trunk/samtools/bcftools/call1.c
-
- * samtools-0.1.12-9 (r891)
- * allow to call SNPs from a subset of samples
-
-------------------------------------------------------------------------
-r889 | lh3lh3 | 2010-12-15 11:28:16 -0500 (Wed, 15 Dec 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.12-12 (r889)
- * set mapQ as 20 if it equals 255
-
-------------------------------------------------------------------------
-r888 | lh3lh3 | 2010-12-14 22:41:09 -0500 (Tue, 14 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
-When -B is applied to mpileup, still use paired reads only unless -A is flagged.
-
-------------------------------------------------------------------------
-r887 | lh3lh3 | 2010-12-14 22:37:05 -0500 (Tue, 14 Dec 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.12-6 (r887)
- * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.
-
-------------------------------------------------------------------------
-r886 | lh3lh3 | 2010-12-14 12:51:03 -0500 (Tue, 14 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-
-(Arguably) improved the indel caller a tiny bit for lowCov data.
-
-------------------------------------------------------------------------
-r885 | petulda | 2010-12-14 04:55:46 -0500 (Tue, 14 Dec 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-
-Fixed the VCF header to pass validation
-------------------------------------------------------------------------
-r884 | lh3lh3 | 2010-12-12 23:02:19 -0500 (Sun, 12 Dec 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
- * samtools-0.1.12-4 (r884)
- * fixed a long-existing flaw in the INDEL calling model
-
-------------------------------------------------------------------------
-r883 | lh3lh3 | 2010-12-11 20:05:42 -0500 (Sat, 11 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcfutils.c
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-compute max SP and max GQ from sample genotypes
-
-------------------------------------------------------------------------
-r880 | lh3lh3 | 2010-12-10 10:50:54 -0500 (Fri, 10 Dec 2010) | 2 lines
-Changed paths:
-   D /trunk/samtools/bcftools/bcf-fix.pl
-
-drop bcf-fix.pl as it is redundant by the latest changes
-
-------------------------------------------------------------------------
-r879 | lh3lh3 | 2010-12-10 10:50:29 -0500 (Fri, 10 Dec 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/vcf.c
-
- * fixed a minor issue in printing VCFs
- * write bcftools specific INFO and FORMAT in the header
-
-------------------------------------------------------------------------
-r878 | lh3lh3 | 2010-12-10 10:09:14 -0500 (Fri, 10 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/bcfutils.c
-   M /trunk/samtools/bcftools/call1.c
-
-Make sure that the GT genotype field is the first
-
-------------------------------------------------------------------------
-r877 | lh3lh3 | 2010-12-08 17:27:05 -0500 (Wed, 08 Dec 2010) | 7 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.12-2 (r877)
-
- * allow to fine control the selection of indel candidates. The current
-   setting is okay for lowCov and highCov with ~100 samples, but it
-   skips too many indels for highCov with >250 samples.
-
-
-------------------------------------------------------------------------
-r874 | lh3lh3 | 2010-12-07 22:40:35 -0500 (Tue, 07 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-
-a spelling error..
-
-------------------------------------------------------------------------
-r873 | lh3lh3 | 2010-12-07 22:39:57 -0500 (Tue, 07 Dec 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.12-1 (r873)
- * added a switch to allow anomalous read pairs in calling
-
-------------------------------------------------------------------------
-r872 | lh3lh3 | 2010-12-07 14:43:54 -0500 (Tue, 07 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-fixed a bug in vcf2fq
-
-------------------------------------------------------------------------
-r869 | lh3lh3 | 2010-12-05 01:18:06 -0500 (Sun, 05 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-
-added a warning for the Windows version
-
-------------------------------------------------------------------------
-r868 | lh3lh3 | 2010-12-05 01:05:51 -0500 (Sun, 05 Dec 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-
-In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
-According to the manual page, this change is valid. However, MinGW seems
-to interpret "%lf" as "%Lf".
-
-------------------------------------------------------------------------
-r867 | lh3lh3 | 2010-12-05 00:35:43 -0500 (Sun, 05 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile.mingw
-   M /trunk/samtools/bam_aux.c
-
-bring back the windows support
-
-------------------------------------------------------------------------
-r866 | lh3lh3 | 2010-12-04 23:33:51 -0500 (Sat, 04 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_reheader.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-Fixed a compiling error when knetfile is not used.
-
-------------------------------------------------------------------------
-r865 | lh3lh3 | 2010-12-04 00:13:22 -0500 (Sat, 04 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-vcf->fastq
-
-------------------------------------------------------------------------
-r864 | lh3lh3 | 2010-12-03 17:12:30 -0500 (Fri, 03 Dec 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/prob1.h
-
- * remove "-f". Instead always compute consensus quality
- * increase the upper limit of quality
-
-------------------------------------------------------------------------
-r863 | lh3lh3 | 2010-12-03 15:28:15 -0500 (Fri, 03 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-
-more informative error message
-
-------------------------------------------------------------------------
-r862 | lh3lh3 | 2010-12-02 16:16:08 -0500 (Thu, 02 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bamtk.c
-
-Release samtools-0.1.12a
-
-------------------------------------------------------------------------
-r861 | lh3lh3 | 2010-12-02 15:55:06 -0500 (Thu, 02 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-
-a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
-
-------------------------------------------------------------------------
-r859 | lh3lh3 | 2010-12-02 11:39:57 -0500 (Thu, 02 Dec 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-
-Release samtools-0.1.12
-
-------------------------------------------------------------------------
-r858 | lh3lh3 | 2010-12-02 11:24:41 -0500 (Thu, 02 Dec 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/bcf.c
-
- * samtools-0.1.11-1 (r858)
- * fixed a bug in mpileup which causes segfaults
- * bcftools: do not segfault when BCF contains errors
-
-------------------------------------------------------------------------
-r857 | lh3lh3 | 2010-11-30 23:52:50 -0500 (Tue, 30 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-
-fixed a memory leak in bam_fetch()
-
-------------------------------------------------------------------------
-r856 | lh3lh3 | 2010-11-26 00:07:31 -0500 (Fri, 26 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
- * fixed a memory violation
- * added splitchr to vcfutils.pl
-
-------------------------------------------------------------------------
-r854 | lh3lh3 | 2010-11-23 09:05:08 -0500 (Tue, 23 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/ld.c
-
-fixed a typo/bug in r^2 computation
-
-------------------------------------------------------------------------
-r852 | lh3lh3 | 2010-11-21 22:20:20 -0500 (Sun, 21 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-
-forget to change the version information
-
-------------------------------------------------------------------------
-r851 | lh3lh3 | 2010-11-21 22:16:52 -0500 (Sun, 21 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bcftools/bcftools.1
-   M /trunk/samtools/samtools.1
-
-Release samtools-0.1.11
-
-------------------------------------------------------------------------
-r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/prob1.h
-
- * samtools-0.1.10-9 (r844)
- * added the "folded" or reference-free mode for variant calling
-
-------------------------------------------------------------------------
-r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bam_sort.c
-
-In merging, if -R is specified, do not abort if the sequence dictionary is different.
-
-------------------------------------------------------------------------
-r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam_sort.c
-
-When merging BAM headers, compare the list of target reference sequences
-strictly (and fail/abort if there is a mismatch), but allow one list to be a
-prefix of the other.  (i.e., check that the lists are identical up until the
-shorter runs out, and add the excess targets from the longer to the output.)
-
-------------------------------------------------------------------------
-r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.10 (r841)
- * fixed a bug in pileup when the first CIGAR operation is D
- * fixed a bug in view with range query
-
-------------------------------------------------------------------------
-r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.10-4 (r840)
-
- * drop the MNP caller. It is slow while does not diliver too much
-   benefit. Possibly I will work on it in future given more time.
-
- * there is a segfault in pileup 
-
- * someone has reported segfault from view/index/sort
-
-
-------------------------------------------------------------------------
-r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.10-6 (r839)
-
- * call MNPs without realignment because it seems to me that it is not
-   worthwhile to significantly slow down SNP calling.
-
- * the result looks quite different from the previous version. I have
-   work to do...
-
-
-------------------------------------------------------------------------
-r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/knetfile.c
-
-Apply a patch by Rob Davis, which improves fault detection.
-
-------------------------------------------------------------------------
-r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-r836
- * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
-
-------------------------------------------------------------------------
-r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
- * modify the filtering rule: also filter SNPs around filtered indels
- * added MNP filter
-
-------------------------------------------------------------------------
-r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.10-4 (r834)
- * fixed a silly bug in printing MNP
- * restrict to at most 1 alternative allele
-
-------------------------------------------------------------------------
-r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bamtk.c
-
-fixed a bug in printing MNPs
-
-------------------------------------------------------------------------
-r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-
-minor change to how seqQ is applied
-
-------------------------------------------------------------------------
-r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.10 (r831)
- * initial MNP caller
-
-------------------------------------------------------------------------
-r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bamtk.c
-
-Release samtools-0.1.10 (r829)
-
-------------------------------------------------------------------------
-r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-
-update version information: samtools-0.1.9-20 (r828)
-
-------------------------------------------------------------------------
-r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-
-bcftools: allow to skip indels
-
-------------------------------------------------------------------------
-r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-
-remove ZQ if both BQ and ZQ are present
-
-------------------------------------------------------------------------
-r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-
- * samtools-0.1.9-18 (r825)
- * change the behaviour of calmd such that by default it does not change the base quality
-
-------------------------------------------------------------------------
-r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/samtools.1
-
- * samtools-0.1.9-17 (r824)
- * added command line options to change the default parameters in indel calling
- * update the manual
-
-------------------------------------------------------------------------
-r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-r823
- * the BQ tag is now 64 shifted, not 33 shifted
-
-------------------------------------------------------------------------
-r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools-0.1.9-16 (r822)
- * keep the raw depth because in indel calling, DP4 may be way off the true depth
-
-------------------------------------------------------------------------
-r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-15 (r821)
- * calmd: write BQ
- * skip realignment if BQ is present
-
-------------------------------------------------------------------------
-r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-14 (r820)
- * penalize reads with excessive differences in indel calling
-
-------------------------------------------------------------------------
-r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-13 (r819)
- * fixed a bug in pileup given refskip
-
-------------------------------------------------------------------------
-r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-r818
- * for indel calling, do two rounds of probabilistic realignments
-
-------------------------------------------------------------------------
-r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
- * samtools-0.1.19-11 (r817)
- * only initiate indel calling when 0.2% of reads contain a gap
-
-------------------------------------------------------------------------
-r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-10 (r816)
-
- * I know why the forward method fails. it is because of zero base
-   qualities. when that is fixed, the forward method seems to give
-   better results than Viterbi, as it should be. I am tired...
-
-
-------------------------------------------------------------------------
-r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam2bcf_indel.c
-
-effectively revert to the viterbi version. The forward realignment gives too many false positives.
-
-------------------------------------------------------------------------
-r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-9 (r810)
- * use forward, instead of viterbi, for realignment
- * realignment is now quality aware
-
-------------------------------------------------------------------------
-r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/kprobaln.c
-   M /trunk/samtools/kprobaln.h
-
- * prepare to replace kaln with kprobaln in realignment
-
-------------------------------------------------------------------------
-r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-
-fixed a typo
-
-------------------------------------------------------------------------
-r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.h
-
-use zlib for direct reading when BCF_LITE is in use
-
-------------------------------------------------------------------------
-r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-
- * do not use reads containing too many mismatches for indel calling
- * fixed a trivial bug in case of multi-allelic indels
-
-------------------------------------------------------------------------
-r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-8 (r809)
- * fixed a bug in the indel caller
-
-------------------------------------------------------------------------
-r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-
-minor change to makefile
-
-------------------------------------------------------------------------
-r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
- * samtools-0.1.9-8 (r807)
- * collect indel candidates only from specified platforms (@RG-PL)
- * merge varFilter and filter4vcf in vcfutils.pl 
-
-------------------------------------------------------------------------
-r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/prob1.h
-
-bcftools: compute equal-tail (Bayesian) credible interval
-
-------------------------------------------------------------------------
-r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-added a double-hit filter to avoid overestimated indel likelihood
-
-------------------------------------------------------------------------
-r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-7 (r804)
- * fixed a bug in the gap caller
-
-------------------------------------------------------------------------
-r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/prob1.c
-
- * samtools-0.1.9-6 (r803)
- * mpileup: apply homopolymer correction when calculating GL, instead of before
- * bcftools: apply a different prior to indels
-
-------------------------------------------------------------------------
-r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-5 (r802)
- * relax tandem penalty. this will be made a command-line option in future.
-
-------------------------------------------------------------------------
-r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-4 (r801)
- * fixed a minor issue in printing indel VCF
-
-------------------------------------------------------------------------
-r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-fixed another silly bug in mpileup's indel caller
-
-------------------------------------------------------------------------
-r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-
-fixed a silly bug in the indel caller
-
-------------------------------------------------------------------------
-r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/sam_view.c
-   M /trunk/samtools/samtools.1
-
-Incorporate patches by Marcel Martin for read counting.
-
-------------------------------------------------------------------------
-r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-2 (r797)
- * mpileup: indel calling seems to be working
-
-------------------------------------------------------------------------
-r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/kaln.c
-
-indel calling is apparently working, but more information needs to be collected
-
-------------------------------------------------------------------------
-r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf_indel.c
-
-fixed a few bugs in the indel caller. Probably there are more.
-
-------------------------------------------------------------------------
-r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   A /trunk/samtools/bam2bcf_indel.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/kaln.c
-   M /trunk/samtools/kaln.h
-
-prepare for the indel caller. It is not ready yet.
-
-------------------------------------------------------------------------
-r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam_plcmd.c
-
-Revert to r790. The recent changes are not good...
-
-------------------------------------------------------------------------
-r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam_plcmd.c
-
- * this revision is UNSTABLE
-
- * indel caller seems working, but it is very insensitive and has
-   several things I do not quite understand.
-
-
-------------------------------------------------------------------------
-r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam_plcmd.c
-
-for backup. no effective changes
-
-------------------------------------------------------------------------
-r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-   M /trunk/samtools/kprobaln.c
-
-fixed a minor problem in the example coming with kprobaln.c
-
-------------------------------------------------------------------------
-r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/kaln.c
-   M /trunk/samtools/kaln.h
-   A /trunk/samtools/kprobaln.c
-   A /trunk/samtools/kprobaln.h
-
-Separate kaln and kprobaln as I am preparing further changes. At
-present, the results should be identical to the previous.
-
-
-------------------------------------------------------------------------
-r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-
-Added -b option: read file names from a file
-------------------------------------------------------------------------
-r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-2 (r787)
-
- * Allow to set a maximum per-sample depth to reduce memory. However,
-   BAQ computation is still applied to every read. The speed is not
-   improved.
-
-
-------------------------------------------------------------------------
-r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/vcf.c
-
- * samtools-0.1.9-1 (r786)
- * samtools: optionally perform exact test for each sample
-
-------------------------------------------------------------------------
-r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bcftools/bcf.c
-
-Optionally output "DP", the individual read depth
-
-------------------------------------------------------------------------
-r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/samtools.1
-
-acknowledge Petr and John who have greatly contributed to the project.
-
-------------------------------------------------------------------------
-r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-
-Release samtools-0.1.9 (r783)
-
-------------------------------------------------------------------------
-r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-
-fixed a silly bug in pileup
-
-------------------------------------------------------------------------
-r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-
- * samtools-0.1.8-22 (r781)
- * made BAQ the default behavior of mpileup
- * updated manual
- * in merge, force to exit given inconsistent header when "-R" is not in use.
-
-------------------------------------------------------------------------
-r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-21 (r780)
- * minor speedup to pileup
-
-------------------------------------------------------------------------
-r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/examples/toy.sam
-
-improve pileup a little bit
-
-------------------------------------------------------------------------
-r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-20 (r778)
- * speed up pileup, although I do not know how much is the improvement
-
-------------------------------------------------------------------------
-r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_maqcns.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/examples/Makefile
-
- * samtools-0.1.8-19 (r777)
- * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
-
-------------------------------------------------------------------------
-r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-
-remove local realignment (probabilistic realignment is still there)
-
-------------------------------------------------------------------------
-r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/sam_view.c
-
-Add the relevant filename or region to error messages, and cause a failure
-exit status where appropriate.  Based on a patch provided by Marcel Martin.
-
-------------------------------------------------------------------------
-r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/examples/toy.sam
-   M /trunk/samtools/kaln.c
-
- * Minor code changes. No real effect.
- * change quality to 30 in toy.sam
-
-------------------------------------------------------------------------
-r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/examples/toy.fa
-   M /trunk/samtools/examples/toy.sam
-
-added another toy example
-
-------------------------------------------------------------------------
-r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/ld.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-improve the LD statistics
-
-------------------------------------------------------------------------
-r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
- * a minor fix to the -L option
- * add ldstats to vcfutils.pl
-
-------------------------------------------------------------------------
-r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-
-a minor change
-
-------------------------------------------------------------------------
-r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   A /trunk/samtools/bcftools/ld.c
-
-forget to add the key file
-
-------------------------------------------------------------------------
-r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
- * vcfutils.pl: fixed a typo in help message
- * added APIs: bcf_append_info() and bcf_cpy()
- * calculate adjacent LD
-
-------------------------------------------------------------------------
-r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-added filter for samtools/bcftools genetated VCFs
-
-------------------------------------------------------------------------
-r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-   M /trunk/samtools/kaln.c
-
- * removed a comment line in kaln.c
- * vcfutils.pl fillac works when GT is not the first field
-
-------------------------------------------------------------------------
-r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
-Changed paths:
-   A /trunk/samtools/bcftools/bcf-fix.pl
-
-Convert VCF output of "bcftools view -bgcv" to a valid VCF file
-------------------------------------------------------------------------
-r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   A /trunk/samtools/bcftools/bcftools.1
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/samtools.1
-
- * samtools-0.1.8-18 (r763)
- * added bcftools manual page
- * minor fix to mpileup and view command lines
-
-------------------------------------------------------------------------
-r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
- * vcfutils.pl qstats: calculate marginal ts/tv
- * allow to call genotypes at variant sites
-
-------------------------------------------------------------------------
-r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-   M /trunk/samtools/misc/HmmGlocal.java
-
-I am changing the gap open probability back to 0.001. It seems that
-being conservative here is a good thing...
-
-------------------------------------------------------------------------
-r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/kaln.c
-   A /trunk/samtools/misc/HmmGlocal.java
-
- * samtools-0.1.8-17 (r760)
- * the default gap open penalty is too small (a typo)
- * added comments on hmm_realn
- * Java implementation
-
-------------------------------------------------------------------------
-r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-
-mark samtools-0.1.8-16 (r759)
-
-------------------------------------------------------------------------
-r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
-round to the nearest integer
-
-------------------------------------------------------------------------
-r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
-I was trying to accelerate ka_prob_glocal() as this will be the
-bottleneck. After an hour, the only gain is to change division to
-multiplication. OK. I will stop.
-
-------------------------------------------------------------------------
-r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
-this is interesting. multiplication is much faster than division, at least on my Mac
-
-------------------------------------------------------------------------
-r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
-minor changes
-
-------------------------------------------------------------------------
-r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/kaln.c
-
-prob_realn() seems working!
-
-------------------------------------------------------------------------
-r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
-minor
-
-------------------------------------------------------------------------
-r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-   M /trunk/samtools/kaln.h
-
-Convert phredQ to probabilities
-
-------------------------------------------------------------------------
-r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-   M /trunk/samtools/kaln.h
-
-Implement the glocal HMM; discard the extention HMM
-
-------------------------------------------------------------------------
-r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
-improve numerical stability
-
-------------------------------------------------------------------------
-r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
-more comments
-
-------------------------------------------------------------------------
-r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
-fixed a bug in banded DP
-
-------------------------------------------------------------------------
-r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
- * fixed that weird issue.
- * the banded version is NOT working
-
-------------------------------------------------------------------------
-r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
-More comments. This version seems working, but something is a little weird...
-
-------------------------------------------------------------------------
-r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
-Changed paths:
-   M /trunk/samtools/kaln.c
-
-A little code cleanup. Now the forward and backback algorithms give
-nearly identical P(x), which means both are close to the correct
-forms. However, I have only tested on toy examples. Minor errors in
-the implementation may not be obvious.
-
-
-------------------------------------------------------------------------
-r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/kaln.c
-   M /trunk/samtools/kaln.h
-
-...
-
-------------------------------------------------------------------------
-r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
-Changed paths:
-   M /trunk/samtools/bam_sort.c
-
-Abort if merge -h's INH.SAM cannot be opened, just as we abort
-if any of the IN#.BAM input files cannot be opened.
-
-Also propagate any error indication returned by bam_merge_core()
-to samtools merge's exit status.
-
-------------------------------------------------------------------------
-r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-
-Use bam_validate1() to detect garbage records in the event of a corrupt
-BAI index file that causes a bam_seek() to an invalid position.  At most
-one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
-call, so the cost is insignificant in the normal case.
-
-------------------------------------------------------------------------
-r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-
-Add bam_validate1().
-
-------------------------------------------------------------------------
-r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-15 (r379)
- * allow to change capQ parameter in calmd
-
-------------------------------------------------------------------------
-r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/sam_view.c
-
-When bam_read1() returns an error (return value <= -2), propagate that error
-to bam_iter_read()'s own return value.  Similarly, also propagate it up to
-bam_fetch()'s return value.  Previously bam_fetch() always returned 0, and
-callers ignored its return value anyway.  With this change, 0 continues to
-indicate success, while <= -2 (which can be written as < 0, as -1 is never
-returned) indicates corrupted input.
-
-bam_iter_read() ought also to propagate errors returned by bam_seek().
-
-main_samview() can now print an error message and fail when bam_fetch()
-detects that a .bai index file is corrupted or otherwise does not correspond
-to the .bam file it is being used with.
-
-------------------------------------------------------------------------
-r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-
-0 is a successful return value from bam_read1().  (In practice, it never
-returns 0 anyway; but all the other callers treat 0 as successful.)
-
-------------------------------------------------------------------------
-r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bam_sort.c
-
- * merge files region-by-region. work on small examples but more tests are needed.
-
-------------------------------------------------------------------------
-r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-improve qstats by checking the alleles as well
-
-------------------------------------------------------------------------
-r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-convert UCSC SNP SQL dump to VCF
-
-------------------------------------------------------------------------
-r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-hapmap2vcf convertor
-
-------------------------------------------------------------------------
-r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/vcf.c
-
- * added comments
- * VCF->BCF is not possible without knowing the sequence dictionary before hand...
-
-------------------------------------------------------------------------
-r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/bcfutils.c
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/vcf.c
-
- * put n_smpl to "bcf1_t" to simplify API a little
-
-------------------------------------------------------------------------
-r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/index.c
-
-fixed a bug in indexing
-
-------------------------------------------------------------------------
-r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_pileup.c
-
- * fixed a bug in capQ
- * valgrind identifies a use of uninitialised value, but I have not fixed it.
-
-------------------------------------------------------------------------
-r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bgzip.c
-   M /trunk/samtools/razip.c
-
- * fixed a bug in razip: -c will delete the input file
- * copy tabix/bgzip to here
-
-------------------------------------------------------------------------
-r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-14 (r727)
- * allow to change the capQ parameter at the command line
-
-------------------------------------------------------------------------
-r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-   M /trunk/samtools/misc/samtools.pl
-
- * added varFilter to vcfutils.pl
- * reimplement realn(). now it performs a local alignment
- * added cap_mapQ() to cap mapping quality when there are many substitutions
-
-------------------------------------------------------------------------
-r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   A /trunk/samtools/bcftools/bcf2qcall.c
-   M /trunk/samtools/bcftools/call1.c
-
- * convert BCF to QCALL input
-
-------------------------------------------------------------------------
-r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-
-dynamic band width in realignment
-
-------------------------------------------------------------------------
-r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_plcmd.c
-
-fixed a bug in realignment
-
-------------------------------------------------------------------------
-r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/prob1.c
-
-fixed a minor issue
-
-------------------------------------------------------------------------
-r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_md.c
-
-fixed a bug in realignment
-
-------------------------------------------------------------------------
-r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-
-minor changes. It is BUGGY now!
-
-------------------------------------------------------------------------
-r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/kaln.c
-   M /trunk/samtools/kaln.h
-
- * aggressive gapped aligner is implemented in calmd.
- * distinguish gap_open and gap_end_open in banded alignment
- * make tview accepts alignment with heading and tailing D
-
-------------------------------------------------------------------------
-r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools
-
-Add svn:ignore properties for generated files that don't appear in "make all".
-
-------------------------------------------------------------------------
-r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools
-   M /trunk/samtools/bcftools
-   M /trunk/samtools/misc
-
-Add svn:ignore properties listing the generated files.
-(Except for *.o, which we'll assume is in global-ignores.)
-
-------------------------------------------------------------------------
-r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/sample.c
-   M /trunk/samtools/sample.h
-
- * samtools-0.1.8-13 (r715)
- * fixed a bug in identifying SM across files
- * bcftools: estimate heterozygosity
- * bcftools: allow to skip sites without reference bases
-
-------------------------------------------------------------------------
-r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/prob1.h
-
-quite a lot changes to the contrast caller, but I still feel something is missing...
-
-------------------------------------------------------------------------
-r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/vcfutils.pl
-
- * changed 3.434 to 4.343 (typo!)
- * fixed a bug in the contrast caller
- * calculate heterozygosity
-
-------------------------------------------------------------------------
-r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/bcfutils.c
-   M /trunk/samtools/bcftools/call1.c
-
-SNP calling from the GL field
-
-------------------------------------------------------------------------
-r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcf.c
-
-fixed another problem
-
-------------------------------------------------------------------------
-r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/vcf.c
-
- * fixed bugs in parsing VCF
- * parser now works with GT/GQ/DP/PL/GL
-
-------------------------------------------------------------------------
-r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   M /trunk/samtools/bcftools/prob1.c
-
-Do not compile _BCF_QUAD by default
-
-------------------------------------------------------------------------
-r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/bcfutils.c
-   M /trunk/samtools/bcftools/call1.c
-
-Write the correct ALT and PL in the SNP calling mode.
-
-------------------------------------------------------------------------
-r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfutils.pl
-
-more commands for my own uses
-
-------------------------------------------------------------------------
-r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
-   A /trunk/samtools/bcftools/vcfutils.pl
-
-Utilities for processing VCF
-
-------------------------------------------------------------------------
-r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/prob1.h
-
-preliminary contrast variant caller
-
-------------------------------------------------------------------------
-r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/call1.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/prob1.h
-
-z' and z'' can be calculated
-
-------------------------------------------------------------------------
-r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
-   M /trunk/samtools/bcftools/prob1.c
-   D /trunk/samtools/bcftools/vcfout.c
-
- * rename vcfout.c as call1.c
- * prepare to add two-sample comparison
-
-------------------------------------------------------------------------
-r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfout.c
-
-fixed a bug in calculating the t statistics
-
-------------------------------------------------------------------------
-r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcftools/kfunc.c
-   M /trunk/samtools/bcftools/vcfout.c
-
- * samtools-0.1.8-13 (r698)
- * perform one-tailed t-test for baseQ, mapQ and endDist
-
-------------------------------------------------------------------------
-r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/kfunc.c
-
-added regularized incomplete beta function
-
-------------------------------------------------------------------------
-r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_plcmd.c
-
-change the default correlation coefficient
-
-------------------------------------------------------------------------
-r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/vcfout.c
-
-print QUAL as floating numbers
-
-------------------------------------------------------------------------
-r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/examples/Makefile
-   A /trunk/samtools/sample.c
-   A /trunk/samtools/sample.h
-
- * samtools-0.1.8-12 (r692)
- * group data by samples in "mpileup -g"
-
-------------------------------------------------------------------------
-r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   D /trunk/samtools/bam_mcns.c
-   D /trunk/samtools/bam_mcns.h
-   M /trunk/samtools/bam_plcmd.c
-
-remove VCF output in mpileup
-
-------------------------------------------------------------------------
-r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-
- * use the revised MAQ error model for mpileup
- * prepare to remove the independent model from mpileup
-
-------------------------------------------------------------------------
-r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_maqcns.h
-   M /trunk/samtools/bam_plcmd.c
-   A /trunk/samtools/errmod.c
-   A /trunk/samtools/errmod.h
-   M /trunk/samtools/ksort.h
-
-added revised MAQ error model
-
-------------------------------------------------------------------------
-r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/prob1.h
-   M /trunk/samtools/bcftools/vcfout.c
-
-allow to read the prior from the error output. EM iteration is working.
-
-------------------------------------------------------------------------
-r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/main.c
-   M /trunk/samtools/bcftools/vcf.c
-
- * write a little more VCF header
- * concatenate BCFs
-
-------------------------------------------------------------------------
-r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/bcf.tex
-
-use float for QUAL
-
-------------------------------------------------------------------------
-r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/prob1.c
-
-faster for large sample size (in principle)
-
-------------------------------------------------------------------------
-r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bcftools/prob1.c
-
- * a numerically stable method to calculate z_{jk}
- * currently slower than the old method but will be important for large sample size
- * in principle, we can speed up for large n, but have not tried
-
-------------------------------------------------------------------------
-r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfout.c
-
-fixed an issue in parsing integer
-
-------------------------------------------------------------------------
-r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-
-do not print refname if file is converted from VCF
-
-------------------------------------------------------------------------
-r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcf.c
-
- * parse PL
- * fixed a bug in parsing VCF
-
-------------------------------------------------------------------------
-r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/bcfutils.c
-   M /trunk/samtools/bcftools/main.c
-   M /trunk/samtools/bcftools/vcf.c
-   M /trunk/samtools/bcftools/vcfout.c
-   M /trunk/samtools/bgzf.c
-   M /trunk/samtools/kstring.c
-
- * fixed a bug in kstrtok@kstring.c
- * preliminary VCF parser (not parse everything for now)
- * improved view interface
-
-------------------------------------------------------------------------
-r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/vcfout.c
-   M /trunk/samtools/kstring.c
-   M /trunk/samtools/kstring.h
-
- * improved kstring (added kstrtok)
- * removed the limit on the format string length in bcftools
- * use kstrtok to parse format which fixed a bug in the old code
-
-------------------------------------------------------------------------
-r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
-Changed paths:
-   A /trunk/samtools/bcftools/README
-   M /trunk/samtools/bcftools/vcfout.c
-
-help messages
-
-------------------------------------------------------------------------
-r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcfout.c
-
-perform single-tail test for ED4
-
-------------------------------------------------------------------------
-r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   M /trunk/samtools/bcftools/kfunc.c
-   M /trunk/samtools/bcftools/vcfout.c
-
- * test depth, end distance and HWE
-
-------------------------------------------------------------------------
-r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/kfunc.c
-
-reimplement incomplete gamma functions. no copy-paste
-
-------------------------------------------------------------------------
-r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bcftools/fet.c
-   M /trunk/samtools/bcftools/prob1.c
-   M /trunk/samtools/bcftools/prob1.h
-   M /trunk/samtools/bcftools/vcfout.c
-
- * bcftools: add HWE (no testing for now)
- * record end dist in a 2x2 table, not avg, std any more
-
-------------------------------------------------------------------------
-r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
-Changed paths:
-   A /trunk/samtools/bcftools/kfunc.c
-
- * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
- * Not using Numerical Recipe due to licensing issues
-
-------------------------------------------------------------------------
-r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
-Changed paths:
-   A /trunk/samtools/bcftools/fet.c
-
-Fisher's exact test
-
-------------------------------------------------------------------------
-r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/examples/Makefile
-
- * samtools-0.1.8-11 (r672)
- * collect more stats for allele balance test in bcftools (not yet)
-
-------------------------------------------------------------------------
-r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/main.c
-
- * the code base is stablized again.
- * I will delay the vcf parser, which is quite complicated but with little value for now
-
-------------------------------------------------------------------------
-r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/examples/Makefile
-
-minor
-
-------------------------------------------------------------------------
-r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcftools/vcf.c
-
-unfinished vcf parser
-
-------------------------------------------------------------------------
-r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bcftools/Makefile
-   M /trunk/samtools/bcftools/bcf.c
-   M /trunk/samtools/bcftools/bcf.h
-   M /trunk/samtools/bcftools/bcfutils.c
-   M /trunk/samtools/bcftools/index.c
-   M /trunk/samtools/bcftools/main.c
-   A /trunk/samtools/bcftools/vcf.c
-   M /trunk/samtools/bcftools/vcfout.c
-
- * added prelimiary VCF parser (not finished)
- * change struct a bit
-
-------------------------------------------------------------------------
-r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bcftools/bcf.c
-
- * allow to set min base q
- * fixed a bug in mpileup -u
-
-------------------------------------------------------------------------
-r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
-Changed paths:
-   A /trunk/samtools/bcftools/bcf.tex
-
-spec
-
-------------------------------------------------------------------------
-r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/examples/Makefile
-
-added more examples
-
-------------------------------------------------------------------------
-r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bcftools/Makefile
-
-fixed compilation error
-
-------------------------------------------------------------------------
-r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   D /trunk/samtools/bcf.c
-   D /trunk/samtools/bcf.h
-   A /trunk/samtools/bcftools
-   A /trunk/samtools/bcftools/Makefile
-   A /trunk/samtools/bcftools/bcf.c
-   A /trunk/samtools/bcftools/bcf.h
-   A /trunk/samtools/bcftools/bcfutils.c
-   A /trunk/samtools/bcftools/index.c
-   A /trunk/samtools/bcftools/main.c
-   A /trunk/samtools/bcftools/prob1.c
-   A /trunk/samtools/bcftools/prob1.h
-   A /trunk/samtools/bcftools/vcfout.c
-
-move bcftools to samtools
-
-------------------------------------------------------------------------
-r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-
-fixed another minor bug
-
-------------------------------------------------------------------------
-r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bcf.c
-
- * samtools-0.1.8-10 (r658)
- * fixed a bug in bam2bcf when the reference is N
-
-------------------------------------------------------------------------
-r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-
- * fixed a bug
- * treat ambiguous ref base as the fifth base
-
-------------------------------------------------------------------------
-r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/bcftools/bcf.c
-   M /trunk/samtools/bcf.c
-
-missing a column in VCF output...
-
-------------------------------------------------------------------------
-r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcf.c
-
-fixed a memory leak
-
-------------------------------------------------------------------------
-r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bcf.c
-
-fixed a bug in bcf reader
-
-------------------------------------------------------------------------
-r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam2bcf.c
-
-fixed a bug
-
-------------------------------------------------------------------------
-r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam2bcf.c
-   M /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-9 (r649)
- * lossless representation of PL in BCF output
-
-------------------------------------------------------------------------
-r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   A /trunk/samtools/bam2bcf.c
-   A /trunk/samtools/bam2bcf.h
-   M /trunk/samtools/bam_plcmd.c
-   A /trunk/samtools/bcf.c
-   A /trunk/samtools/bcf.h
-
-Generate binary VCF
-
-------------------------------------------------------------------------
-r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-8 (r644)
- * mpileup becomes a little stable again
- * the method is slightly different, but is more theoretically correct
- * snp calling is O(n^2) instead of O(n^3)
-
-------------------------------------------------------------------------
-r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-
- * fixed a STUPID bug, which cost me a lot of time.
- * I am going to clean up mcns a little bit
-
-------------------------------------------------------------------------
-r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bam_mcns.h
-   M /trunk/samtools/bam_plcmd.c
-
-supposedly this is THE correct implementation, but more testing is needed
-
-------------------------------------------------------------------------
-r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-
-NOT ready yet. Going to make further changes...
-
-------------------------------------------------------------------------
-r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-7 (r639)
- * fixed the reference allele assignment
-
-------------------------------------------------------------------------
-r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bam_mcns.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-6 (r638)
- * skip isnan/isinf in case of float underflow
- * added the flat prior
- * fixed an issue where there are no reads supporting the reference
-
-------------------------------------------------------------------------
-r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-
-minor changes
-
-------------------------------------------------------------------------
-r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bam_mcns.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
-minor tweaks
-
-------------------------------------------------------------------------
-r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bam_mcns.h
-   M /trunk/samtools/bam_plcmd.c
-
-posterior expectation FINALLY working. I am so tired...
-
-------------------------------------------------------------------------
-r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-
-another minor fix to mpileup
-
-------------------------------------------------------------------------
-r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-
-added the format column
-
-------------------------------------------------------------------------
-r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bam_mcns.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
-added an alternative prior
-
-------------------------------------------------------------------------
-r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bam_mcns.h
-   M /trunk/samtools/bam_plcmd.c
-
-calculate posterior allele frequency
-
-------------------------------------------------------------------------
-r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-3 (r627)
- * multi-sample snp calling appears to work. More tests needed.
-
-------------------------------------------------------------------------
-r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bam_mcns.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bam_tview.c
-
- * preliminary multisample SNP caller.
- * something looks not so right, but it largely works
-
-------------------------------------------------------------------------
-r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_mcns.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-2 (r617)
- * allele frequency calculation apparently works...
-
-------------------------------------------------------------------------
-r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   A /trunk/samtools/bam_mcns.c
-   A /trunk/samtools/bam_mcns.h
-   M /trunk/samtools/bam_plcmd.c
-
- * added mutli-sample framework. It is not working, yet.
- * improved the mpileup interface
-
-------------------------------------------------------------------------
-r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/Makefile
-
- * samtools-0.1.8-1 (r615)
- * allow to get mpileup at required sites
-
-------------------------------------------------------------------------
-r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-
-Release samtools-0.1.8
-
-------------------------------------------------------------------------
-r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/knetfile.c
-
-fixed a compiling issue for Windows
-
-------------------------------------------------------------------------
-r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_sort.c
-
-fixed a bug in sorting when output to stdout (by Peter Chines)
-
-------------------------------------------------------------------------
-r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bam_plcmd.c
-
-change the command line option of pileup
-
-------------------------------------------------------------------------
-r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_pileup.c
-   A /trunk/samtools/examples/toy.fa
-   A /trunk/samtools/examples/toy.sam
-
-make pileup work with CIGAR with I/D at the beginning or in the end
-
-------------------------------------------------------------------------
-r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_maqcns.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bam_tview.c
-
- * make tview more friendly
- * a temporary remedy for an issue in indel calling
-
-------------------------------------------------------------------------
-r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-r607
- * improved the genotype accuracy for indels
- * use the SOAPsnp model for SNP calling by default.
-
-------------------------------------------------------------------------
-r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/Makefile
-
-removed a debugging example
-
-------------------------------------------------------------------------
-r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-.1.7-18 (r605)
- * fixed an issue when a deletion and mismatch occur at the same time
-   and the base quality is higher than 40 (if -I40).
-
-------------------------------------------------------------------------
-r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/misc/Makefile
-
-fixed a minor bug in idxstats
-
-------------------------------------------------------------------------
-r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-
-fixed a minor bug in indexing
-
-------------------------------------------------------------------------
-r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam.c
-
-change printf() to puts in exporting
-
-------------------------------------------------------------------------
-r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-
-minor fix. No actual effect.
-
-------------------------------------------------------------------------
-r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-
-added Makefile targets to compile shared/dynamic library
-
-------------------------------------------------------------------------
-r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-17 (r596)
- * also keep the number of coor-less reads in the index file
-
-------------------------------------------------------------------------
-r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-16 (r595)
- * write additional information to bam index
-
-------------------------------------------------------------------------
-r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-
-fixed a bug for unmapped sequences in indexing
-
-------------------------------------------------------------------------
-r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/samtools.1
-
-rename iterf as iter
-
-------------------------------------------------------------------------
-r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-15 (r592)
- * fixed a few minor memory leaks in the new pileup code
- * improved the functionality of mpileup
-
-------------------------------------------------------------------------
-r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-14 (r591)
- * elementary multi-way pileup. More testing and more functionality to be done.
-
-------------------------------------------------------------------------
-r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-13 (r590)
- * added mpileup APIs. No compiling errors, but not tested at all. It is late.
-
-------------------------------------------------------------------------
-r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-12 (r589)
- * added iterator-like APIs for pileup
-
-------------------------------------------------------------------------
-r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-11 (r588)
- * ported a few improvements from tabix back to samtools
-
-------------------------------------------------------------------------
-r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-10 (r587)
- * added iterator interface for bam_fetch (ported back from tabix)
-
-------------------------------------------------------------------------
-r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   A /trunk/samtools/bam_reheader.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bgzf.c
-
- * samtools-0.1.7-9 (r586)
- * added "reheader" to replace the BAM header
-
-------------------------------------------------------------------------
-r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/kstring.h
-
- * samtools-0.1.7-8 (r585)
- * speed up "view"
-
-------------------------------------------------------------------------
-r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bgzf.c
-   M /trunk/samtools/bgzf.h
-   M /trunk/samtools/kstring.h
-   M /trunk/samtools/misc/wgsim_eval.pl
-
- * samtools-0.1.7-7 (r584)
- * ported tabix BGZF to samtools
- * flush BGZF after writing the BAM header and between alignment boundaries
-
-------------------------------------------------------------------------
-r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
-Changed paths:
-   A /trunk/samtools/misc/varfilter.py
-
-Initial release on behalf of Aylwyn Scally
-------------------------------------------------------------------------
-r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/samtools.1
-
-Added a note about the indels coordinates
-------------------------------------------------------------------------
-r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/misc/sam2vcf.pl
-
-Added the possibility to print or not to print the reference allele
-------------------------------------------------------------------------
-r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/sam_header.c
-
-More descriptive message for space separated tags
-------------------------------------------------------------------------
-r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/misc/sam2vcf.pl
-
-Speedup with -i, no need to query the reference all the time
-------------------------------------------------------------------------
-r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/sam_header.c
-
-Fixed the order of sequences in the header
-------------------------------------------------------------------------
-r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/misc/sam2vcf.pl
-
-Added possibility to select indels only and fixed a bug in reporting homozygous indels.
-------------------------------------------------------------------------
-r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-
-Improve the invalid 'BAM\1' magic number error message, and also print it
-when no bytes can be read from the alleged BAM file, e.g., in the common
-user error case when a SAM file has accidentally been supplied.
-
-------------------------------------------------------------------------
-r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/AUTHORS
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/sam_header.c
-
-Improved efficiency of header parsing
-------------------------------------------------------------------------
-r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/export2sam.pl
-
-Updated export2sam.pl by Chris Saunders from Illumina.
-
-
-------------------------------------------------------------------------
-r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
-Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
-------------------------------------------------------------------------
-r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/misc/sam2vcf.pl
-
-Print an error for pileups in simple format
-------------------------------------------------------------------------
-r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-
-added a hidden option in pileup to output the base position (for Erin)
-
-------------------------------------------------------------------------
-r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/misc/sam2vcf.pl
-
-Added possibility to specify a custom column title for the data column
-------------------------------------------------------------------------
-r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-
-Added the -d option to limit maximum depth for indels.
-------------------------------------------------------------------------
-r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
-Changed paths:
-   M /trunk/samtools/misc/sam2vcf.pl
-
-Added VCF header
-------------------------------------------------------------------------
-r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/samtools.pl
-   M /trunk/samtools/misc/wgsim.c
-
- * samtools-0.1.7-6
- * fixed a bug in faidx
-
-------------------------------------------------------------------------
-r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
-Changed paths:
-   M /trunk/samtools/faidx.c
-
-Put the right filename in the error message.
-
-------------------------------------------------------------------------
-r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-5 (r528)
- * further add new consensus generation strategy
-
-------------------------------------------------------------------------
-r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
-Changed paths:
-   M /trunk/samtools/knetfile.c
-
-Fixed a bug in knet_seek
-------------------------------------------------------------------------
-r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
-Changed paths:
-   M /trunk/samtools/misc/sam2vcf.pl
-
-Small fix in VCF format: dot for the empty INFO field
-------------------------------------------------------------------------
-r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
-Changed paths:
-   M /trunk/samtools/sam_header.c
-
-Allow tabs in the CO header field
-------------------------------------------------------------------------
-r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/Makefile.mingw
-
-Depend on libbam.a rather than the phony target, so that samtools is not
-unnecessarily rebuilt every time.  Also clean bgzip.
-
-------------------------------------------------------------------------
-r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/Makefile.mingw
-
-Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
-is defined.  Also introduce $(KNETFILE_O) which can be set to empty to
-facilitate non-knet builds.
-
-------------------------------------------------------------------------
-r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.7-4 (r522)
- * fixed a bug in "view -r"
- * added a new option "view -R" to read required read groups from a file
-
-------------------------------------------------------------------------
-r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-3 (r521)
- * calmd: optionally mask matching bases as N
-
-------------------------------------------------------------------------
-r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools-0.1.7-2 (r520)
- * fixed a few issues with compilation in Windows (on behalf of John)
- * choose a random base as the consensus (for population genetics studies)
-
-------------------------------------------------------------------------
-r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-
-Put libraries at the end, so they can resolve references from libbam.a
-as well, even with old-fashioned linkers.
-
-Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
-the freshly built library, not some other libbam.a lying around the system.
-
-------------------------------------------------------------------------
-r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/misc/Makefile
-
-Also clean *.exe (for Cygwin users using this makefile).
-
-------------------------------------------------------------------------
-r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-
-Index files should be opened in binary mode, not text mode.
-
-------------------------------------------------------------------------
-r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
-Changed paths:
-   A /trunk/samtools/examples/bam2bed.c
-
-another example program
-
-------------------------------------------------------------------------
-r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/wgsim_eval.pl
-   M /trunk/samtools/sam.c
-
- * samtools-0.1.7-1 (r515)
- * report an error when .fai contains duplicated names, instead of segfault
-
-------------------------------------------------------------------------
-r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-
-Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
-
-------------------------------------------------------------------------
-r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile.mingw
-
-Update Makefile.mingw for the same reason
-
-------------------------------------------------------------------------
-r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-
-Fixed a bug in compiling razip
-
-------------------------------------------------------------------------
-r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-
-Release samtools-0.1.7 (r510)
-
-------------------------------------------------------------------------
-r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-22 (r509)
- * forget to fix a similar problem in glfgen
-
-------------------------------------------------------------------------
-r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.6-21 (r508)
- * fixed a potential bug in the indel caller towards the end of a chromosome
-
-------------------------------------------------------------------------
-r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.6-19 (r494)
- * allow to convert Illumina quality (64 based) to the BAM quality
-
-------------------------------------------------------------------------
-r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam_header.c
-
- * samtools-0.1.6-18 (r493)
- * fixed the bugs due to improperly incorporating Petr's header parser
- * a little code clean up in sam_header.c
-
-------------------------------------------------------------------------
-r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
-Changed paths:
-   M /trunk/samtools/sam_header.c
-
-Added sam_header_line_free call for sam_header_parse2
-------------------------------------------------------------------------
-r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/sam_view.c
-
- * BUGGY VERSION
- * fixed a minor bug
-
-------------------------------------------------------------------------
-r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/sam.c
-
- * BUGGY VERSION
- * improved the interface a bit
- * bug unfixed
-
-------------------------------------------------------------------------
-r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/sam_header.c
-   M /trunk/samtools/sam_header.h
-
- * BUGGY VERSION. Please NOT use it.
- * Fixed a minor bug, but the major bug is still there.
-
-------------------------------------------------------------------------
-r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_rmdup.c
-   M /trunk/samtools/bam_rmdupse.c
-   M /trunk/samtools/kaln.c
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam_header.c
-   M /trunk/samtools/sam_header.h
-   M /trunk/samtools/sam_view.c
-
- * This revision is SERIOUSLY BUGGY. Please NOT use it.
- * Start to incorporate header parsing from Petr Danecek
-
-------------------------------------------------------------------------
-r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
-Changed paths:
-   M /trunk/samtools/sam_header.c
-   M /trunk/samtools/sam_header.h
-
-Now possible to merge multiple HeaderDict dictionaries
-------------------------------------------------------------------------
-r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
-Changed paths:
-   M /trunk/samtools/sam_header.c
-
-
-------------------------------------------------------------------------
-r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
-Changed paths:
-   A /trunk/samtools/sam_header.c
-   A /trunk/samtools/sam_header.h
-
-
-------------------------------------------------------------------------
-r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_rmdupse.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/examples/Makefile
-
- * samtools-0.1.6-17 (r484)
- * fixed a memory leak in rmdupse
- * fixed a bug in parsing @RG header lines
- * test rmdup in examples/
-
-------------------------------------------------------------------------
-r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_rmdup.c
-   M /trunk/samtools/bam_rmdupse.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-16 (r483)
- * unify the interface of rmdup and rmdupse
- * a new bug found in rg2lib(). Have not been fixed yet.
-
-------------------------------------------------------------------------
-r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_rmdup.c
-   M /trunk/samtools/bam_rmdupse.c
-   M /trunk/samtools/bamtk.c
-   A /trunk/samtools/klist.h
-
- * samtools-0.1.6-15 (r482)
- * rewrite rmdupse
- * rmdupse is now library aware
-
-------------------------------------------------------------------------
-r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_rmdup.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-14 (r480)
- * rmdup is now RG aware
-
-------------------------------------------------------------------------
-r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
-added a small unitity to parse SRA XML files
-
-------------------------------------------------------------------------
-r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_maqcns.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-13 (r479)
- * merge: optionally use file names as RG tags
-
-------------------------------------------------------------------------
-r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/kaln.c
-
- * samtools-0.1.6-12 (r478)
- * fixed a bug in the indel caller
-
-------------------------------------------------------------------------
-r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-11 (r477)
- * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
-
-------------------------------------------------------------------------
-r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
-Changed paths:
-   A /trunk/samtools/misc/sam2vcf.pl
-
-Added the sam2vcf.pl script.
-------------------------------------------------------------------------
-r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bamtk.c
-   A /trunk/samtools/kaln.c
-   A /trunk/samtools/kaln.h
-
-Unfinished modification. Please do not use this revision...
-
-------------------------------------------------------------------------
-r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
-Changed paths:
-   M /trunk/samtools/knetfile.c
-
-Removed the offending knet_seek message.
-------------------------------------------------------------------------
-r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
-Changed paths:
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/razf.c
-
-Bug fix - faidx on RAZF compressed files now working.
-------------------------------------------------------------------------
-r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/samtools.1
-
-Clarify the meaning of a region like "chr2:1,000,000".
-
-------------------------------------------------------------------------
-r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/novo2sam.pl
-
-Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
-
-------------------------------------------------------------------------
-r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile.mingw
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/knetfile.h
-
- * samtools-0.1.6-9 (r470)
- * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
-
-------------------------------------------------------------------------
-r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-9 (r469)
- * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
-
-------------------------------------------------------------------------
-r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools-0.1.6-7 (r468)
- * make merge stable
-
-------------------------------------------------------------------------
-r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
-Changed paths:
-   M /trunk/samtools/bgzf.c
-   M /trunk/samtools/bgzip.c
-   M /trunk/samtools/razf.c
-   M /trunk/samtools/razip.c
-
-Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
-------------------------------------------------------------------------
-r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-6 (r466)
- * do not crash calmd when some sequences are absent from the reference.
-
-------------------------------------------------------------------------
-r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/knetfile.c
-
-Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
-no way to seek on a pipe and the messages always appear.
-
-------------------------------------------------------------------------
-r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
-Changed paths:
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/razf.c
-
-A bug fix, "samtools view" is now working again.
-------------------------------------------------------------------------
-r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/faidx.c
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/knetfile.h
-   M /trunk/samtools/razf.c
-   M /trunk/samtools/razf.h
-
- * samtools-0.1.6-5 (r462)
- * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
-
-------------------------------------------------------------------------
-r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/samtools.1
-
-fixed a formatting issue
-
-------------------------------------------------------------------------
-r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-4 (r459)
- * make sort output the result to stdout when -o is in use
-
-------------------------------------------------------------------------
-r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/faidx.c
-   M /trunk/samtools/faidx.h
-   M /trunk/samtools/samtools.1
-
- * samtools-0.1.6-2 (r458)
- * added more interface to faidx (by Nils)
- * updated documentation
-
-------------------------------------------------------------------------
-r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-2 (r457)
- * get rid of three assert() in bam_sort.c
-
-------------------------------------------------------------------------
-r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/razf.c
-
-Return NULL from _razf_open() (and hence razf_open()/razf_open2())
-when opening the file fails.
-
-------------------------------------------------------------------------
-r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-   D /trunk/samtools/source.dot
-
-Release samtools-0.1.6
-
-------------------------------------------------------------------------
-r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_rmdup.c
-   M /trunk/samtools/bam_rmdupse.c
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-
- * samtools-0.1.5-34 (r451)
- * applied the patch by John
- * improved the help message a little bit
-
-------------------------------------------------------------------------
-r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_color.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-33 (r450)
- * fixed a bug in bam_color.c (on behalf of Nils Homer)
-
-------------------------------------------------------------------------
-r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools-0.1.5-32 (r449)
- * fillmd: fixed a bug in modifying MD/NM tags
- * in import, give a warning if the read is aligned but there is no CIGAR.
-
-------------------------------------------------------------------------
-r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/wgsim_eval.pl
-
- * samtools-0.1.5-31 (r448)
- * fixed an issue when the last CIGAR is I or D
-
-------------------------------------------------------------------------
-r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-30 (r447)
- * fixed a bug in bam_aux_get(): 'A' is not checked
-
-------------------------------------------------------------------------
-r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bamtk.c
-
- * 
-
-------------------------------------------------------------------------
-r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-28 (r444)
- * bug in "merge -n"
-
-------------------------------------------------------------------------
-r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-27 (r443)
- * SEQ and QUAL can be "*"
- * parse CIGAR "=" and "X" as "M"
-
-------------------------------------------------------------------------
-r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/md5.c
-   M /trunk/samtools/misc/md5.h
-   M /trunk/samtools/misc/md5fa.c
-
- * samtools-0.1.5-26 (r442)
- * replace RSA Inc md5.* with ones under permissive lincense
- * fixed a bug in detecting unsorted bam in pileup
-
-------------------------------------------------------------------------
-r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bgzf.c
-   M /trunk/samtools/bgzf.h
-   M /trunk/samtools/bgzip.c
-
-Change copyright notices now that MIT has approved open source distribution.
-
-------------------------------------------------------------------------
-r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_stat.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-25 (r436)
- * in flagstats, do not report singletons if both ends are unmapped
-
-------------------------------------------------------------------------
-r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/maq2sam.c
-
-fixed a SERIOUS bug in setting 0x20 flag
-
-------------------------------------------------------------------------
-r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
-fixed two minor bugs (suggested by Tim M Storm)
-
-------------------------------------------------------------------------
-r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/samtools.pl
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-24 (r435)
- * fixed a typo
-
-------------------------------------------------------------------------
-r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-23 (r434)
- * in tview, press 'r' to show read names rather than sequences
-
-------------------------------------------------------------------------
-r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/knetfile.c
-
- * tried to fixed the buggy FTP random access in Windows. FAILED.
- * anyway, MinGW seems to have problem with "%lld".
-
-------------------------------------------------------------------------
-r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/Makefile.mingw
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/faidx.c
-   M /trunk/samtools/razf.c
-   A /trunk/samtools/win32/libcurses.a
-   A /trunk/samtools/win32/xcurses.h
-
- * samtools-0.1.5-22 (r432)
- * faidx: fixed compitability issue with _WIN32
- * razf: fixed potential compitability issue with _WIN32
- * PDCurses support in Windows
-
-------------------------------------------------------------------------
-r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/win32/libz.a
-
-replace the GnuWin32 version of libz.a with my own build with MinGW.
-
-------------------------------------------------------------------------
-r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/knetfile.c
-
-add comments
-
-------------------------------------------------------------------------
-r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile.mingw
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/knetfile.h
-
- * samtools-0.1.5-21 (r428)
- * knetfile.c is now compatible with mingw-winsock
-
-------------------------------------------------------------------------
-r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile.mingw
-
-simplify MinGW Makefile
-
-------------------------------------------------------------------------
-r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
-Changed paths:
-   A /trunk/samtools/Makefile.mingw
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-   A /trunk/samtools/win32
-   A /trunk/samtools/win32/libz.a
-   A /trunk/samtools/win32/zconf.h
-   A /trunk/samtools/win32/zlib.h
-
- * samtools-0.1.5-20 (r427)
- * MinGW support. At least SAM<->BAM conversion is working. Other
-   functionality are not tested at the moment.
- * zlib headers and Windows version of libz.a are included in win32/
-
-------------------------------------------------------------------------
-r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-19 (r426)
- * fixed a bug caused by recent modifications. Sorry.
-
-------------------------------------------------------------------------
-r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bgzf.c
-
-compatible with Windows binary files
-
-------------------------------------------------------------------------
-r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_maqcns.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools-0.1.5-18 (r423)
- * output additional information in pileup indel lines, for the purepose
-   of debugging at the moment
- * in tview, optionally allow to treat reference skip as deletion
-
-------------------------------------------------------------------------
-r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
-Changed paths:
-   A /trunk/samtools/misc/psl2sam.pl
-
-convert BLAT psl to SAM.
-
-------------------------------------------------------------------------
-r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bgzf.c
-   M /trunk/samtools/bgzf.h
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-17 (r422)
- * fixed a but in knetfile.c when seek type is not SEEK_SET
- * write an empty BGZF block to every BGZF file
- * check BGZF EOF marker in bam_header_read()
- * update ChangeLog
-
-------------------------------------------------------------------------
-r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/samtools.pl
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam.h
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-16 (r421)
- * in view and pileup, load header from FASTA index if the input is SAM.
-
-------------------------------------------------------------------------
-r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/maq2sam.c
-
-do not set "read 1" if reads are not mapped in the PE mode of maq
-
-------------------------------------------------------------------------
-r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/samtools.pl
-   M /trunk/samtools/misc/wgsim_eval.pl
-
- * samtools-0.1.5-15 (r419)
- * in sam_open(), return NULL when the file cannot be opened.
- * make wgsim_eval.pl more robust to imperfect SAM
- * add "unique" command to samtools.pl
-
-------------------------------------------------------------------------
-r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/wgsim_eval.pl
-
-skip @header lines in SAM
-
-------------------------------------------------------------------------
-r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-14 (r417)
- * more help in "samtools view" due to the recent changes.
-
-------------------------------------------------------------------------
-r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam.h
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-17 (r416)
- * support import/export SAM with string tags
-
-------------------------------------------------------------------------
-r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam.h
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-12 (r415)
- * FLAG now can be in HEX
-
-------------------------------------------------------------------------
-r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/kstring.h
-
-fixed a compiling error (thank Ken for fixing it)
-
-------------------------------------------------------------------------
-r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/kstring.c
-   M /trunk/samtools/kstring.h
-
-Implemented Boyer-Moore search in the kstring library.
-
-------------------------------------------------------------------------
-r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-
-do not include knetfile.h when _USE_KNETFILE is not defined
-
-------------------------------------------------------------------------
-r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bgzf.c
-
- * samtools-0.1.5-11 (r408)
- * force to overwirte existing MD if it is different from the one calculated
-   from fillmd.
- * bgzf.c: improved the compatibility with Windows headers
-
-------------------------------------------------------------------------
-r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.h
-
- * samtools-0.1.5-10 (r407)
- * implemented bam_aux_del() to remove a tag
- * fillmd: generate the NM tag
- * fillmd: cmd interface improvement
-
-------------------------------------------------------------------------
-r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-
-Sorry. The old Makefile is for PDCurses...
-
-------------------------------------------------------------------------
-r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-9 (r405)
- * improved the compatibility with PDCurses a little bit
-
-------------------------------------------------------------------------
-r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-8 (r404)
- * compatible with PDCurses
-
-------------------------------------------------------------------------
-r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/kseq.h
-
- * samtools-0.1.5-7 (r403)
- * fixed a bug in kseq.h for binary files (text files are fine)
-
-------------------------------------------------------------------------
-r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bgzf.c
-
- * samtools-0.1.5-6 (r402)
- * fixed compiling error when "-D_USE_NETFILE" is not applied
- * improve portability to MinGW
-
-------------------------------------------------------------------------
-r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
-Changed paths:
-   A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
-   A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
-   D /trunk/samtools/bam_lite.c
-
- * move bam_lite.c to bam-lite
- * copy bam.h to bam-lite
-
-------------------------------------------------------------------------
-r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_lite.c
-   M /trunk/samtools/bam_lpileup.c
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-5 (r395)
- * added bam_pileup_file() and removed bam_lpileup_file()
-
-------------------------------------------------------------------------
-r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/knetfile.h
-
- * samtools-0.1.5-4 (r394)
- * http_proxy support in knetfile library (check http_proxy ENV)
-
-------------------------------------------------------------------------
-r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/knetfile.h
-
- * samtools-0.1.5-3 (r393)
- * knetfile now supports HTTP (no proxy at the moment)
- * fixed a potential issue in knetfile on opening ordinary file, although I have
-   not seen the sideeffect so far.
-
-------------------------------------------------------------------------
-r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/samtools.1
-
-Remove the warning in tview
-
-------------------------------------------------------------------------
-r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-2 (r391)
- * do not show a blank screen when no reads mapped
-
-------------------------------------------------------------------------
-r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   A /trunk/samtools/bam_lite.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-1 (r390)
- * removed useless _IOLIB in bam.h. This should cause no change at all.
- * added bam_lite.c for light-weight BAM reading
-
-------------------------------------------------------------------------
-r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/knetfile.c
-
-Release samtools-0.1.5c (fixed a bug in piping)
-
-------------------------------------------------------------------------
-r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-
-Release samtools-0.1.5b (BUG! so embarrassing!)
-
-------------------------------------------------------------------------
-r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bamtk.c
-
-Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
-
-------------------------------------------------------------------------
-r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-
-Release samtools-0.1.5
-
-------------------------------------------------------------------------
-r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-
- * samtools-0.1.4-23 (r372)
- * keep header text if "view -t" is used (by Gerton)
-
-------------------------------------------------------------------------
-r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/samtools.1
-
-update documentation
-
-------------------------------------------------------------------------
-r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-
-Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
-
-------------------------------------------------------------------------
-r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-22 (r369)
- * in pileup, optionally print E2 and U2
- * remove the debugging code in bam_aux_get() (Drat!)
-
-------------------------------------------------------------------------
-r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bam_lpileup.c
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bam_rmdup.c
-   M /trunk/samtools/bam_stat.c
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/faidx.c
-   M /trunk/samtools/faidx.h
-   M /trunk/samtools/glf.c
-
- * samtools-0.1.4-21 (r368)
- * propagate errors rather than exit or complain assertion failure. Assertion
-   should be only used for checking internal bugs, but not for external input
-   inconsistency. I was just a bit lazy.
- * small memory leak may be present on failure, though
-
-------------------------------------------------------------------------
-r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/knetfile.c
-
-reduce the chance of blocking in FTP connection
-
-------------------------------------------------------------------------
-r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/knetfile.c
-
-minor changes to knetfile: invalid fd equals -1 rather than 0
-
-------------------------------------------------------------------------
-r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/knetfile.h
-
- * samtools-0.1.4-20 (r365)
- * download the BAM index file if it is not found in the current working directory.
-
-------------------------------------------------------------------------
-r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/knetfile.c
-
- * samtools-0.1.4-19 (r364)
- * knetfile: report error when the file is not present on FTP
-
-------------------------------------------------------------------------
-r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bgzf.c
-   M /trunk/samtools/bgzf.h
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/knetfile.h
-
- * samtools-0.1.4-18 (r363)
- * knetfile: do not trigger network communication in FTP seek (lazy seek)
- * bgzf: cache recent blocks (disabled by default)
-
-------------------------------------------------------------------------
-r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bgzf.c
-
-write changelog
-
-------------------------------------------------------------------------
-r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-17 (r361)
- * if a file is given on FTP, search locally for the BAM index
-
-------------------------------------------------------------------------
-r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bgzf.c
-   M /trunk/samtools/bgzf.h
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/knetfile.h
-
- * samtools-0.1.4-16 (r360)
- * report more information in index when the input is not sorted
- * change the behaviour of knet_seek() such that it returns 0 on success
- * support knetfile library in BGZF
-
-------------------------------------------------------------------------
-r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/knetfile.c
-   M /trunk/samtools/knetfile.h
-
-fixed bugs in knetfile.*
-
-------------------------------------------------------------------------
-r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
-Changed paths:
-   A /trunk/samtools/knetfile.h
-
-this is the header file
-
-------------------------------------------------------------------------
-r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
-Changed paths:
-   A /trunk/samtools/knetfile.c
-
- * open a file at FTP
- * preliminary version
-
-------------------------------------------------------------------------
-r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-15 (r354)
- * fixed a memory leak in bam_view1(), although samtools is not using this routine.
-
-------------------------------------------------------------------------
-r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/faidx.c
-
- * samtools-0.1.4-13 (r351)
- * make faidx more tolerant to empty lines right before or after > lines
- * hope this does not introduce new bugs...
-
-------------------------------------------------------------------------
-r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-13 (r350)
- * fixed a small memory leak in pileup, caused by recent modifications
-
-------------------------------------------------------------------------
-r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.4-12 (r347)
- * added `-S' to pileup, similar to `view -S' 
-
-------------------------------------------------------------------------
-r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam_view.c
-   M /trunk/samtools/samtools.1
-
- * samtools-0.1.4-11 (r346)
- * allow to select a read group at view command-line
-
-------------------------------------------------------------------------
-r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/examples/calDepth.c
-
-added more comments
-
-------------------------------------------------------------------------
-r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/examples/calDepth.c
-
-nothing really
-
-------------------------------------------------------------------------
-r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/examples/Makefile
-   A /trunk/samtools/examples/calDepth.c
-
-added an example of calculating read depth
-
-------------------------------------------------------------------------
-r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   A /trunk/samtools/bam_color.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam.h
-
- * samtools-0.1.4-10 (r341)
- * only include key APIs in libbam.a
- * move color-specific routines to bam_color.c
- * update documentations
- * remove the support of -q in pileup
-
-------------------------------------------------------------------------
-r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
-Changed paths:
-   M /trunk/samtools/INSTALL
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/razf.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.4-9 (r340)
- * added a warning to razf.c if zlib<1.2.2.1
- * fixed a compilation warning
- * fixed a segfault caused by @RG parsing
- * detect NCURSES in bam_tview.c
-
-------------------------------------------------------------------------
-r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/INSTALL
-
-update INSTALL
-
-------------------------------------------------------------------------
-r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/kstring.h
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.4-8 (r338)
- * parse the @RG header lines and allow to choose library at the "samtools view"
-   command line
-
-------------------------------------------------------------------------
-r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bgzf.c
-   M /trunk/samtools/bgzf.h
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.4-7 (r337)
- * bgzf.c: support mode string "wu": uncompressed output
- * "samtools view" support "-u" command-line option
-
-------------------------------------------------------------------------
-r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/misc/Makefile
-   M /trunk/samtools/razf.c
-   M /trunk/samtools/razf.h
-   M /trunk/samtools/razip.c
-
- * no changes to samtools itself
- * remove zlib source codes
- * make RAZF reading compatible with old version of zlib
- * on old version of zlib, writing is not available
-
-------------------------------------------------------------------------
-r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
-Changed paths:
-   D /trunk/samtools/zlib
-
-remove zlib for simplification...
-
-------------------------------------------------------------------------
-r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-6 (r334)
- * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
-   been implemented in that.
- * this version works with the latest Bio::DB::Sam (20090612)
-
-------------------------------------------------------------------------
-r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-
-update ChangeLog
-
-------------------------------------------------------------------------
-r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/AUTHORS
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/misc/Makefile
-
-fixed minor things in Makefile
-
-------------------------------------------------------------------------
-r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-5 (r3310
- * no change to samtools itself. Version number is increased to reflect the
-   changes in the Makefile building system.
-
-------------------------------------------------------------------------
-r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/AUTHORS
-   D /trunk/samtools/README
-
-update information...
-
-------------------------------------------------------------------------
-r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/novo2sam.pl
-
- * updated novoalign converter by Colin Hercus et al.
- * this version works with indels
-
-------------------------------------------------------------------------
-r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/INSTALL
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/misc/Makefile
-   M /trunk/samtools/zlib/Makefile
-
- * update Makefile
- * update INSTALL instruction
-
-------------------------------------------------------------------------
-r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
-Changed paths:
-   A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
-   D /trunk/samtools/Makefile.am
-   D /trunk/samtools/Makefile.generic
-   D /trunk/samtools/Makefile.lite
-   D /trunk/samtools/autogen.sh
-   D /trunk/samtools/cleanup.sh
-   D /trunk/samtools/configure.ac
-   A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
-   D /trunk/samtools/misc/Makefile.am
-   D /trunk/samtools/misc/Makefile.generic
-   M /trunk/samtools/razf.c
-   A /trunk/samtools/zlib
-   A /trunk/samtools/zlib/Makefile
-   A /trunk/samtools/zlib/adler32.c
-   A /trunk/samtools/zlib/compress.c
-   A /trunk/samtools/zlib/crc32.c
-   A /trunk/samtools/zlib/crc32.h
-   A /trunk/samtools/zlib/deflate.c
-   A /trunk/samtools/zlib/deflate.h
-   A /trunk/samtools/zlib/gzio.c
-   A /trunk/samtools/zlib/infback.c
-   A /trunk/samtools/zlib/inffast.c
-   A /trunk/samtools/zlib/inffast.h
-   A /trunk/samtools/zlib/inffixed.h
-   A /trunk/samtools/zlib/inflate.c
-   A /trunk/samtools/zlib/inflate.h
-   A /trunk/samtools/zlib/inftrees.c
-   A /trunk/samtools/zlib/inftrees.h
-   A /trunk/samtools/zlib/trees.c
-   A /trunk/samtools/zlib/trees.h
-   A /trunk/samtools/zlib/uncompr.c
-   A /trunk/samtools/zlib/zconf.h
-   A /trunk/samtools/zlib/zlib.h
-   A /trunk/samtools/zlib/zutil.c
-   A /trunk/samtools/zlib/zutil.h
-   D /trunk/samtools/zutil.h
-
- * added zlib-1.2.3 as razip requires that
- * prepare to changed back to the Makefile building system
- * unfinished! (will be soon)
-
-------------------------------------------------------------------------
-r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
-Unfinished
-
-------------------------------------------------------------------------
-r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-4 (r325)
- * further avoid wrong consensus calls in repetitive regions.
-
-------------------------------------------------------------------------
-r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam.h
-
- * samtools-0.1.4-3 (r324)
- * make maqcns generate the correct call in repetitive regions.
- * allow filtering on mapQ at the pileup command line
-
-------------------------------------------------------------------------
-r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.3.2 (r322)
- * indels and SNPs use different mapping quality threshold
-
-------------------------------------------------------------------------
-r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/export2sam.pl
-
-fixed a typo
-
-------------------------------------------------------------------------
-r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
-just typo. no real change
-
-------------------------------------------------------------------------
-r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
-a little bit code cleanup
-
-------------------------------------------------------------------------
-r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.3.1
- * change default parameters
- * optionally print filtered variants
-
-------------------------------------------------------------------------
-r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.3.0
- * combine snpFilter and indelFilter
-
-------------------------------------------------------------------------
-r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.2.3
- * change a default parameter
-
-------------------------------------------------------------------------
-r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_maqcns.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-
- * samtools-0.1.4-2 (r316)
- * pileup: cap mapping quality at 60 (by default)
- * pileup: always calculate RMS mapq
- * pileup: allow to output variant sites only
-
-------------------------------------------------------------------------
-r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.2.2
- * added pileup2fq
-
-------------------------------------------------------------------------
-r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
- * in snpFilter, suppress non-SNP sites
-
-------------------------------------------------------------------------
-r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.2.1
- * fixed a typo
-
-------------------------------------------------------------------------
-r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.2.0
- * snpFilter
-
-------------------------------------------------------------------------
-r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bgzf.c
-
- * minor changes to bgzf: return NULL if fd == -1
- * suggested by {kdj,jm18}@sanger.ac.uk
-
-------------------------------------------------------------------------
-r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
-Changed paths:
-   A /trunk/samtools/misc/interpolate_sam.pl
-
-Script for paired-end pileup, contributed by Stephen Montgomery.
-
-------------------------------------------------------------------------
-r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-
- * samtools-0.1.4-1 (r304)
- * fixed a minor bug in printing headers
-
-------------------------------------------------------------------------
-r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/maq2sam.c
-   M /trunk/samtools/samtools.1
-
-Release samtools-0.1.4
-
-------------------------------------------------------------------------
-r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-24 (r296)
- * another similar bug in the indel caller
-
-------------------------------------------------------------------------
-r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-23 (r295)
- * fixed a critical bug in the indel caller
-
-------------------------------------------------------------------------
-r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_stat.c
-
-added a missing header file
-
-------------------------------------------------------------------------
-r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-22 (r293)
- * open tview in the dot-view mode by default
-
-------------------------------------------------------------------------
-r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
-Changed paths:
-   M /trunk/samtools/samtools.1
-
-Added a note to the manual. Currently SAMtools used unaligned words in
-several places. Although this does not cause bus errors to me, it may
-affect portability. Please see the "Bus error" wiki page for more
-information. Also thank James Bonfields for pointing this out.
-
-
-------------------------------------------------------------------------
-r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-21 (286)
- * declare bam_aux_get_core() in bam.h
-
-------------------------------------------------------------------------
-r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-20 (r276)
- * remove bam1_t::hash again. We need to modify the Perl API anyway to
-   make it work with the latest SVN.
- * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
-
-------------------------------------------------------------------------
-r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-19 (r275)
- * a minor change to the bam1_t struct: added back "void *hash" for the
-   backward compatibility with Bio::DB::Sam
-
-------------------------------------------------------------------------
-r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_rmdupse.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-18 (r273)
- * rmdupse: do not remove unmapped reads
-
-------------------------------------------------------------------------
-r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_rmdupse.c
-
-change a parameter. It does nothing
-
-------------------------------------------------------------------------
-r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile.am
-   M /trunk/samtools/Makefile.generic
-   M /trunk/samtools/Makefile.lite
-   A /trunk/samtools/bam_rmdupse.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/configure.ac
-
- * samtools-0.1.3-17 (r271)
- * added 'rmdupse' command
-
-------------------------------------------------------------------------
-r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.3-16 (r267)
- * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
-
-------------------------------------------------------------------------
-r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-15 (r266)
- * report an error if a non-* reference is present while @SQ is absent
-
-------------------------------------------------------------------------
-r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.3-14 (r262)
- * make samopen() recognize @SQ header lines
-
-------------------------------------------------------------------------
-r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bgzf.c
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam_view.c
-
- * samtools-0.1.3-13 (r260)
- * report error for file I/O error
-
-------------------------------------------------------------------------
-r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile.am
-
-update Makefile.am
-
-------------------------------------------------------------------------
-r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/sam.c
-   M /trunk/samtools/sam.h
-
- * samtools-0.1.3-12 (r259)
- * use the new I/O interface in pileup
-
-------------------------------------------------------------------------
-r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile.generic
-   M /trunk/samtools/Makefile.lite
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-   A /trunk/samtools/sam.c
-   A /trunk/samtools/sam.h
-   A /trunk/samtools/sam_view.c
-
- * samtools-0.1.3-11 (r258)
- * unify the interface to BAM and SAM I/O
-
-------------------------------------------------------------------------
-r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile.lite
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-10 (r257)
- * allow hex with "pileup -m"
-
-------------------------------------------------------------------------
-r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_lpileup.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-9 (r256)
- * fixed a bug in bam_lpileup.c
- * I do not know if this also fixes the bug causing assertion failure in the tview
-
-------------------------------------------------------------------------
-r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-8 (r251)
- * fixed a bug when there are reads without coordinates
-
-------------------------------------------------------------------------
-r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
-Changed paths:
-   A /trunk/samtools/AUTHORS
-   A /trunk/samtools/README
-   M /trunk/samtools/cleanup.sh
-
-added missing files
-
-------------------------------------------------------------------------
-r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile.generic
-   M /trunk/samtools/Makefile.lite
-   M /trunk/samtools/configure.ac
-   M /trunk/samtools/misc/Makefile.generic
-
-improve large file support in compilation
-
-------------------------------------------------------------------------
-r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/INSTALL
-
-update INSTALL
-
-------------------------------------------------------------------------
-r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile.am
-   M /trunk/samtools/autogen.sh
-   M /trunk/samtools/cleanup.sh
-   M /trunk/samtools/configure.ac
-   A /trunk/samtools/misc/Makefile.am
-
-fixed various issues about the GNU building scripts
-
-------------------------------------------------------------------------
-r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   D /trunk/samtools/Makefile
-   A /trunk/samtools/Makefile.am
-   A /trunk/samtools/Makefile.generic
-   A /trunk/samtools/autogen.sh
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-   A /trunk/samtools/cleanup.sh
-   A /trunk/samtools/configure.ac
-   D /trunk/samtools/misc/Makefile
-   A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
-
- * samtools-0.1.3-7 (r246)
- * incorporated revisions from Nils Homer
- * enhanced support of displaying color-space reads
-
-------------------------------------------------------------------------
-r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-6 (r244)
- * fixed segfault for unmapped reads
-
-------------------------------------------------------------------------
-r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-5 (r243)
- * fixed a long existing bug which may cause memory leak
- * check MD
- * consensus calling now works with "=", but indel calling not
-
-------------------------------------------------------------------------
-r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_md.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-4 (r242)
- * fixed a memory leak
-
-------------------------------------------------------------------------
-r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/Makefile.lite
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   A /trunk/samtools/bam_md.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-3 (r240)
- * generate MD tag
- * generate "=" bases
- * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
-
-------------------------------------------------------------------------
-r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_aux.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-2 (r239)
- * fixed bugs in bam_aux.c (these functions nevered used by samtools)
- * removed bam_aux_init()/bam_aux_destroy()
- * added tagview for testing bam_aux
-
-------------------------------------------------------------------------
-r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-1
- * fixed a bug in pileup: the first read in a chromosome may not be printed
-
-------------------------------------------------------------------------
-r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile.lite
-
-a missing file in Makefile.lite
-
-------------------------------------------------------------------------
-r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bamtk.c
-
-Release samtools-0.1.3
-
-------------------------------------------------------------------------
-r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-28
- * make samtools more robust to weird input such as empty file
-
-------------------------------------------------------------------------
-r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/samtools.1
-
-prepare for release 0.1.3
-
-------------------------------------------------------------------------
-r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
-Changed paths:
-   A /trunk/samtools/misc/blast2sam.pl
-
-convert NCBI-BLASTN to SAM
-
-------------------------------------------------------------------------
-r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_lpileup.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-27
- * fixed a small memory leak in tview
-
-------------------------------------------------------------------------
-r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_rmdup.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-26
- * fixed a bug in rmdup when there are unmapped reads
-
-------------------------------------------------------------------------
-r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-
-proposed NEWS for the new release (have not yet)
-
-------------------------------------------------------------------------
-r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.1.1
- * improve indelFilter to avoid filtering true indels. The new filter relies
-   on the new pileup indel line implemented in samtools-0.1.2-25
-
-------------------------------------------------------------------------
-r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-
- * samtools-0.1.2-25
- * change the pileup indel line to shows the number of alignments actually
-   containing indels
-
-------------------------------------------------------------------------
-r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-
-update ChangeLog from "svn log"
-
-------------------------------------------------------------------------
-r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/kseq.h
-
- * samtools-0.1.2-24
- * in merge, gives a warning rather than error if the target sequence length is different
- * allow empty header
-
-------------------------------------------------------------------------
-r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-23
- * recognize '*' at the QUAL field
-
-------------------------------------------------------------------------
-r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/kseq.h
-
- * samtools-0.1.2-22
- * the field separater is TAB only, now
-
-------------------------------------------------------------------------
-r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/examples/ex1.sam.gz
-
- * fixed the problem in the example alignment due to the bug in fixmate
-
-------------------------------------------------------------------------
-r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_mate.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/soap2sam.pl
-
- * samtools-0.1.2-21
- * fixed a nasty bug in `fixmate'
-
-------------------------------------------------------------------------
-r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/bowtie2sam.pl
-   M /trunk/samtools/misc/soap2sam.pl
-   M /trunk/samtools/misc/wgsim_eval.pl
-
-make the script robust to the bugs in SOAP-2.1.7
-
-------------------------------------------------------------------------
-r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_stat.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-20
- * check if file is truncated in flagstat
-
-------------------------------------------------------------------------
-r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-19
- * print the header if requested
-
-------------------------------------------------------------------------
-r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-18
- * fixed a minor bug reported by Nils Homer
-
-------------------------------------------------------------------------
-r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
-Changed paths:
-   A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
-   D /trunk/samtools/Makefile.std
-   A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
-   D /trunk/samtools/misc/Makefile.std
-
-rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
-
-------------------------------------------------------------------------
-r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
-Changed paths:
-   D /trunk/samtools/Makefile
-   A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bam_tview.c
-   M /trunk/samtools/bamtk.c
-   D /trunk/samtools/misc/Makefile
-   A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
-   M /trunk/samtools/samtools.1
-
- * samtools-0.1.2-17
- * incorporating Nils' changes
- * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
-
-------------------------------------------------------------------------
-r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_maqcns.h
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/kseq.h
-   A /trunk/samtools/kstring.c
-   A /trunk/samtools/kstring.h
-
- * samtools-0.1.2-16
- * made pileup take a list of proposed indels. An insertion is N at the moment.
- * added my kstring library for a bit complex parsing of the position list.
-
-------------------------------------------------------------------------
-r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/soap2sam.pl
-
- * soap2sam.pl-0.1.2
- * more robust to truncated soap output
-
-------------------------------------------------------------------------
-r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile.lite
-
-added bam_stat.o to Makefile.lite
-
-------------------------------------------------------------------------
-r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-15
- * generate RMS of mapQ instead of max mapQ
-
-------------------------------------------------------------------------
-r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/glf.c
-   M /trunk/samtools/glf.h
-   M /trunk/samtools/misc/Makefile
-
- * samtools-0.1.2-14
- * implemented GLFv3
-
-------------------------------------------------------------------------
-r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-13
- * fixed a minor bug in displaying pileup
-
-------------------------------------------------------------------------
-r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-12
- * optionally print SAM header
-
-------------------------------------------------------------------------
-r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/glf.c
-
- * samtools-0.1.2-11
- * use "GLF\3" as the magic for GLFv3 files
-
-------------------------------------------------------------------------
-r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/glf.c
-   M /trunk/samtools/glf.h
-
- * samtools-0.1.2-10
- * fixed a bug in import: core.bin is undefined for unmapped reads
- * this bug can be alleviated (not completely solved) in bam_index.c
- * update to GLFv3: pos is changed to offset for better compression
-
-------------------------------------------------------------------------
-r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/wgsim.c
-
- * wgsim-0.2.3
- * fixed a bug in simulating indels
-
-------------------------------------------------------------------------
-r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/misc/wgsim.c
-
- * wgsim-0.2.2
- * allow to print mismatch information as fastq comment. MAQ does
-   not like long read names.
-
-------------------------------------------------------------------------
-r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/misc/wgsim.c
-   M /trunk/samtools/misc/wgsim_eval.pl
-
- * wgsim-0.2.1
- * fixed a bug about color read coordinates
- * fixed a bug in read names
- * wgsim_eval.pl-0.1.3
- * make the script work with color reads
-
-------------------------------------------------------------------------
-r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/Makefile
-   M /trunk/samtools/misc/wgsim.c
-
- * wgsim: added a note
-
-------------------------------------------------------------------------
-r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
-Changed paths:
-   M /trunk/samtools/misc/wgsim.c
-   M /trunk/samtools/misc/wgsim_eval.pl
-
- * wgsim-0.2.0
- * considerable code clean up
- * print number of substitutions/indels/errors on each read
- * potentially support SOLiD simulation, though not tested at the moment
- * wgsim_eval.pl-0.1.2
- * change in accordant with wgsim
-
-------------------------------------------------------------------------
-r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-9
- * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
-
-------------------------------------------------------------------------
-r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bamtk.c
-
-Fix annoying segv when invalid region specified.
-
-------------------------------------------------------------------------
-r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
-Changed paths:
-   D /trunk/samtools/misc/indel_filter.pl
-   A /trunk/samtools/misc/samtools.pl
-
- * move indel_filter.pl to samtools.pl
-
-------------------------------------------------------------------------
-r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_mate.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-7
- * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
-
-------------------------------------------------------------------------
-r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_stat.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-7
- * fixed a minor bug in flagstat
-
-------------------------------------------------------------------------
-r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/misc/indel_filter.pl
-
- * samtools-0.1.2-6
- * improve indel caller by setting maximum window size
-
-------------------------------------------------------------------------
-r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bamtk.c
-
- * output max mapping quality in indel line
-
-------------------------------------------------------------------------
-r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/misc/maq2sam.c
-
-fixed a bug in generating tag AM
-
-------------------------------------------------------------------------
-r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bamtk.c
-
-fixed a potential memory problem in indexing
-
-------------------------------------------------------------------------
-r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-
-Pass LIBS to recursive targets to facilitate building at Broad.
-
-------------------------------------------------------------------------
-r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/bam_plcmd.c
-   M /trunk/samtools/bam_stat.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-3
- * fixed a bug in generating GLFv2 for indels
- * improve flagstat report a little bit
-
-------------------------------------------------------------------------
-r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/Makefile
-   A /trunk/samtools/bam_stat.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-1
- * added flagstat command
-
-------------------------------------------------------------------------
-r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/NEWS
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/samtools.1
-
-Release SAMtools-0.1.2
-
-------------------------------------------------------------------------
-r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
-Changed paths:
-   A /trunk/samtools/misc/indel_filter.pl
-
-Script for filtering indel results
-
-------------------------------------------------------------------------
-r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
-Changed paths:
-   A /trunk/samtools/misc/zoom2sam.pl
-
-convert ZOOM to SAM
-
-------------------------------------------------------------------------
-r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
-Changed paths:
-   A /trunk/samtools/misc/novo2sam.pl
-
-add a script to convert novo alignment to SAM
-
-------------------------------------------------------------------------
-r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/ChangeLog
-   M /trunk/samtools/ChangeLog.old
-   M /trunk/samtools/samtools.1
-
-update documentation and ChangeLog
-
-------------------------------------------------------------------------
-r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-
- * samtools-0.1.1-19
- * fixed a bug in "merge" command line
-
-------------------------------------------------------------------------
-r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/misc/Makefile
-   A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
-   M /trunk/samtools/misc/export2sam.pl
-   A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
-   A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
-   A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
-
- * merge from branches/dev/
- * all future development will happen here
-
-------------------------------------------------------------------------
-r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
-Changed paths:
-   M /trunk/samtools/COPYING
-   M /trunk/samtools/ChangeLog
-   A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
-   M /trunk/samtools/Makefile
-   A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
-   M /trunk/samtools/bam.c
-   M /trunk/samtools/bam.h
-   M /trunk/samtools/bam_import.c
-   M /trunk/samtools/bam_index.c
-   M /trunk/samtools/bam_lpileup.c
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_maqcns.h
-   A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
-   M /trunk/samtools/bam_pileup.c
-   M /trunk/samtools/bam_plcmd.c
-   A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
-   M /trunk/samtools/bam_sort.c
-   M /trunk/samtools/bamtk.c
-   M /trunk/samtools/bgzf.h
-   M /trunk/samtools/examples/00README.txt
-   A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
-   D /trunk/samtools/examples/ex1.fa.fai
-   M /trunk/samtools/examples/ex1.sam.gz
-   M /trunk/samtools/faidx.c
-   A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
-   M /trunk/samtools/glf.h
-   M /trunk/samtools/misc/Makefile
-   M /trunk/samtools/misc/maq2sam.c
-   M /trunk/samtools/razf.c
-   M /trunk/samtools/source.dot
-
- * Merge from branches/dev/
- * all future development will happen here at trunk/
-
-------------------------------------------------------------------------
-r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
-Changed paths:
-   M /trunk/samtools/bam_maqcns.c
-   M /trunk/samtools/bam_tview.c
-
-Fix problem with compiling without curses.
-
-------------------------------------------------------------------------
-r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
-Changed paths:
-   A /trunk/samtools (from /branches/dev/samtools:62)
-
-Create trunk copy
-
-------------------------------------------------------------------------
-r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
-Changed paths:
-   A /branches/dev/samtools/NEWS
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/samtools.1
-
-Release samtools-0.1.1
-
-------------------------------------------------------------------------
-r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
-Changed paths:
-   M /branches/dev/samtools/bam_aux.c
-   M /branches/dev/samtools/bam_index.c
-   M /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bam_tview.c
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/razf.c
-   M /branches/dev/samtools/samtools.1
-
- * samtools-0.1.0-66
- * fixed a bug in razf.c: reset z_eof when razf_seek() is called
- * fixed a memory leak in parsing a region
- * changed pileup a little bit when -s is in use: output ^ and $
- * when a bam is not indexed, output more meaningful error message
- * fixed a bug in indexing for small alignment
- * fixed a bug in the viewer when we come to the end of a reference file
- * updated documentation
- * prepare to release 0.1.1
-
-------------------------------------------------------------------------
-r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
-Changed paths:
-   A /branches/dev/samtools/examples
-   A /branches/dev/samtools/examples/00README.txt
-   A /branches/dev/samtools/examples/ex1.fa
-   A /branches/dev/samtools/examples/ex1.fa.fai
-   A /branches/dev/samtools/examples/ex1.sam.gz
-
-example
-
-------------------------------------------------------------------------
-r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/ChangeLog
-
-update ChangeLog
-
-------------------------------------------------------------------------
-r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/misc/export2sam.pl
-
- * added comments
- * fixed several bugs 
-
-------------------------------------------------------------------------
-r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
-Changed paths:
-   A /branches/dev/samtools/misc/export2sam.pl
-
-convert Export format to SAM; not thoroughly tested
-
-------------------------------------------------------------------------
-r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
-Changed paths:
-   M /branches/dev/samtools/bam_import.c
-   M /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bam_tview.c
-   M /branches/dev/samtools/bamtk.c
-   A /branches/dev/samtools/source.dot
-
- * samtools-0.1.0-65
- * pileup: generate maq-like simple output
- * pileup: allow to output pileup at required sites
- * source.dot: source file relationship graph
- * tview: fixed a minor bug
-
-------------------------------------------------------------------------
-r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
-Changed paths:
-   D /branches/dev/samtools/misc/all2sam.pl
-
-remove all2sam.pl
-
-------------------------------------------------------------------------
-r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
-Changed paths:
-   A /branches/dev/samtools/COPYING
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/faidx.h
-   M /branches/dev/samtools/khash.h
-   M /branches/dev/samtools/kseq.h
-   M /branches/dev/samtools/ksort.h
-   M /branches/dev/samtools/samtools.1
-
-Added copyright information and a bit more documentation. No code change.
-
-------------------------------------------------------------------------
-r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/bam.c
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/bam_index.c
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-64
- * improved efficiency of the indel caller for spliced alignments
-
-------------------------------------------------------------------------
-r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/bam.c
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/bam_aux.c
-   M /branches/dev/samtools/bam_index.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-63
- * a bit code cleanup: reduce the dependency between source files
-
-------------------------------------------------------------------------
-r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-62
- * fixed a memory leak
-
-------------------------------------------------------------------------
-r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/ChangeLog
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/samtools.1
-
-update documentation, ChangeLog and a comment
-
-------------------------------------------------------------------------
-r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
-Changed paths:
-   M /branches/dev/samtools/Makefile
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bam_maqcns.h
-   M /branches/dev/samtools/bam_pileup.c
-   A /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/samtools.1
-
- * samtools-0.1.0-61
- * moved pileup command to a separate source file
- * added indel caller
- * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
- * updated documentation
-
-------------------------------------------------------------------------
-r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-60
- * fixed another bug in maqcns when there is a nearby deletion
-
-------------------------------------------------------------------------
-r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
-Changed paths:
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bam_pileup.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-59
- * pileup: outputing consensus is now optional
- * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
-   I am not quite sure why the previous version may have problem.
-
-------------------------------------------------------------------------
-r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
-Changed paths:
-   M /branches/dev/samtools/bam_pileup.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-58
- * add maq consensus to pileup. However, I will move this part to a new
-   command as strictly speaking, consensus callin is not part of pileup,
-   and imposing it would make it harder to generate for other language
-   bindings.
-
-------------------------------------------------------------------------
-r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/bgzf.c
-
-Fix bug in tell() after reads that consume to the exact end of a block.
-
-------------------------------------------------------------------------
-r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/samtools.1
-
-update manual
-
-------------------------------------------------------------------------
-r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
-Changed paths:
-   M /branches/dev/samtools/bam_import.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-57
- * fixed a bug in parser when there is auxiliary fields
- * made the parser a bit more robust
-
-------------------------------------------------------------------------
-r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
-Changed paths:
-   M /branches/dev/samtools/bam_index.c
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/bgzf.c
-
- * samtools-0.1.0-56
- * fixed a bug in bgzf (only reading is affected)
- * fixed a typo in bam_index.c
- * in bam_index.c, check potential bugs in the underlying I/O library
-
-------------------------------------------------------------------------
-r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/samtools.1
-
-update manual
-
-------------------------------------------------------------------------
-r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
-Changed paths:
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/bam_pileup.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-55
- * tried to make pileup work with clipping (previously not), though NOT tested
- * removed -v from pileup
- * made pileup take the reference sequence
-
-------------------------------------------------------------------------
-r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
-Changed paths:
-   M /branches/dev/samtools/bam_import.c
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/samtools.1
-
- * samtools-0.1.0-54
- * in parser, recognize "=", rather than ",", as a match
- * in parser, correctl parse "=" at the MRNM field.
-
-------------------------------------------------------------------------
-r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/misc/maq2sam.c
-
-fixed a bug in handling maq flag 64 and 192
-
-------------------------------------------------------------------------
-r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/misc/md5fa.c
-
-also calculate unordered md5sum check
-
-------------------------------------------------------------------------
-r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/misc/md5fa.c
-
-fixed a minor bug when there are space in the sequence
-
-------------------------------------------------------------------------
-r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/misc/md5fa.c
-
-fixed a potential memory leak
-
-------------------------------------------------------------------------
-r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/bam_import.c
-   M /branches/dev/samtools/bam_index.c
-   M /branches/dev/samtools/bamtk.c
-
- * fixed a bug in import: bin is wrongly calculated
-
-------------------------------------------------------------------------
-r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/misc/all2sam.pl
-
-nothing, really
-
-------------------------------------------------------------------------
-r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/Makefile
-   M /branches/dev/samtools/kseq.h
-   M /branches/dev/samtools/misc/Makefile
-   A /branches/dev/samtools/misc/md5.c
-   A /branches/dev/samtools/misc/md5.h
-   A /branches/dev/samtools/misc/md5fa.c
-
- * fixed two warnings in kseq.h
- * added md5sum utilities
-
-------------------------------------------------------------------------
-r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
-Changed paths:
-   M /branches/dev/samtools/Makefile
-   M /branches/dev/samtools/bam_import.c
-   M /branches/dev/samtools/bamtk.c
-   A /branches/dev/samtools/kseq.h
-   D /branches/dev/samtools/kstream.h
-
- * samtools-0.1.0-52
- * replace kstream with kseq. kseq is a superset of kstream. I need the
-   extra functions in kseq.h.
- * also compile stand-alone faidx
-
-------------------------------------------------------------------------
-r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/bam_sort.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-51
- * sorting by read names is available
-
-------------------------------------------------------------------------
-r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/bam.c
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/bam_import.c
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bam_pileup.c
-   M /branches/dev/samtools/bam_sort.c
-   M /branches/dev/samtools/bam_tview.c
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/misc/maq2sam.c
-
- * samtools-0.1.0-50
- * format change to meet the latest specification
-
-------------------------------------------------------------------------
-r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/misc/maq2sam.c
-
- * minor change in maqcns: special care when n==0
- * change maq2sam to meet the latest specification
-
-------------------------------------------------------------------------
-r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/razf.c
-   M /branches/dev/samtools/razf.h
-
-considerable code clean up in razf
-
-------------------------------------------------------------------------
-r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/ChangeLog
-   M /branches/dev/samtools/Makefile
-   M /branches/dev/samtools/faidx.c
-
-make RAZF optional in faidx.c
-
-------------------------------------------------------------------------
-r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/Makefile
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/bam_aux.c
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/samtools.1
-
- * samtools-0.1.0-49
- * added routines for retrieving aux data, NOT TESTED YET!
-
-------------------------------------------------------------------------
-r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
-Changed paths:
-   M /branches/dev/samtools/bam.c
-   M /branches/dev/samtools/bam_import.c
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/bgzf.c
-   M /branches/dev/samtools/samtools.1
-
- * samtools-0.1.0-48
- * bgzf: fixed a potential integer overflow on 32-it machines
- * maqcns: set the minimum combined quality as 0
- * supporting hex strings
-
-------------------------------------------------------------------------
-r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-47
- * fixed the bug in maqcns
-
-------------------------------------------------------------------------
-r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/Makefile
-   M /branches/dev/samtools/bam.h
-   A /branches/dev/samtools/bam_maqcns.c
-   A /branches/dev/samtools/bam_maqcns.h
-   M /branches/dev/samtools/bam_tview.c
-   M /branches/dev/samtools/bamtk.c
-   A /branches/dev/samtools/glf.h
-
- * samtools-0.1.0-46
- * add MAQ consensus caller, currently BUGGY!
-
-------------------------------------------------------------------------
-r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
-Changed paths:
-   M /branches/dev/samtools/bam_pileup.c
-   M /branches/dev/samtools/bam_tview.c
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-45
- * tview: display padded alignment (but not P operation)
- * better coordinates and reference sequence
-
-------------------------------------------------------------------------
-r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
-Changed paths:
-   A /branches/dev/samtools/ChangeLog
-
-new ChangeLog
-
-------------------------------------------------------------------------
-r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
-Changed paths:
-   D /branches/dev/samtools/ChangeLog
-   A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
-
-Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
-the log of my personal SVN repository.
-
-------------------------------------------------------------------------
-r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
-Changed paths:
-   M /branches/dev/samtools/Makefile
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/bgzf.c
-
- * samtools-0.1.0-44
- * declare fseeko and ftello as some Linux may not do this by default and
-   missing these declarations will make bgzf buggy
- * get rid of some harmless warings
- * use BGZF by default, now
-
-------------------------------------------------------------------------
-r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
-Changed paths:
-   M /branches/dev/samtools/bam_index.c
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/razf.c
-
- * samtools-0.1.0-43
- * fixed a bug in razf_read()
- * give more warnings when the file is truncated (or due to bugs in I/O library)
-
-------------------------------------------------------------------------
-r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/bgzf.c
-
-fixed a bug in bgzf.c at the end of the file
-
-------------------------------------------------------------------------
-r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
-Changed paths:
-   M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-42
- * a lot happened to RAZF, although samtools itself is untouched. Better
-   also update the version number anyway to avoid confusion
-
-------------------------------------------------------------------------
-r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/razf.c
-
-a change from Jue, but I think it should not matter
-
-------------------------------------------------------------------------
-r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
-Changed paths:
-   M /branches/dev/samtools/razf.c
-
-fixed a potential bug in razf. However, it seems still buggy, just
-rarely happens, very rarely.
-
-------------------------------------------------------------------------
-r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/razf.c
-
-fixed a bug in razf, with the help of Jue
-
-------------------------------------------------------------------------
-r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/bam_index.c
-
-remove a comment
-
-------------------------------------------------------------------------
-r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
-Changed paths:
-   M /branches/dev/samtools/Makefile
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/razf.c
-   M /branches/dev/samtools/razf.h
-
- * Jue has updated razf to realize Bob's scheme
-
-------------------------------------------------------------------------
-r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
-Changed paths:
-   A /branches/dev/samtools/samtools.1
-
-the manual page
-
-------------------------------------------------------------------------
-r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
-Changed paths:
-   A /branches/dev/samtools/ChangeLog
-   A /branches/dev/samtools/Makefile
-   A /branches/dev/samtools/bam.c
-   A /branches/dev/samtools/bam.h
-   A /branches/dev/samtools/bam_aux.c
-   A /branches/dev/samtools/bam_endian.h
-   A /branches/dev/samtools/bam_import.c
-   A /branches/dev/samtools/bam_index.c
-   A /branches/dev/samtools/bam_lpileup.c
-   A /branches/dev/samtools/bam_pileup.c
-   A /branches/dev/samtools/bam_sort.c
-   A /branches/dev/samtools/bam_tview.c
-   A /branches/dev/samtools/bamtk.c
-   A /branches/dev/samtools/bgzf.c
-   A /branches/dev/samtools/bgzf.h
-   A /branches/dev/samtools/bgzip.c
-   A /branches/dev/samtools/faidx.c
-   A /branches/dev/samtools/faidx.h
-   A /branches/dev/samtools/khash.h
-   A /branches/dev/samtools/ksort.h
-   A /branches/dev/samtools/kstream.h
-   A /branches/dev/samtools/misc
-   A /branches/dev/samtools/misc/Makefile
-   A /branches/dev/samtools/misc/all2sam.pl
-   A /branches/dev/samtools/misc/maq2sam.c
-   A /branches/dev/samtools/razf.c
-   A /branches/dev/samtools/razf.h
-   A /branches/dev/samtools/razip.c
-   A /branches/dev/samtools/zutil.h
-
-The initial version of samtools, replicated from my local SVN repository.
-The current version is: 0.1.0-42. All future development will happen here.
-
-------------------------------------------------------------------------
-r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
-Changed paths:
-   A /branches/dev/samtools
-
-samtools (C version)
-
-------------------------------------------------------------------------
diff --git a/sam/ChangeLog.old b/sam/ChangeLog.old
new file mode 100644 (file)
index 0000000..19aefae
--- /dev/null
@@ -0,0 +1,3875 @@
+commit db2ad3e19068cbafde72ecde75d0638bbb3598ba
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 16 14:45:17 2012 -0500
+
+    removed downsample.c
+
+commit 6c55c576903992c6fef148fe3b606fbc8bd10655
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 16 14:45:06 2012 -0500
+
+    print to output
+
+commit db1044a34e6049c87eaa63c39ed6e56f03e7d4c1
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 16 14:39:34 2012 -0500
+
+    removed sample
+    
+    Downsampling already exists in "view". View also keeps pairing while "sample" does not.
+
+commit ffdeed3e5d4a530bfdf6f9ba97fff0ba7add6cba
+Merge: 2daad7b accf026
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 16 14:22:15 2012 -0500
+
+    Merge branch 'master' of github.com:lh3/samtools
+
+commit accf0260fd1117e10047344345d40b31a9ec31bb
+Merge: 9134e0d c554160
+Author: Heng Li <lh3@me.com>
+Date:   Thu Feb 16 11:21:14 2012 -0800
+
+    Merge pull request #8 from nh13/master
+    
+    Patches
+
+commit c554160df16ec7748cfdda4c7b54c641be7b809f
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 14:06:52 2012 -0500
+
+    * more README.md work
+
+commit 2a81ffe349208d917666808fbc9f3041e0cb57de
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 14:06:10 2012 -0500
+
+    * more README work
+
+commit fb3125f732715f62cded8685a23a002a96ce009b
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 14:05:19 2012 -0500
+
+    * more README work
+
+commit 444d41002c37e1c3d0f9208b4a88126c47276386
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 14:02:13 2012 -0500
+
+    * updating README
+
+commit dec53cb1043fe7efadfde75fa2fd39b76de22e54
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 13:55:01 2012 -0500
+
+    updating the README for markdown syntax
+
+commit 798da18c346dca8ec6005582a0ddb1d5420b04ca
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 13:48:35 2012 -0500
+
+    adding a README with the current differences between this repository and
+    the official one
+
+commit 4d22d86c0f28636662f2144a88cd168e104c4275
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 13:35:03 2012 -0500
+
+    adding "samtools sample" to the main
+
+commit 893c25a37c21005dc42f45d45e9ad78ddc5f29bb
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 13:33:51 2012 -0500
+
+    * removing some compile flags to work with OS X
+
+commit 7ac22f72fdc32edd5c24af6baebfa7db5faf8e7b
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date:   Thu Feb 16 10:47:14 2012 -0500
+
+    Check write filehandle after opening for write. tamw/tamr is a union type, so change is only semantic.
+    
+    Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit fef53330416631690f60fdff42b6e43d764170dc
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date:   Thu Feb 16 10:44:59 2012 -0500
+
+    Catch and report invalid BAM header, instead of segfaulting later on.
+    
+    Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 5cc013fe4930bf9b6e7963aab1cd4a3c94f695bc
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date:   Thu Feb 16 10:44:16 2012 -0500
+
+    Add downsample to examples.
+    
+    Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit b3fa9e7071532905a81dc7aa48eadc24b8c8846b
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date:   Thu Feb 16 10:43:48 2012 -0500
+
+    Adjust for leading hard clip on colorspace reads.
+    
+    Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 1a9296c1389469d1c1db5b8069f0e11ffcc8abb2
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date:   Thu Feb 16 10:42:52 2012 -0500
+
+    Add samtools sample command, contributed by Davide Cittaro <davide.cittaro@ifom-ieo-campus.it>.
+    
+    Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 2a804f3379748aeba944f1dec306dd726ff3235e
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date:   Thu Feb 16 10:42:07 2012 -0500
+
+    Add samtools qa command, contributed by Roman Valls Guimera <roman.valls.guimera@scilifelab.se>.
+    
+    Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 0f3207fe8fd93e44d40fcf57204079c8c06d24a6
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date:   Thu Feb 16 10:39:08 2012 -0500
+
+    Makefile cleanup - allow CC, CFLAGS, LDFLAGS to be passed on make command line. Use LDFLAGS in samtools compile.
+    
+    Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 6e7df604025f6a86881bf7f4a16f30e15d31538a
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date:   Thu Feb 16 10:31:15 2012 -0500
+
+    Allow max_mem for sort to be specified with units.
+    
+    Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit f12ebcaf6e60d34180a27d70e09b743cef140b98
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date:   Thu Feb 16 10:29:11 2012 -0500
+
+    Allow user defined [lowercase] tags in header elements.
+    
+    Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 50b931fa3312dc109537a4260698ddecd0f06a05
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date:   Thu Feb 16 10:27:11 2012 -0500
+
+    Check lowerbound in text entry box to avoid segfault in tview. Remove redundant call to bam_aux_get.
+    
+    Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 5e729da5190949a813d20d329eab7ddb661816bd
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 10:31:48 2012 -0500
+
+    * fixing overflow/underflow in integer parsing
+
+commit fa50a4330b9abedaf07c26e13d31f05e57f1d319
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 10:30:40 2012 -0500
+
+    * updating help message for samtools depth
+
+commit 79e52c9624b6dd3bdfdf439f4b4bc6f774c230a4
+Author: Nils Homer <nils.homer@lifetech.com>
+Date:   Thu Feb 16 10:29:32 2012 -0500
+
+    * adding support for outputting a circos histogram file in "samtools depth".  Use
+    the "-c/-B" options.
+
+commit 2daad7b52daa86561c0fb65fe366691fad9f5ed3
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 16 09:31:57 2012 -0500
+
+    bugfix: wrong SP; missing DV in the VCF hdr
+
+commit 9134e0d5047c281ef3bd53da91771d4814a5131c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 8 11:19:12 2012 -0500
+
+    missing support of DV
+
+commit 34ebf12078c1d1015a0b8b9a9221243a60b22893
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 8 11:08:56 2012 -0500
+
+    new BCF DV format: number of variant reads
+
+commit 9589d3312fa2d076f48bdd68e2a5edd419c8070c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Jan 10 10:30:27 2012 -0500
+
+    scale depth to quality (hidden option)
+
+commit 704473e14668333ecaca5fb7b238af405c43e3b1
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Jan 10 10:18:17 2012 -0500
+
+    really nothing
+
+commit 01b307fd287962372bbf07461c88b54f41636817
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Dec 7 13:07:42 2011 -0500
+
+    added an example containing 'B'
+
+commit c678791f0451ceb9205c1ab5c52c84641863c99a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Dec 3 12:10:30 2011 -0500
+
+    'B' now moves backward w.r.t. the query
+
+commit 152119bc06a073933ca830e8e1407538e44626cc
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Dec 2 10:50:12 2011 -0500
+
+    better consensus; a little more robust
+
+commit 454da4754ac503edda5b1329b67757d797e46e07
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Dec 2 00:20:22 2011 -0500
+
+    in pileup call remove_B()
+
+commit ff2bcac1cc078ba1879f18c89cfae314439d7086
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Dec 2 00:17:32 2011 -0500
+
+    working on a few toy examples
+
+commit 745ca7260158d6df7897b52598033ffb055a9e4f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Dec 1 22:55:39 2011 -0500
+
+    bam_remove_B(); not tested
+
+commit 07e4cdc7300abfcc82e03105b4689f95cab551cd
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Nov 10 12:58:55 2011 -0500
+
+    baseQ threshold on plain pipleup; removed -E
+
+commit 322ebf2082dfa91df44b3a996d26c85357e5d5a2
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Oct 19 09:28:04 2011 -0400
+
+    fixed two gcc warnings
+
+commit a632457b4c4adc50d833b56b5a5231feafaf8193
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Oct 4 10:13:23 2011 -0400
+
+    change size_t to uint32_t in bam_header_t
+    
+    This may cause issues on 64-bit big-endian machines. Reported and fixed by Paolo Emilio Mazzon.
+
+commit af31bf5a78aea03baf6eb90fe50076549d499f6e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Sep 26 20:17:57 2011 -0400
+
+    rename pad2unpad to depad
+
+commit 77b198b73dfad1048e5d1c5a64aa75ee7b90f596
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Sep 23 01:22:40 2011 -0400
+
+    convert padded BAM to unpadded BAM
+
+commit adb9e2342b7b7501d9527d3c23afab10469ae2c6
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Sep 7 11:40:50 2011 -0400
+
+    generate template cigar with "fixmate"
+
+commit 46e5ab445a0fe880216cbc0daf1225725b569d7a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Sep 2 12:50:18 2011 -0400
+
+    update kseq.h to the latest version
+
+commit 68e9e4a73eb91405bb3e56bf0cdaf12d1b487abb
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Sep 2 12:44:45 2011 -0400
+
+    Release samtools-0.1.18
+
+commit aa06bdadb2d109a79f927f478102f96a1f5fd258
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Sep 2 12:14:17 2011 -0400
+
+    updated the revision number
+
+commit 267e1e1b6e54c0ab24f94cd9aee9cbd2d1923f9f
+Merge: 19ff1d3 aebab30
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Sep 2 12:13:08 2011 -0400
+
+    Merge https://github.com/lh3/samtools into reduce
+    
+    Conflicts:
+       bam_md.c
+    
+    Fixed a few typos in the merge
+
+commit aebab302399c24eaa6c5ab79d13d6bd5e2e9ea9a
+Merge: c2c63d0 da62663
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Sep 2 09:03:49 2011 -0700
+
+    Merge pull request #4 from peterjc/x_equals2
+    
+    Implement basic support for =/X CIGAR operations
+
+commit 19ff1d3d7f47d7e61b121292aefe5a74bb8a18d2
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Aug 25 16:38:12 2011 -0400
+
+    reduce BAM size (experimental)
+
+commit da626630fd98fd4e07ceb4d58c5c9a42d312a85d
+Author: peterjc <p.j.a.cock@googlemail.com>
+Date:   Mon Aug 22 06:58:08 2011 +0100
+
+    Support =/X CIGAR operations (treated like M)
+
+commit 461d8003529db77a4d5ecbd108312e868b051a3d
+Author: peterjc <p.j.a.cock@googlemail.com>
+Date:   Mon Aug 22 05:52:56 2011 +0100
+
+    Define CIGAR equals and X operationss (7 and 8)
+
+commit c2c63d067113baab41f3bc35fb28f4f00578accb
+Merge: 7ab3ef3 9a0ed9a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Aug 18 17:21:54 2011 -0700
+
+    Merge pull request #3 from peterjc/x_equals
+    
+    Accept SAM files using = in CIGAR (treats X and = as M)
+
+commit 9a0ed9a6b85c7981465f459300208dbd93e3c6f5
+Author: peterjc <p.j.a.cock@googlemail.com>
+Date:   Thu Aug 18 19:28:52 2011 +0100
+
+    Accept SAM files using = in CIGAR (treats X and = as M)
+
+commit 7ab3ef388c1eb34d7912fd70cc5656c955240263
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Aug 8 10:22:22 2011 -0400
+
+    bugfix: indexing takes huge memory
+    
+    This happens when an unmapped mate has coordinate 1. Thank Joel Martin for the fix.
+
+commit a3f6738593e944354a8f75306687d8b3acf08bf1
+Merge: a8bdca9 bc67ea2
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Aug 8 09:52:26 2011 -0400
+
+    Merge branch 'master' of github.com:lh3/samtools
+
+commit bc67ea225da653f36a70b38382d6111dd494f659
+Author: Petr Danecek <pd3@sanger.ac.uk>
+Date:   Thu Jul 28 20:03:16 2011 +0100
+
+    Variant Distance Bias
+
+commit deb578f0c49d0b7d8c3bc6be220b4d67e2e7dfdf
+Author: Petr Danecek <pd3@sanger.ac.uk>
+Date:   Tue Jul 26 09:57:37 2011 +0100
+
+    If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but use the tag instead.
+
+commit a8bdca9cf482a637b89ee4f98469a93e0ab5e69b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Jul 25 10:10:55 2011 -0400
+
+    bugfix: LRT2=nan
+
+commit 0afe33137d046a3e849eeb4a54590f27cbad4228
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Jul 22 21:55:38 2011 -0400
+
+    fixed a bug/typo
+
+commit 62d5849658c10222d40308c6b53ab4f99a448494
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Jul 15 16:04:19 2011 -0400
+
+    allow to set see in subsampling
+
+commit 5f46243824cc9435b167973e1d51e13128794ea1
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Jul 15 15:54:47 2011 -0400
+
+    support subsampling
+
+commit 5e55b6f34fc86cba7cf98d52ccaed405c3ffabbc
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Jul 15 15:53:38 2011 -0400
+
+    support indels
+
+commit f31c162926d6f43e8b60171789a258d02e1f9be5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jul 7 17:02:33 2011 -0400
+
+    do not count indel with "view -Y"
+
+commit e412dae587883b4c17e5fbf4b7c33f38bfa8458a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jul 7 00:35:25 2011 -0400
+
+    for WIN32 compatibility
+
+commit 70a52501bcfa63824749893a5ab8ed3c38e34958
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jul 7 00:32:46 2011 -0400
+
+    for WIN32 compatibility
+
+commit 00438f14ed5984f08e8f7645a9b95644a812f969
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jul 6 23:41:45 2011 -0400
+
+    fixed an uninitialized variable
+
+commit 7609c4a01059c326544b3d0142dfe9c4229d68c6
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jul 6 23:39:31 2011 -0400
+
+    fixed an uninitialized variable
+
+commit cec7189a412f80ccb068a73bd28528915c16b0bf
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jul 6 22:53:19 2011 -0400
+
+    Release samtools-0.1.17
+
+commit 93c06a249de3bb666029bf07b66de5e8e5e314fa
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jul 6 09:46:09 2011 -0400
+
+    bugfix: incorrect idxstats for the last seq
+    
+    Again, this bug is caused by 3rd-party code for the sorting order checking.
+
+commit 84f6ca62db6e27b8c4c711e7b5f3ca704bf27b4f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Jul 5 23:30:23 2011 -0400
+
+    output mapping quality in the old pileup format
+
+commit 362e05fd670886acaede69b864903d730b9db3ca
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Jul 5 21:59:22 2011 -0400
+
+    added a brief description of the VCF format
+
+commit e690a696468205e0cc4560016361c997660dd496
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Jul 5 16:23:10 2011 -0400
+
+    improved samtools manual page
+
+commit 362b4a1408ef3c32311d638aa8d85ce39c1c7b2d
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Jul 5 15:58:29 2011 -0400
+
+    merge bcftools.1 to samtools.1
+
+commit 643e0e61ba7266efbc9e5bfcb8e41f369ba2ce0a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Jul 5 13:39:02 2011 -0400
+
+    mpileup: when region set, set reference properly
+
+commit 613e4d67624a94f62563935fbd5cc294df69605a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Jul 4 23:29:02 2011 -0400
+
+    compute the min PL diff
+
+commit 5b7d5d3f52b97ca42c8500eede808dab88a46a53
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Jul 4 22:57:48 2011 -0400
+
+    rename trio.c to mut.c
+
+commit 84fe96ad64b0365ead93a4115d1684b9bebb98fc
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Jul 3 15:38:51 2011 -0400
+
+    added pair caller interface; not tested
+
+commit 2f2867b87b84c35319cc416d6173819d5c8a4e8c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Jul 3 15:24:23 2011 -0400
+
+    inital implementation of a pair caller
+
+commit e97653cf2ad653c95886933c42a2b5492ccab5ff
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Jul 3 00:06:28 2011 -0400
+
+    convert bam to single-end fastq
+
+commit e8013e11f7a8db0a8d18c60d130169cca39bf2bd
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Jul 2 14:39:18 2011 -0400
+
+    improve BED parsing
+
+commit 1025714325fdc636aeee47a76db8dafbbbfde64b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Jul 1 14:19:54 2011 -0400
+
+    update the manual page
+
+commit 8022d0039dff47b1c11b2421357d510c1f28ae15
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Jul 1 14:17:03 2011 -0400
+
+    output the best constrained genotypes in trio
+
+commit 18c87295e12f5bebafdcae00d52000fb94c8a566
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Jul 1 11:18:14 2011 -0400
+
+    added documentations for view -T
+
+commit daf7a8d96bd495296bf7c7d99cddb808a3ced7d5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jun 30 22:45:20 2011 -0400
+
+    fixed a bug in writing SP
+
+commit e5c32bf9b28c6e3e861db88de56b5dbe11058b61
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jun 30 22:35:25 2011 -0400
+
+    optionally output read positions in mpileup
+
+commit 1008051155ec994c1901e18f3eb03ea32a62e5d7
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jun 30 22:17:25 2011 -0400
+
+    make faidx works with <2GB lines
+
+commit 2daebb63762425dd3074ddf71582ad189001e394
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jun 30 17:28:58 2011 -0400
+
+    fixed an issue in the trio caller and the indel caller
+
+commit 9fdd52cf0716fb342a94946433d564b28b230835
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jun 30 13:34:01 2011 -0400
+
+    Added trio caller; NOT tested yet
+
+commit ea22a8ed83625e9c82382b56acc42a2d9cfd17e5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jun 30 11:42:29 2011 -0400
+
+    convert PL to 10-likelihood GL
+
+commit 10d7065267b0d12c2bfcb6c70204fb6944cd395d
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jun 30 10:49:05 2011 -0400
+
+    fix a compatibility issue with the new bcftools
+
+commit d340f01f609c61b719d38a6a55629a3fc899e1cd
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Jun 26 23:41:20 2011 -0400
+
+    allow to ignore RG
+
+commit d6321faf98ebfe899b9409fb23c90a4aa8c6b542
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Jun 5 23:05:21 2011 -0400
+
+    fixed a bug in SO checking due to a recent change
+
+commit bc995abf666d0c9ab4258f6c1b3518a45a89209f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Jun 3 14:45:36 2011 -0400
+
+    update the version number
+
+commit 9e7cd83a08383858d008e0ccb2238a2b93831d6c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Jun 3 14:43:12 2011 -0400
+
+    smarter way to parse a region string
+
+commit e58a90a0fde54053dac65352b34c13c3fea815fc
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jun 1 14:36:22 2011 -0400
+
+    output LRT2 instead of LRT1
+
+commit 08f78c9af3e5661f04f80bef424232de721dba03
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jun 1 14:02:28 2011 -0400
+
+    genotype test, but assuming 1-degree
+
+commit 587b852340d7e60f6f7cf474a92ef77aeab46018
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jun 1 12:55:19 2011 -0400
+
+    perform 2-degree test by default
+
+commit 3d38e403c5c830478b7eb157a484776997440501
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jun 1 12:44:34 2011 -0400
+
+    fixed a typo; but the result is still not good
+
+commit 06291624f7dcc57445676f3be25d0bc355dd7110
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jun 1 12:24:18 2011 -0400
+
+    fixed a typo
+
+commit 63b98aa33636b0d82a435bf49153c8c1502e7d42
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jun 1 12:23:37 2011 -0400
+
+    added HWE+F<0 filter
+
+commit 37d926e8999999b593d0637ab7dc379dbd3d6006
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed May 4 10:11:59 2011 -0400
+
+    improved sorting order checking in index
+    
+    Patches from Jonathan Manning
+
+commit 1c2dc6762c5f7cd946046b53346513f2f9761dbf
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue May 3 23:09:05 2011 -0400
+
+    added r^2 estimate; added Brent's method
+
+commit c2d3bcd8f98e31668b5f1321222fbc6fd6336e75
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun May 1 23:45:23 2011 -0400
+
+    combine several utilites into vcfutils.lua
+
+commit be2e7362d7593ea4d03fb33cdb6af2aa096ca6c4
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Apr 27 21:09:22 2011 -0400
+
+    minor warning
+
+commit 683ef0443860813d743cf84fa86dda9bfaf5445a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Apr 27 10:10:38 2011 -0400
+
+    added versioning
+
+commit ed72f25ec85671f7646dbc92fa7b5b1dda427f7d
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Apr 27 10:04:02 2011 -0400
+
+    Output ML allele count
+
+commit 2a9e36d2d6c405b2411ca47458f028ada8fe1000
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Apr 26 16:14:20 2011 -0400
+
+    use ar -s
+
+commit 7a4f54e6dbcd7c94acbb3f1050a93f94b8a07949
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Apr 23 01:22:31 2011 -0400
+
+    added another type of LRT
+
+commit b9c5e84762a4aacce3a3771b51ea80967c79a2e5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 22 16:00:31 2011 -0400
+
+    added version
+
+commit 8fad6677c5952efd67391581d64e67e02e7f6e68
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 22 00:30:19 2011 -0400
+
+    remove the pileup command
+
+commit 3a962fb6ebf779de70f9e6effb2d8701a9aa3dd9
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Apr 21 23:10:45 2011 -0400
+
+    Release 0.1.16 (r963:234)
+
+commit b4d683cffbd98c43f05aff8610b37d63dd7e54aa
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Apr 21 12:44:44 2011 -0400
+
+    fixed a bug when coordinate-less reads are on the reverse strand
+
+commit c5ec45a128f409debc6a56a798024f53004037dc
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Apr 20 11:36:52 2011 -0400
+
+    added option '-f' to merge to avoid overwritting
+
+commit 68d431531370d24907c01a27f166f2341d7c4d35
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Apr 20 10:26:58 2011 -0400
+
+    do not print a warning
+
+commit 32922607e51ad2260c337eb022b9e4aedacb049f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Apr 20 10:21:06 2011 -0400
+
+    Added ldpair to compute LD between requested pairs
+
+commit b8d6fa71b91678fa02338257e0707d1e5ca098dd
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Apr 17 21:51:43 2011 -0400
+
+    On a toy sample, type "B" seems to be accepted
+
+commit 0e7ee9a6bb4029184202aa6e6738105ba0c0510b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Apr 17 21:21:20 2011 -0400
+
+    added type "B"; not tested yet
+
+commit a513dfad0ac0062b03871eb6ecf26cb8d18dc895
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Apr 17 19:25:54 2011 -0400
+
+    fixed a bug in bedidx.c: input BED not sorted
+
+commit de1e192bb0a8a762a54a6eee81d882fab01c3d32
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Apr 17 18:51:08 2011 -0400
+
+    by default, always perform posterior chi^2
+
+commit df6e0d1099895fc6cd7a19dc89fba95ed6654d35
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Apr 16 12:33:28 2011 -0400
+
+    added debugging
+
+commit 8ce52e024dc2ef361dbd5399c232163055057e70
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Apr 16 00:59:05 2011 -0400
+
+    avoid a segfault given wrong input
+
+commit e66b6684fc9a397f91ec29fdeecae9f8eb986a55
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 15 19:55:39 2011 -0400
+
+    do not segfault when there is no PL
+
+commit 9ce3c584ec0cebfa45576f2ef538df4dad2b7e55
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 15 11:59:55 2011 -0400
+
+    remove another unused part
+
+commit f53a051d68bf312ac8d5865210fae7a9808c0fb9
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 15 10:41:25 2011 -0400
+
+    print G3 if HWE is small
+
+commit 4b2c08bb86ca4ed4959e4cb77a28f7d6fc19f5c9
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 15 10:04:34 2011 -0400
+
+    fixed a bug
+    
+    actually not fix, but hide it
+
+commit 088e13c32453fb533b7bb1c65a573f9b90a23625
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 15 09:48:47 2011 -0400
+
+    added LRT based permutation; not used though
+
+commit 1e3c2001afcb80b5eaa4c3f88df9da7b01b62524
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 15 09:28:55 2011 -0400
+
+    Perform posterior contrast for small LRT
+    
+    Posterior contrast is much slower than LRT. Nonetheless, posterior P-value is
+    more robust to sequencing artifacts. Thus we may combine the two to achieve a
+    balance between speed and low FPR.
+
+commit 6f1b066270902198a7175ff6c1b05ebc8d1919be
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 15 01:36:06 2011 -0400
+
+    Added Brent's method
+
+commit 3d061e5db25b67b25f6ff87afe4162e121354232
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Apr 14 23:30:10 2011 -0400
+
+    fixed a typo in printing
+
+commit 7fd14ceb5990bb350b8e97346ef3537d80058def
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Apr 14 23:14:23 2011 -0400
+
+    fixed a stupid bug
+
+commit f5b2c3459ec098b3cafd9619b9077132516baf58
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Apr 14 22:42:35 2011 -0400
+
+    separate EM and posterior
+    
+    Now, constrast is not performed unless -C is in use. EM can be invoked
+    independently with -e without computing the posterior.
+
+commit 9eefcac963697fae554789b11ae3cb2c23f224d0
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Apr 14 22:00:19 2011 -0400
+
+    further code cleanup; prepare to add EM interface
+
+commit c2cce52355262743711e4742b0c8542bfcab1cdd
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Apr 14 21:44:03 2011 -0400
+
+    drop EM from prob1
+
+commit 24016f04bd3bdffb7eeb50cb25854f5007feb70f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Apr 14 21:08:33 2011 -0400
+
+    drop posterior LRT; prepare for clean up
+
+commit 3670d8bd88c3eb22873f0a80e2a5913f64ca8c9a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Apr 14 20:57:43 2011 -0400
+
+    better initial values for LD
+
+commit d48a8873c060b18b57799cfe3a0e5496ba069457
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Apr 14 20:36:25 2011 -0400
+
+    finished EM
+
+commit b101f2db476188a950c23f5c1b6185fdb7f8f40b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Apr 13 01:19:04 2011 -0400
+
+    genotype frequency estimate
+
+commit d79bdcbf6242ecfb8accba9ac9a22fbcbd543cf2
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Apr 13 00:37:22 2011 -0400
+
+    prepare for code clean up
+
+commit e0ce416abfc094f0c090957080b1404fd0edf752
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Apr 13 00:34:15 2011 -0400
+
+    rename ld.c to em.c
+
+commit 45ede3ad181f35c1be24bed5d75841e472357ab7
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Apr 13 00:22:10 2011 -0400
+
+    implemeted EM likelihood ratio test
+    
+    The idea is learned from a brief chat with Rasmus Nielsen.
+
+commit 0454a346b60e42b75a2f742272089810279c7131
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Apr 12 15:45:52 2011 -0400
+
+    added likelihood-ratio test (idea from Nick)
+
+commit f6287c8646c690440a1554c8958e7268f4134dc2
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Apr 10 18:24:37 2011 -0400
+
+    Release samtools-0.1.15 (r949:203)
+
+commit de6023f38f4d652438557cf7a0ac6eec324e7416
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Apr 10 15:54:58 2011 -0400
+
+    improved help information
+
+commit d3b337f2b7eda1e6f8f5575a19d1b5ed55cae279
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Apr 9 16:28:01 2011 -0400
+
+    fixed a minor issue
+
+commit 82f6e4f49247e75fbd8ec08c285b8d3047b3d235
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Apr 9 15:49:04 2011 -0400
+
+    separate QC-pass and QC-fail reads
+
+commit 8362b4a255081ee7ca0a4ca2eabc8c76758b6863
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 8 17:45:19 2011 -0400
+
+    added verbose level
+
+commit f7bf419c290462be7d289249a4a6d28f825b4c93
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 8 16:08:14 2011 -0400
+
+    fixed a bug
+
+commit 890cbb1ac93b3004fb6cf42ff47195077dcfc8ad
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 8 16:00:37 2011 -0400
+
+    drop unrelated @RG when "-R" is in use
+
+commit a62dc929c950fb51311b705f5b5bfba8e3f704d7
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 8 16:00:14 2011 -0400
+
+    skip header validation
+
+commit 39da810e2c56c8f0eff1ab726600b41f26d3d8e9
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Apr 5 23:52:22 2011 -0400
+
+    change error message
+
+commit c0c50a34df250ef8a7a29b172058cd229be582b5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Apr 5 23:50:46 2011 -0400
+
+    fixed a bug caused by recent modifications
+
+commit 25226e8c468404cb5e1b5272efcea57e4193c762
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Apr 5 13:31:19 2011 -0400
+
+    reduce the indel filtering window
+
+commit 5e18d7014437734f9dac9ab45a95e43ec2526101
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Apr 4 13:56:20 2011 -0400
+
+    only output hwe if it is small enough
+
+commit 614941fb7dd276de662e7820eb8c7bae871a18cc
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Apr 4 13:34:02 2011 -0400
+
+    added HWE back
+
+commit 7abe8825aa0bacccdeb38125934ae94d18f0ad4d
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Apr 4 12:46:24 2011 -0400
+
+    EM estimate of genotype frequency
+
+commit 2bfeff9c645d177416664f1cb811e85cac3ff9e3
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Apr 4 11:29:12 2011 -0400
+
+    minor
+
+commit 401e40647e7e3abbac6e4ec3d8bb68eb6f2d401b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Apr 4 11:24:04 2011 -0400
+
+    Added genotype freq estimate and association test
+
+commit 6cc226df6e3b480f1bd6e763ce8ef47f785bbb74
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Apr 3 20:57:23 2011 -0400
+
+    minor changes
+
+commit 7e47a39630e812f09b80369f14606245976f687e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 1 15:21:59 2011 -0400
+
+    print the grayscale
+
+commit 2f675d9c0dde3c166c99e335fa17c7873a5ae8d5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 1 08:55:16 2011 -0400
+
+    change to comment
+
+commit 0592bb514994544ed84f51e509b233cf8821e0cf
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Apr 1 08:54:35 2011 -0400
+
+    added base quality filtering
+
+commit fc1b47e04a7b94f6362c45856cbeb89d9d0b5ca5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Mar 31 23:31:14 2011 -0400
+
+    fixed a few typos in comments
+
+commit 60be79bc8f0d24656e5e8a329af7e9b5b91d4c8b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Mar 31 23:13:23 2011 -0400
+
+    comments
+
+commit 2432864acc25ebe5cee4217dbb0120439077a7f8
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Mar 31 22:42:46 2011 -0400
+
+    added bam2depth.c, a demo program
+
+commit 39625f7c6bea9ccbfd9af0feb22348d52079f012
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Mar 31 16:37:22 2011 -0400
+
+    added bgzf_check_bgzf() (used by tabix)
+
+commit 6de6bd3fb67fd22753a5f07d4cc25bf94e1b5a8c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Mar 31 16:37:08 2011 -0400
+
+    fixed a bug in bedidx.c
+
+commit 3b9e257d25b2e81eed1625bc5d2882ed486ef20e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 30 13:27:15 2011 -0400
+
+    added bed support to bcftools
+
+commit 47bcce3d14ec4d205283b61e5e653803996c42e0
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 30 12:56:40 2011 -0400
+
+    Added BED support to "samtools view"
+
+commit a812386017faedfc86c0e6562adbb2138329cfeb
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 30 12:47:04 2011 -0400
+
+    support BED file
+
+commit 3052dddc929f1825e6e7f7f6f6724d9465d6cf9a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Mar 28 15:51:55 2011 -0400
+
+    relax RG matching; proper mismatching message
+
+commit f86d60c8fe25785523f01fae1486d2a6df4ee6ef
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Mar 26 10:38:23 2011 -0400
+
+    Avoid reporting association when something unexpected, which I do not understand, happens.
+
+commit dd41e6b26fd9fe30218748b9a0a1f49bdb1862b9
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Mar 26 10:38:01 2011 -0400
+
+    Added -1 to merge
+
+commit 4a0364b0d7f87f1c88d71ec5857a1f1d40710681
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 23 16:56:55 2011 -0400
+
+    plot pairwise r^2
+
+commit 452629a711582e612bec22b3b082e234bd37039b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 23 14:31:01 2011 -0400
+
+    pairwise LD; case-control AF2
+
+commit 52862951adcaecde26ba8f0d9c1897944640a674
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Mar 21 23:03:14 2011 -0400
+
+    Release samtools-0.1.14 (r933:170)
+
+commit 59a5a8ba8e2940f0e38238f9339f02c91a8a0ce4
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Mar 21 13:52:55 2011 -0400
+
+    optionally skip loci with too low sample coverage
+
+commit 6434264b5c69514d4fafe62cbd30b3bbaddc1d41
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Mar 19 14:38:25 2011 -0400
+
+    mpileup support Illumina1.3+ quality; skip non-variant sites when "view -v" is in use
+
+commit 5f59e01987e1d5eca7d6359cae64a9734b18beea
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Mar 18 17:19:18 2011 -0400
+
+    update version to r933:167
+
+commit 4d2c3c950910aa3d2c87760c3532e458fe01c0fa
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Mar 18 16:25:01 2011 -0400
+
+    added "-1" to the command-line help
+
+commit 55313a015a7bd6369cf5a66fed7fab2333201dc9
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Mar 18 16:22:12 2011 -0400
+
+    added the "cat" command (by Chris Saunders)
+
+commit b670272cadf3efa4dc456ac4c76104f73477d60d
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Mar 18 15:59:46 2011 -0400
+
+    support varying the compression level
+
+commit c5dd3c9ca5f75f880e52c8cd2beae983bcb8d3b1
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 16 14:33:45 2011 -0400
+
+    update the manual pages
+
+commit 12fb4b596dc51bccd154fc4bd0593442f7937a46
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 16 12:49:26 2011 -0400
+
+    update changelog
+
+commit e7fe4fd66e02d60a1ca7952ad1938809e77729a9
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 16 12:10:05 2011 -0400
+
+    do not call indels when the depth is very high
+
+commit 7455eeaa32b949bb3856f75810890aabf7cacb18
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 16 11:56:56 2011 -0400
+
+    code clean up
+
+commit 5f16679e54ced8e67a75d949f9175c50480b914e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Mar 15 14:45:24 2011 -0400
+
+    when -s is specified, change the sample order
+
+commit 7ba95adee09d3b06a7eaf797d25efef837e592f5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Mar 15 14:11:42 2011 -0400
+
+    compute the rank in permutation
+
+commit d219783cea7643fc7e10e1bd3a98e9b3165b4506
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Mar 13 21:35:13 2011 -0400
+
+    I have found a SERIOUS BUG!!!
+
+commit 8e20d04ecdac1a7788eef71c4bb91b8479cf7150
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Mar 13 17:04:04 2011 -0400
+
+    optionally shuffle samples in a BCF (debugging)
+
+commit fc7b261f181f2a411427bc9ee5d586c883ca9cdc
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Mar 11 09:34:20 2011 -0500
+
+    fixed a bug
+
+commit b3bbcc3d40994ae85705ab6fef9866ec8c142201
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Mar 10 20:25:59 2011 -0500
+
+    use mode instead of mean
+
+commit f1161262d137098a19143b5cb0de810e5db3243e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Mar 10 20:09:16 2011 -0500
+
+    start from the mean instead of the mode
+
+commit 2ba56f5e99e90674855c4ffc8bf583340b932e1e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Mar 10 17:13:34 2011 -0500
+
+    fixed an error in Chi^2 test
+
+commit b4ce7ae400290bc43dd287240479667f99b3b11e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Mar 10 00:23:39 2011 -0500
+
+    minor
+
+commit 8487fa5d3a73a43443964e731ea2a4c873c9d4e5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 9 21:33:19 2011 -0500
+
+    added -F to accept BCFs generated by old samtools
+
+commit fd51d2093f7fd775a7eaaeea57fa34716ab59ac2
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 9 17:39:09 2011 -0500
+
+    update version
+
+commit b6da54335df943015a998a934075331b467abb5b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 9 17:37:14 2011 -0500
+
+    compute pseudo-chi2 probability
+
+commit 9f73cefdb8935421d872b989dd98fbc8e1295029
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 9 15:54:04 2011 -0500
+
+    remove a comment which is wrong
+
+commit b10b1e47ece522e97ab8ef23417bcb6454f8b9db
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 9 15:51:12 2011 -0500
+
+    clean up
+
+commit 353bfae2c6ff59205bd9223db04084cf7f507f01
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 9 15:45:29 2011 -0500
+
+    for backup
+
+commit 53915d1c6410c2537d18bfa8eb8c657a2233c35e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 9 15:27:56 2011 -0500
+
+    having debugging code
+
+commit 0d0dbf66995b1511390d593981eae7b5d36fe17b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Mar 9 14:58:23 2011 -0500
+
+    temporary backup
+
+commit 5b74a174a8b637dee43b7f30250df6fb96580e12
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Mar 8 15:46:11 2011 -0500
+
+    the output makes sense, but there may be a typo...
+
+commit d81ec654b6c0c1eef6b0625d96f14b3155cee7c6
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Mar 8 15:19:09 2011 -0500
+
+    added contrast2(); fixed a bug in haploid mode
+
+commit 0cfd896fad5f7737cca49efa94a11892dafcd812
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Mar 7 21:40:17 2011 -0500
+
+    fixed a bug in haploid genotyping
+
+commit ccd52155ef61273f2b42ad9c7b31ff1915f81b24
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Mar 5 18:10:35 2011 -0500
+
+    fixed a few bugs; still not fully working
+
+commit edc3af753f96f831968ae32f2e0f915b74f31e6e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Mar 4 17:31:33 2011 -0500
+
+    drop HWE calculation
+
+commit 92dac194debb66ca0718c21c871822dda2dd5bc1
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Mar 4 17:28:35 2011 -0500
+
+    implemented hap/dipoind mode; probably BUGGY!
+
+commit 7f26804bc27937e36fdc967e5c76514653ea40f5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Mar 4 16:01:27 2011 -0500
+
+    read ploidy
+
+commit e7b7213475b5e61a69aab77ffb02b4983c8e7678
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Mar 4 14:12:14 2011 -0500
+
+    added math notes
+
+commit 46023e2f21321da83fc8e83e9229757a4e821acb
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Mar 4 13:34:10 2011 -0500
+
+    update BCF spec
+
+commit 13190c49eeb006ad7013b7f1e9fc1b3beca3ae78
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Mar 1 14:45:19 2011 -0500
+
+    Release samtools-0.1.13 (r926:134)
+
+commit be8fabbb6001d9fd5263a70a3e21ed6dfe5a9837
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Mar 1 14:07:15 2011 -0500
+
+    prepare to finalize 0.1.13
+
+commit 1e8c753660978bed7e9289fe50becd596d9314bb
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Mar 1 09:40:17 2011 -0500
+
+    allow to change whether to drop ambiguous reads
+
+commit 412210bfdb46606023f2e4b9086f2787f0cf1c62
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 28 22:01:29 2011 -0500
+
+    revert to the old behavior of phase
+
+commit 46035589518cf84738de8666b866e2619457c1fb
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 28 16:46:23 2011 -0500
+
+    change version number
+
+commit 7f40c33e37fc16fcb0a375ce46ae1d09cafb6d50
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 28 16:37:42 2011 -0500
+
+    bugfix in indel calling: interger overflow
+
+commit 75849470efbe30042e5ddd516f9bcbe3b9bf6062
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 28 15:35:47 2011 -0500
+
+    fixed a typo
+
+commit 9e6fb569885f906fabaab7fc2f02eae82f4bd602
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 28 15:34:09 2011 -0500
+
+    minor changes to heuristic rules
+
+commit 30a799a91f5e2c10b761aa5437f902c6649fceb3
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 28 15:20:26 2011 -0500
+
+    fixed a bug in the latest change
+
+commit e21ba9df950ea37f5c1b35c2af9ba9a4e0bba02a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 28 12:47:06 2011 -0500
+
+    put version in bam.h
+
+commit 918b14780c1dceb39c7010638ecd61c626e17166
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 28 12:00:38 2011 -0500
+
+    frag_t::phased==0 reads are dumped to chimera.bam
+
+commit 657293c7bdba3ac69f53cd1ffa2874ed8756475e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 28 11:05:29 2011 -0500
+
+    change default -q to 37 (previously 40)
+
+commit 33d8d3bea76e466798ea322d68d34deb8d2dff06
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 28 10:39:57 2011 -0500
+
+    fixed a minor bug in BAM reading
+
+commit daa25d426d42465d76c7317c95772bbb36bb3f47
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Feb 26 21:07:24 2011 -0500
+
+    suppress gzopen64() warning
+
+commit 9cec4256eb9e7848d4711adb67b540659c141e32
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 22:14:52 2011 -0500
+
+    fixed a long existing bug in vcf2fq
+
+commit 304487c83067a733add71cbc3886fa8c49f7ef2a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 16:37:40 2011 -0500
+
+    change version number
+
+commit 10ba6bf4f16692760f696f7b17f3719065786f77
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 16:34:08 2011 -0500
+
+    Change the order of PL; change SP to int32_t
+
+commit c5cc2a8036a9c3579fbfde651efec4f6763b0228
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 14:52:03 2011 -0500
+
+    claim X defined in the header
+
+commit 4ee8cb29f6092fd14a89f0cc5d3575112a204f39
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 14:40:24 2011 -0500
+
+    minor changes
+
+commit 00065e9336a2831dc53bee7da2f4719845be1a2a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 11:39:06 2011 -0500
+
+    fixed an error in the BCF spec
+
+commit 1e2a73afcb72a02aa448718cb017c0438de89f90
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 11:36:40 2011 -0500
+
+    update BCF spec
+
+commit dbf8eedaa38a405cb2fba5b3952b85776f51d035
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 11:28:43 2011 -0500
+
+    update BCF spec
+
+commit eed1d91af9fad3c9d965333a55e623757f9c4e9d
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 09:51:39 2011 -0500
+
+    fixed a flaw in targetcut
+
+commit 59bc980bb832b92a8b0cc244cf106e6150e4db6f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 00:54:35 2011 -0500
+
+    update manual page
+
+commit fcc4738c4abdca79e3de159e21208df1b98ac76c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 00:45:39 2011 -0500
+
+    update version format
+
+commit 5748639ae542b7f6b853562edc2bb3faf43030e4
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 00:45:12 2011 -0500
+
+    update version number
+
+commit 06b44cc366cf27ce8976ee6a05810a0b3c48b56d
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 00:44:21 2011 -0500
+
+    update version number
+
+commit ab7f4529d12739ff66fd4c09af9d992ab59c53ef
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 25 00:42:55 2011 -0500
+
+    various help message
+
+commit a092e1f6f963272f8bb23616986ddaf604fd0f82
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 24 23:43:13 2011 -0500
+
+    disable unfinished functionality
+
+commit f00a78db72b14ee4c6689fc13f20ed31aeaecd40
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 24 10:04:56 2011 -0500
+
+    added "const" to bcf_p1_cal()
+
+commit 91049c4a8db3bf50dcc9d07506f22fa4ca5b5a96
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 23 11:53:47 2011 -0500
+
+    randomly allocate unphased reads
+
+commit f4405354a8d4cb3441141fa734573031059d7f57
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 22 15:36:07 2011 -0500
+
+    fixed a typo
+
+commit 3075e4dc5c7c9d954426aabda6a73fa788357100
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 22 15:33:40 2011 -0500
+
+    make output more informative
+
+commit 628cf3235e2815a40acf089fb1d3357be6437787
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 22 14:50:06 2011 -0500
+
+    change the scoring rule; change default k to 13
+
+commit f22fd99831e4b5c74f898719216f359dbe987bbf
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 22 14:45:15 2011 -0500
+
+    update scoring in masking
+
+commit 2f23547b81984555032aa0eefd064b8e07986fdc
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 22 14:37:17 2011 -0500
+
+    remove dropreg()
+
+commit 4d8b6b1f1f331ca9041983c66e34a857c3b8f1bb
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 22 13:10:16 2011 -0500
+
+    accept files from stdin
+
+commit 9b50c5038e6fc0185e29ca5b50fe0806a9a939b9
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 22 11:16:57 2011 -0500
+
+    fixed a bug in consensus generation
+
+commit 1332ab32fb788fdc81b2ba8653b905d106238fad
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 21 22:53:23 2011 -0500
+
+    print dropped fragments
+
+commit a288761b4ca1584e51076a71cbc4d72fe923dda1
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 21 22:37:04 2011 -0500
+
+    bugfix: singletons are not phased
+
+commit 683365f534c0223dea7d72532015ac16a45ba22b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 21 17:27:10 2011 -0500
+
+    output singleton blocks
+
+commit 841a4609084d81f1bc81e0b00dd806002461e7d9
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 21 15:58:55 2011 -0500
+
+    fixed a bug; not working with -l right now
+
+commit fdd57ea31732b5516dc212d72174b60206952636
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 21 15:17:00 2011 -0500
+
+    skip mapQ==0 reads
+
+commit 4eb6ba75c23c1c9be5f76814fa1b93a2e304b2af
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 21 14:03:03 2011 -0500
+
+    print the "targetcut" command
+
+commit 0123d9559ba58b026c0dfd15bc26019a193cd21a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 21 11:22:13 2011 -0500
+
+    allow to set the maximum depth
+
+commit 0f92eb248a4d06645b2c3d736a0faea8a7a9f731
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 21 09:56:41 2011 -0500
+
+    use a proper error model to call hets
+
+commit 587a01504af5aea6288740d121dccf48fb8a75f4
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 21 09:16:38 2011 -0500
+
+    phase is UNFINISHED; strip RG when merging
+
+commit 723bf3cd79e4f4a558373d4c707fa6b3db0fb357
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Feb 19 23:38:11 2011 -0500
+
+    use a proper model to compute consensus
+
+commit 891a6b02d4a9af2ed98fbaac4915bf1f0da4f6c8
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Feb 19 22:14:19 2011 -0500
+
+    added comment
+
+commit 8b55e0a581ecc9e4ba754d1f3c8784f3038b6e48
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 18 17:23:39 2011 -0500
+
+    change the output format
+
+commit 75c36e8c563eddd0a362ba3b38cf0aea21aafb1f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 15 20:31:00 2011 -0500
+
+    fixed a bug in writing BAM
+
+commit bb0ce52f066cfebaa35a125d57b353bb717a5165
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 23:39:09 2011 -0500
+
+    skip uncovered; unknown alleles taken as X
+
+commit ba67f4d119c7d06907db3015d337d9a01a3fc9fe
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 23:21:19 2011 -0500
+
+    fixed a bug
+
+commit e4448d49e6129a5e1ee9c7f04f43612f12d6aad6
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 22:43:09 2011 -0500
+
+    prepare to read hets from a list; unfinished
+
+commit 129ea29c1f12177c0a7c3e21676f6210370fc59b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 16:32:22 2011 -0500
+
+    updated khash.h to 0.2.5
+
+commit 15b44ed93bd949dffcf79ac8dbea6d9b7dfcb58c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 16:15:04 2011 -0500
+
+    use the latest version of khash
+
+commit 486c05f06f44d981dfb2069bcb43e4b35fd8389c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 15:04:40 2011 -0500
+
+    change the default -k to 11
+
+commit 07cf9d1e443d73cf053de38dd01671e3781f6e29
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 14:50:51 2011 -0500
+
+    sort fragments by vpos instead of by beg
+
+commit d0d3e7faabf5cbb7e5ff7b294f7e220da807c4c0
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 14:45:41 2011 -0500
+
+    shuffling the two haplotypes for better randomness
+
+commit 3be28eaf5f6033229aedf12ddb11a0084ba01cd8
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 14:09:17 2011 -0500
+
+    write chimeras to a separate BAM
+
+commit 80ccbc26f43918fe42be123cc1da9d3d7ce30816
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 13:54:13 2011 -0500
+
+    no mem leak/violation on small files; correctness is not checked
+
+commit 5c923867432fa14c26a19e3782e7f48d4080f6ac
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 14 13:50:25 2011 -0500
+
+    bam separation; at least not immediate segfault
+
+commit cea2643ec30a59735bf89b2f562b563bf7263e79
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Feb 13 23:24:11 2011 -0500
+
+    on the way to implement BAM separation; unfinished
+
+commit 964269cd15036a470ca89e43d0952201a0825671
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Feb 13 18:07:56 2011 -0500
+
+    keep singletons in the hash table
+
+commit 2d4aa649bd670d5e038a1acaefd33c5fe24ae0e8
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Feb 13 17:42:24 2011 -0500
+
+    Revert "prepare to add bam separation"
+    
+    This reverts commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f.
+
+commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Feb 13 00:24:28 2011 -0500
+
+    prepare to add bam separation
+
+commit d211e652d93791d2e112d334added243ffe5fc3e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Feb 12 18:50:20 2011 -0500
+
+    accelerate kstrtok
+
+commit 2d6af49d331ff5afe7b9e9b102e79d7d4512fdbe
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 11 21:08:21 2011 -0500
+
+    split unlinked blocks
+
+commit 68e4cd1b560b0a6fd4c77e5e51eadde9fda26ea4
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 11 10:47:58 2011 -0500
+
+    remove heading and tailing ambiguous positions
+
+commit d2b685141426a902ae76660c1fbe8020da150cf8
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 11 10:02:21 2011 -0500
+
+    code clean up for further features
+
+commit c6980e062d55928b59f287c03e599dd5a37ed509
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 11 08:00:08 2011 -0500
+
+    change /64 to >>6; the latter is faster
+
+commit 91635b9c2687f24d72ee6a8aad2050a79bb8400f
+Merge: 41d4df2 9a7e155
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 11 01:22:55 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit 9a7e155cc591c1b6c9f7f9cb939364a6becb65b2
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 11 01:21:07 2011 -0500
+
+    output an unrecognized field as '.'; autofix GL/PL
+
+commit 41d4df2e9545e9abe97151cfe5d6c763f3d00db1
+Merge: c00c41c aacce0c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 10 23:00:14 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit aacce0ce7276f451e4fddf81832f9e5f7f65198b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 10 22:57:53 2011 -0500
+
+    finished VCF->BCF conversion
+
+commit 0e875df643e41d848b709e2fa877de8ae53cdd4c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 10 21:57:28 2011 -0500
+
+    fixed a bug in reading VCF files
+
+commit c00c41c2a5da69cccea64adb542a0b365e56b4fc
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 10 16:28:37 2011 -0500
+
+    suppres one-allele blocks
+
+commit 2e2354b673722e2f00d72970a043f80a66270da1
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 10 16:06:56 2011 -0500
+
+    fixed the bug in filtering
+
+commit d971e1fe24de4ecaf94055efffc5f641e2bdb563
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 10 12:24:23 2011 -0500
+
+    prepare to add filtering; buggy right now
+
+commit a0a5a3fbf504c3b02f7b9212e72315c1047cc249
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 10 11:55:02 2011 -0500
+
+    make masking optional
+
+commit 28db71ccd95054a5f8a47c2332794f8968f6a822
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 10 11:40:47 2011 -0500
+
+    routine to mask poorly called regions
+
+commit a3f6c439262bc10a4067860440f4d4dde9e0c515
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 9 17:18:33 2011 -0500
+
+    code clean up: remove globals
+
+commit 0b711978492f6ad39d459d78723c299468906818
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 9 16:52:54 2011 -0500
+
+    output more information
+
+commit f69d217ae5b691bf42ad07a97f29a7cc6456046f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 9 16:11:54 2011 -0500
+
+    fixed another bug in flipping
+
+commit d47882d549337fbcc251597508a2c7faf1bb92e2
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 9 16:01:35 2011 -0500
+
+    fixed a stupid bug in flipping
+
+commit e33f89de499496537f5fbde396a66557f0353f1b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 9 15:54:42 2011 -0500
+
+    fix chimeras; a little weird...
+
+commit 03d3c1d0b945245108ce0942d4772536a32212c7
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 9 13:27:35 2011 -0500
+
+    no effective change; prepare to fix chimera
+
+commit 6bc0a4676dd2252085a6e67bb06daa5ae05a554f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 9 11:52:58 2011 -0500
+
+    better count output
+
+commit dcac515439d25f71125d6de8111da417776ab9ce
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 9 10:31:07 2011 -0500
+
+    prepare for another way of filtering
+
+commit ca7e4f1899b86d2e077994c789e8f69d699b3cd9
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 8 16:10:08 2011 -0500
+
+    fixed the bug; I can do better.
+
+commit 0733f77b98af121bdcb198cea6151d159831bb9c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 8 15:55:38 2011 -0500
+
+    fixed two bugs; still not working...
+
+commit 80f18cba9ba73c9592380fc1ecd53c351d294782
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 8 15:42:58 2011 -0500
+
+    filter false SNPs; NOT working right now
+
+commit 69a66e2f96d5b102cd712ff1527a3802fa84c590
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 8 14:39:09 2011 -0500
+
+    write sequence in the SAM format for debugging
+
+commit b6f1c9d160822af2b713be206f37bd6dde00546a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 7 11:51:21 2011 -0500
+
+    fixed two bugs
+
+commit 400aa5c06100af9c47cd5e4ce8b95b7deb84f54b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 7 11:22:38 2011 -0500
+
+    Optionally apply BAQ
+
+commit 4c82e0e19682e424f5cdb8381364114c307b329e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Feb 7 01:23:31 2011 -0500
+
+    improved output; the result makes sense at a glance
+
+commit dc7853a581ab24bcc496e96b123ccf637e32ed1d
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Feb 6 14:12:43 2011 -0500
+
+    process per linked block instead of per chr
+
+commit e867d9c6c2e61d9e748e78163e5481dca5697a36
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sun Feb 6 00:45:46 2011 -0500
+
+    DP seems to work on toy examples
+
+commit 445ad72fc43d4354d56f5f759790e8ae0be73d02
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Feb 5 01:24:42 2011 -0500
+
+    implemented backtrack; not tested
+
+commit ba38e180b9cd545956583b22e97e09b4bb12073e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 4 23:55:23 2011 -0500
+
+    More "correct" DP; backtrack not implemented
+
+commit d69761fd9351273ccd37ea431b10509add91e7cf
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 4 17:22:31 2011 -0500
+
+    scratch of dynamic programming; unfinished...
+
+commit 769ffcb44e26e59300791658801d321559b33858
+Author: Heng Li <lh3@live.co.uk>
+Date:   Fri Feb 4 16:29:55 2011 -0500
+
+    UNFINISHED commit.
+
+commit 9adab9591317c3467f3d8cdf2d19ec1f65d1b5b7
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 3 16:20:59 2011 -0500
+
+    another way of counting; can be even faster
+
+commit bbafbdc01ed1ceaab44927def1ad47c4c78aeb9c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Feb 3 14:48:20 2011 -0500
+
+    for backup
+
+commit eba7446389cad62a19133bced1386a4334dcab79
+Merge: a44a98e f01a593
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 2 14:06:07 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit f01a5930445b5fda7e6b5b813ed63c652160ada2
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 2 11:31:54 2011 -0500
+
+    Better truncation warning when EOF is absent
+
+commit dd3ee5ed26c8bbef4a62fa5b2bfb0a75833f2c31
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 2 10:38:28 2011 -0500
+
+    fixed a typo in BCF/VCF headers
+
+commit b9d1137c55f401387113d1ad8a387489afe741db
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Feb 2 09:13:44 2011 -0500
+
+    fixed an out-of-boundary bug (fixed by Roel Kluin)
+
+commit a44a98e16559b9672e8a3492c8f8c640074b7ee2
+Merge: ef68a14 d0443d5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 1 21:54:48 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit d0443d5c2f648e0f69bd4c56eaac7868e501c18b
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 1 17:31:52 2011 -0500
+
+    improved sorting order checking
+
+commit ef68a14fab91399b2ecd38345936c3d6e7391cf3
+Merge: 1e597b3 1a39a2e
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 1 15:12:37 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit 1a39a2eb08a270e20a34a0983e8bed6ffb3e2008
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 1 15:12:14 2011 -0500
+
+    more precise error message
+
+commit e028e7a47c02232e06a9dd3009262c00dede1060
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 1 14:48:01 2011 -0500
+
+    improved sorting order validation in index
+
+commit 1e597b3356744e2b791b12c9187f91c8054511d5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Tue Feb 1 14:44:27 2011 -0500
+
+    testing only; not working
+
+commit 5753ace1e54228822d8ee95f69943f586e42f6e8
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Jan 31 17:37:08 2011 -0500
+
+    reduce the effect of seq errors at the cost of SN
+
+commit 6f239ce5e0abd47babee33174476d48b723260d8
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Jan 31 17:29:34 2011 -0500
+
+    added testing code
+
+commit 3db42fe22d27d61ab5735cd2308f73d93def8ebe
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Jan 31 14:33:21 2011 -0500
+
+    routine for phasing fosmid resequencing (incomplete)
+
+commit ed88f2797323229ae8f38fbcd107b231007956a8
+Author: Heng Li <lh3@live.co.uk>
+Date:   Mon Jan 31 10:12:53 2011 -0500
+
+    SAM output
+
+commit abc6acae28dc4794f6422255f077cf370d34e414
+Merge: f1985a9 b133dbf
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Jan 29 22:56:10 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit b133dbf82de4e8cea5eb56e5bbf0c4b3e9368fd5
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Jan 29 22:37:11 2011 -0500
+
+    fixed a bug in tview on big-endian by Nathan Weeks
+
+commit 9d3fdaef29f91e21dbfcb9ff0165b9573e7c1042
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Jan 29 22:24:00 2011 -0500
+
+    update INSTALL
+
+commit 9d074a38bde53961f96157b6fb3683b6dded38d7
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Jan 29 21:56:25 2011 -0500
+
+    avoid a segfault when network connect fails
+
+commit f1985a93f7455b3ea1b0ef9b959d50b896ccd620
+Author: Heng Li <lh3@live.co.uk>
+Date:   Sat Jan 29 21:53:18 2011 -0500
+
+    fixed a bug about bit ordering
+
+commit d09797db6fef648a6823cbe718d67664660c6ebe
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jan 27 16:53:19 2011 -0500
+
+    point out there are 4 or fewer free parameters
+
+commit 5fd1717650ed68ab6c55d094d1648c16a054891a
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jan 27 16:09:18 2011 -0500
+
+    updated .gitignore
+
+commit fccb19fbe8f9de91f59d85bb49a248683dc6266c
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jan 27 16:08:14 2011 -0500
+
+    fixed a bug; better scoring
+
+commit b4dcb844bde3d09eedcd9f6832186ece60ae5afd
+Merge: ffc3e89 6f502de
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jan 27 14:50:30 2011 -0500
+
+    Merge branch 'master' into devel
+
+commit 6f502dec46b18dae4bb5b2319715d028b5e193d0
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jan 27 14:47:31 2011 -0500
+
+    skip unmapped and ref-skip reads in indel calling
+
+commit 3639f37dd8257b24560c35effcc3b6c16c3c1bcb
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jan 27 14:19:15 2011 -0500
+
+    fixed an out-of-boundary bug in rare cases
+
+commit ffc3e89678ab9052b84f403da1e43044b045e73f
+Author: Heng Li <lh3@live.co.uk>
+Date:   Thu Jan 27 14:00:17 2011 -0500
+
+    targetcut can be compiled, though probably buggy
+
+commit f452b3ac51306865ddde31a8d715b155d4d3e6e6
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jan 26 18:58:43 2011 -0500
+
+    this is for a very special application...
+
+commit ca1451c6406c7ee757cb31349ea0b8de70db0656
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jan 26 18:48:09 2011 -0500
+
+    fixed compiling errors
+
+commit 085b87a7642865f17239fb6a436e626e25417838
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jan 26 18:45:09 2011 -0500
+
+    This script was put in a wrong place...
+
+commit 090d360828622520de60385af4928ce1aebe0e48
+Author: Heng Li <lh3@live.co.uk>
+Date:   Wed Jan 26 18:33:58 2011 -0500
+
+    Imported from samtools-r902
+------------------------------------------------------------------------
+r108 | lh3lh3 | 2009-01-20 11:56:45 +0000 (Tue, 20 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/examples/Makefile
+
+made it a little more convenient
+
+------------------------------------------------------------------------
+r107 | lh3lh3 | 2009-01-20 11:53:30 +0000 (Tue, 20 Jan 2009) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/examples/Makefile
+
+added a Makefile
+
+------------------------------------------------------------------------
+r106 | lh3lh3 | 2009-01-20 11:25:05 +0000 (Tue, 20 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/maq2sam.c
+
+support RG tag
+
+------------------------------------------------------------------------
+r105 | lh3lh3 | 2009-01-18 17:37:20 +0000 (Sun, 18 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/ChangeLog
+
+update changelog
+
+------------------------------------------------------------------------
+r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_lpileup.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-18
+ * fixed a bug in bam_lpileup.c: segment start and end are not correctly recognized
+
+------------------------------------------------------------------------
+r103 | lh3lh3 | 2009-01-18 16:34:03 +0000 (Sun, 18 Jan 2009) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-17
+ * fixed a bug when there are reads without coordinates
+ * also recognize type 'c' as 'A'      
+ * found a bug in bam_lpileup.c; NOT fixed yet
+
+------------------------------------------------------------------------
+r102 | lh3lh3 | 2009-01-17 19:46:49 +0000 (Sat, 17 Jan 2009) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/INSTALL
+
+Instruction for compilation
+
+------------------------------------------------------------------------
+r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   A /branches/dev/samtools/Makefile.lite
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/faidx.c
+   M /branches/dev/samtools/misc/Makefile
+   M /branches/dev/samtools/razf.c
+
+ * replaced HAVE_RAZF with _NO_RAZF
+ * added Makefile.lite for people who have trouble with razf.c
+
+------------------------------------------------------------------------
+r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_mate.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/misc/wgsim.c
+
+ * samtools-0.1.1-15
+ * fixed another bug in fixmate: unmapped pair has non-zero isize
+
+------------------------------------------------------------------------
+r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/ChangeLog
+   M /branches/dev/samtools/bam_mate.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-14
+ * fixed a bug in fixmate: isize not equal to zero if two ends mapped to
+   different chr
+
+------------------------------------------------------------------------
+r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-13
+ * fixed the prior for hom indels (Richard pointed this out)
+
+------------------------------------------------------------------------
+r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/COPYING
+   M /branches/dev/samtools/bam_sort.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/source.dot
+
+ * samtools-0.1.1-12
+ * fixed a bug in sort
+ * update source file graph and copyright information
+
+------------------------------------------------------------------------
+r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/glf.c
+
+fixed a typo
+
+------------------------------------------------------------------------
+r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/glf.c
+
+added a main function for glf.c
+
+------------------------------------------------------------------------
+r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/bgzf.h
+   A /branches/dev/samtools/glf.c
+   M /branches/dev/samtools/glf.h
+
+ * samtools-0.1.1-11
+ * generate binary GLFv2
+ * added glfview command to dump GLFv2 binary file
+
+------------------------------------------------------------------------
+r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_rmdup.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/glf.h
+
+ * samtools-0.1.1-10
+ * fixed several bugs in rmdup
+ * prepare to generate GLF2
+
+------------------------------------------------------------------------
+r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_import.c
+   A /branches/dev/samtools/bam_rmdup.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-9
+ * implemented rmdup; NOT tested yet
+
+------------------------------------------------------------------------
+r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/examples/00README.txt
+
+update README for typos
+
+------------------------------------------------------------------------
+r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/examples/ex1.sam.gz
+
+update example
+
+------------------------------------------------------------------------
+r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.c
+   A /branches/dev/samtools/bam_mate.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-8
+ * added fixmate command
+
+------------------------------------------------------------------------
+r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-7
+ * change the reported indel position to the previous way
+
+------------------------------------------------------------------------
+r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-6
+ * addd glt output
+ * allow to change indel calling parameters at the command line
+
+------------------------------------------------------------------------
+r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-5
+ * added two more flags
+ * allowed to select reads shown in pileup with a mask
+
+------------------------------------------------------------------------
+r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-4
+ * fixed a bug in indexing (linear index)
+ * prepare to add glt output from pileup
+
+------------------------------------------------------------------------
+r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-3
+ * fixed a bug in outputing the coordinate of an indel
+
+------------------------------------------------------------------------
+r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-2
+ * pileup: allows to output indel sites only
+
+------------------------------------------------------------------------
+r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_maqcns.h
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.1-1
+ * implemented a Bayesian indel caller
+
+------------------------------------------------------------------------
+r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/examples/00README.txt
+   D /branches/dev/samtools/examples/ex1.fa.fai
+
+Let users generate ex1.fa.fai.
+
+------------------------------------------------------------------------
+r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/bowtie2sam.pl
+
+make the bowtie converter works for "-k 2"
+
+------------------------------------------------------------------------
+r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/export2sam.pl
+
+fixed a bug for "QC" reads
+
+------------------------------------------------------------------------
+r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines
+Changed paths:
+   A /branches/dev/samtools/misc/bowtie2sam.pl
+   M /branches/dev/samtools/misc/soap2sam.pl
+
+ * soap2sam.pl: added NM tag
+ * bowtie2sam.pl: converter for bowtie
+
+------------------------------------------------------------------------
+r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/misc/soap2sam.pl
+
+soap2sam.pl: convert soap output to SAM
+
+------------------------------------------------------------------------
+r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/misc/wgsim_eval.pl
+
+ * wgsim_eval.pl-0.1.1
+ * fixed a bug for a contig name like "NT_012345"
+
+------------------------------------------------------------------------
+r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/misc/wgsim_eval.pl
+
+ * evaluate alignment for reads generated by wgsim
+
+------------------------------------------------------------------------
+r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/Makefile
+   M /branches/dev/samtools/misc/wgsim.c
+
+fixed compiling warnings for wgsim
+
+------------------------------------------------------------------------
+r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bam_tview.c
+
+remove an unused variable (a compiler warning only)
+
+------------------------------------------------------------------------
+r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/Makefile
+   A /branches/dev/samtools/misc/wgsim.c
+
+wgsim: Paired-end reads simulator
+
+------------------------------------------------------------------------
+r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_tview.c
+
+Move definition of bam_nt16_nt4_table so we can build without curses.
+
+------------------------------------------------------------------------
+r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/NEWS
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/samtools.1
+
+Release samtools-0.1.1
+
+------------------------------------------------------------------------
+r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
+Changed paths:
+   M /branches/dev/samtools/bam_aux.c
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bam_tview.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/razf.c
+   M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-66
+ * fixed a bug in razf.c: reset z_eof when razf_seek() is called
+ * fixed a memory leak in parsing a region
+ * changed pileup a little bit when -s is in use: output ^ and $
+ * when a bam is not indexed, output more meaningful error message
+ * fixed a bug in indexing for small alignment
+ * fixed a bug in the viewer when we come to the end of a reference file
+ * updated documentation
+ * prepare to release 0.1.1
+
+------------------------------------------------------------------------
+r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/examples
+   A /branches/dev/samtools/examples/00README.txt
+   A /branches/dev/samtools/examples/ex1.fa
+   A /branches/dev/samtools/examples/ex1.fa.fai
+   A /branches/dev/samtools/examples/ex1.sam.gz
+
+example
+
+------------------------------------------------------------------------
+r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/ChangeLog
+
+update ChangeLog
+
+------------------------------------------------------------------------
+r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/misc/export2sam.pl
+
+ * added comments
+ * fixed several bugs 
+
+------------------------------------------------------------------------
+r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/misc/export2sam.pl
+
+convert Export format to SAM; not thoroughly tested
+
+------------------------------------------------------------------------
+r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
+Changed paths:
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bam_tview.c
+   M /branches/dev/samtools/bamtk.c
+   A /branches/dev/samtools/source.dot
+
+ * samtools-0.1.0-65
+ * pileup: generate maq-like simple output
+ * pileup: allow to output pileup at required sites
+ * source.dot: source file relationship graph
+ * tview: fixed a minor bug
+
+------------------------------------------------------------------------
+r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
+Changed paths:
+   D /branches/dev/samtools/misc/all2sam.pl
+
+remove all2sam.pl
+
+------------------------------------------------------------------------
+r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/COPYING
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/faidx.h
+   M /branches/dev/samtools/khash.h
+   M /branches/dev/samtools/kseq.h
+   M /branches/dev/samtools/ksort.h
+   M /branches/dev/samtools/samtools.1
+
+Added copyright information and a bit more documentation. No code change.
+
+------------------------------------------------------------------------
+r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam.c
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-64
+ * improved efficiency of the indel caller for spliced alignments
+
+------------------------------------------------------------------------
+r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam.c
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_aux.c
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-63
+ * a bit code cleanup: reduce the dependency between source files
+
+------------------------------------------------------------------------
+r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-62
+ * fixed a memory leak
+
+------------------------------------------------------------------------
+r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/ChangeLog
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/samtools.1
+
+update documentation, ChangeLog and a comment
+
+------------------------------------------------------------------------
+r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_maqcns.h
+   M /branches/dev/samtools/bam_pileup.c
+   A /branches/dev/samtools/bam_plcmd.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-61
+ * moved pileup command to a separate source file
+ * added indel caller
+ * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
+ * updated documentation
+
+------------------------------------------------------------------------
+r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-60
+ * fixed another bug in maqcns when there is a nearby deletion
+
+------------------------------------------------------------------------
+r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-59
+ * pileup: outputing consensus is now optional
+ * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
+   I am not quite sure why the previous version may have problem.
+
+------------------------------------------------------------------------
+r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
+Changed paths:
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-58
+ * add maq consensus to pileup. However, I will move this part to a new
+   command as strictly speaking, consensus callin is not part of pileup,
+   and imposing it would make it harder to generate for other language
+   bindings.
+
+------------------------------------------------------------------------
+r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bgzf.c
+
+Fix bug in tell() after reads that consume to the exact end of a block.
+
+------------------------------------------------------------------------
+r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/samtools.1
+
+update manual
+
+------------------------------------------------------------------------
+r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-57
+ * fixed a bug in parser when there is auxiliary fields
+ * made the parser a bit more robust
+
+------------------------------------------------------------------------
+r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/bgzf.c
+
+ * samtools-0.1.0-56
+ * fixed a bug in bgzf (only reading is affected)
+ * fixed a typo in bam_index.c
+ * in bam_index.c, check potential bugs in the underlying I/O library
+
+------------------------------------------------------------------------
+r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/samtools.1
+
+update manual
+
+------------------------------------------------------------------------
+r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-55
+ * tried to make pileup work with clipping (previously not), though NOT tested
+ * removed -v from pileup
+ * made pileup take the reference sequence
+
+------------------------------------------------------------------------
+r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-54
+ * in parser, recognize "=", rather than ",", as a match
+ * in parser, correctl parse "=" at the MRNM field.
+
+------------------------------------------------------------------------
+r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/maq2sam.c
+
+fixed a bug in handling maq flag 64 and 192
+
+------------------------------------------------------------------------
+r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/md5fa.c
+
+also calculate unordered md5sum check
+
+------------------------------------------------------------------------
+r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/md5fa.c
+
+fixed a minor bug when there are space in the sequence
+
+------------------------------------------------------------------------
+r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/md5fa.c
+
+fixed a potential memory leak
+
+------------------------------------------------------------------------
+r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bamtk.c
+
+ * fixed a bug in import: bin is wrongly calculated
+
+------------------------------------------------------------------------
+r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/misc/all2sam.pl
+
+nothing, really
+
+------------------------------------------------------------------------
+r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/kseq.h
+   M /branches/dev/samtools/misc/Makefile
+   A /branches/dev/samtools/misc/md5.c
+   A /branches/dev/samtools/misc/md5.h
+   A /branches/dev/samtools/misc/md5fa.c
+
+ * fixed two warnings in kseq.h
+ * added md5sum utilities
+
+------------------------------------------------------------------------
+r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bamtk.c
+   A /branches/dev/samtools/kseq.h
+   D /branches/dev/samtools/kstream.h
+
+ * samtools-0.1.0-52
+ * replace kstream with kseq. kseq is a superset of kstream. I need the
+   extra functions in kseq.h.
+ * also compile stand-alone faidx
+
+------------------------------------------------------------------------
+r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_sort.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-51
+ * sorting by read names is available
+
+------------------------------------------------------------------------
+r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam.c
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bam_sort.c
+   M /branches/dev/samtools/bam_tview.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/misc/maq2sam.c
+
+ * samtools-0.1.0-50
+ * format change to meet the latest specification
+
+------------------------------------------------------------------------
+r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/misc/maq2sam.c
+
+ * minor change in maqcns: special care when n==0
+ * change maq2sam to meet the latest specification
+
+------------------------------------------------------------------------
+r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/razf.c
+   M /branches/dev/samtools/razf.h
+
+considerable code clean up in razf
+
+------------------------------------------------------------------------
+r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/ChangeLog
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/faidx.c
+
+make RAZF optional in faidx.c
+
+------------------------------------------------------------------------
+r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/bam_aux.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-49
+ * added routines for retrieving aux data, NOT TESTED YET!
+
+------------------------------------------------------------------------
+r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
+Changed paths:
+   M /branches/dev/samtools/bam.c
+   M /branches/dev/samtools/bam_import.c
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/bgzf.c
+   M /branches/dev/samtools/samtools.1
+
+ * samtools-0.1.0-48
+ * bgzf: fixed a potential integer overflow on 32-it machines
+ * maqcns: set the minimum combined quality as 0
+ * supporting hex strings
+
+------------------------------------------------------------------------
+r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/bam_maqcns.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-47
+ * fixed the bug in maqcns
+
+------------------------------------------------------------------------
+r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.h
+   A /branches/dev/samtools/bam_maqcns.c
+   A /branches/dev/samtools/bam_maqcns.h
+   M /branches/dev/samtools/bam_tview.c
+   M /branches/dev/samtools/bamtk.c
+   A /branches/dev/samtools/glf.h
+
+ * samtools-0.1.0-46
+ * add MAQ consensus caller, currently BUGGY!
+
+------------------------------------------------------------------------
+r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_pileup.c
+   M /branches/dev/samtools/bam_tview.c
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-45
+ * tview: display padded alignment (but not P operation)
+ * better coordinates and reference sequence
+
+------------------------------------------------------------------------
+r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/ChangeLog
+
+new ChangeLog
+
+------------------------------------------------------------------------
+r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
+Changed paths:
+   D /branches/dev/samtools/ChangeLog
+   A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
+
+Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
+the log of my personal SVN repository.
+
+------------------------------------------------------------------------
+r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/bgzf.c
+
+ * samtools-0.1.0-44
+ * declare fseeko and ftello as some Linux may not do this by default and
+   missing these declarations will make bgzf buggy
+ * get rid of some harmless warings
+ * use BGZF by default, now
+
+------------------------------------------------------------------------
+r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bam_index.c
+   M /branches/dev/samtools/bamtk.c
+   M /branches/dev/samtools/razf.c
+
+ * samtools-0.1.0-43
+ * fixed a bug in razf_read()
+ * give more warnings when the file is truncated (or due to bugs in I/O library)
+
+------------------------------------------------------------------------
+r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bgzf.c
+
+fixed a bug in bgzf.c at the end of the file
+
+------------------------------------------------------------------------
+r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/dev/samtools/bamtk.c
+
+ * samtools-0.1.0-42
+ * a lot happened to RAZF, although samtools itself is untouched. Better
+   also update the version number anyway to avoid confusion
+
+------------------------------------------------------------------------
+r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/razf.c
+
+a change from Jue, but I think it should not matter
+
+------------------------------------------------------------------------
+r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/dev/samtools/razf.c
+
+fixed a potential bug in razf. However, it seems still buggy, just
+rarely happens, very rarely.
+
+------------------------------------------------------------------------
+r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/razf.c
+
+fixed a bug in razf, with the help of Jue
+
+------------------------------------------------------------------------
+r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/bam_index.c
+
+remove a comment
+
+------------------------------------------------------------------------
+r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/dev/samtools/Makefile
+   M /branches/dev/samtools/bam.h
+   M /branches/dev/samtools/razf.c
+   M /branches/dev/samtools/razf.h
+
+ * Jue has updated razf to realize Bob's scheme
+
+------------------------------------------------------------------------
+r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools/samtools.1
+
+the manual page
+
+------------------------------------------------------------------------
+r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
+Changed paths:
+   A /branches/dev/samtools/ChangeLog
+   A /branches/dev/samtools/Makefile
+   A /branches/dev/samtools/bam.c
+   A /branches/dev/samtools/bam.h
+   A /branches/dev/samtools/bam_aux.c
+   A /branches/dev/samtools/bam_endian.h
+   A /branches/dev/samtools/bam_import.c
+   A /branches/dev/samtools/bam_index.c
+   A /branches/dev/samtools/bam_lpileup.c
+   A /branches/dev/samtools/bam_pileup.c
+   A /branches/dev/samtools/bam_sort.c
+   A /branches/dev/samtools/bam_tview.c
+   A /branches/dev/samtools/bamtk.c
+   A /branches/dev/samtools/bgzf.c
+   A /branches/dev/samtools/bgzf.h
+   A /branches/dev/samtools/bgzip.c
+   A /branches/dev/samtools/faidx.c
+   A /branches/dev/samtools/faidx.h
+   A /branches/dev/samtools/khash.h
+   A /branches/dev/samtools/ksort.h
+   A /branches/dev/samtools/kstream.h
+   A /branches/dev/samtools/misc
+   A /branches/dev/samtools/misc/Makefile
+   A /branches/dev/samtools/misc/all2sam.pl
+   A /branches/dev/samtools/misc/maq2sam.c
+   A /branches/dev/samtools/razf.c
+   A /branches/dev/samtools/razf.h
+   A /branches/dev/samtools/razip.c
+   A /branches/dev/samtools/zutil.h
+
+The initial version of samtools, replicated from my local SVN repository.
+The current version is: 0.1.0-42. All future development will happen here.
+
+------------------------------------------------------------------------
+r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/dev/samtools
+
+samtools (C version)
+
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+r703 | lh3 | 2008-11-25 20:20:02 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/samtools.1
+
+rename bamtk to samtools
+
+------------------------------------------------------------------------
+r702 | lh3 | 2008-11-25 20:15:09 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   D /branches/prog/bam/bamtk.1
+   A /branches/prog/bam/samtools.1 (from /branches/prog/bam/bamtk.1:679)
+
+rename bamtk.1 to samtools.1
+
+------------------------------------------------------------------------
+r701 | lh3 | 2008-11-25 13:29:10 +0000 (Tue, 25 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/misc/Makefile
+
+ * samtools-0.1.0-41
+ * small (but a bit dangerous) changes to meet the latest specification
+
+------------------------------------------------------------------------
+r700 | lh3 | 2008-11-25 13:15:11 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/misc/all2sam.pl (from /branches/prog/bam/misc/all2tam.pl:649)
+   D /branches/prog/bam/misc/all2tam.pl
+   A /branches/prog/bam/misc/maq2sam.c (from /branches/prog/bam/misc/maq2tam.c:699)
+   D /branches/prog/bam/misc/maq2tam.c
+
+rename tam to sam
+
+------------------------------------------------------------------------
+r699 | lh3 | 2008-11-25 13:14:49 +0000 (Tue, 25 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/misc/maq2tam.c
+
+change for the new specification
+
+------------------------------------------------------------------------
+r698 | lh3 | 2008-11-24 13:15:20 +0000 (Mon, 24 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/razf.c
+   M /branches/prog/bam/razf.h
+
+ * add a fake BGZF mode to razf. It is fake in that it loads razf index into
+   memory but gives BGZF like virtual offset
+
+------------------------------------------------------------------------
+r697 | lh3 | 2008-11-24 09:53:44 +0000 (Mon, 24 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/ChangeLog
+
+change log
+
+------------------------------------------------------------------------
+r696 | lh3 | 2008-11-24 09:53:23 +0000 (Mon, 24 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bgzf.c
+
+updated bgzf, on behalf of Bob
+
+------------------------------------------------------------------------
+r695 | lh3 | 2008-11-23 11:40:31 +0000 (Sun, 23 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/razf.c
+
+fixed a bug in razf
+
+------------------------------------------------------------------------
+r694 | lh3 | 2008-11-22 16:23:52 +0000 (Sat, 22 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_lpileup.c
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bam-0.1.0-40
+ * fixed two small memory leaks
+ * fixed a memory problem when seek outside the length of the sequence
+
+------------------------------------------------------------------------
+r693 | lh3 | 2008-11-22 16:10:04 +0000 (Sat, 22 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+
+ * bam-0.1.0-39
+ * fixed an uninitialized warning. This does not matter in fact
+
+------------------------------------------------------------------------
+r692 | lh3 | 2008-11-22 15:44:05 +0000 (Sat, 22 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/razf.c
+   M /branches/prog/bam/razf.h
+
+Jue's new razf
+
+------------------------------------------------------------------------
+r691 | lh3 | 2008-11-21 21:30:39 +0000 (Fri, 21 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/bgzip.c
+
+ * bam-0.1.0-38
+ * get rid of some warings in bgzip.c
+ * potentially improve performance in indexing for BGZF
+
+------------------------------------------------------------------------
+r690 | lh3 | 2008-11-21 21:15:51 +0000 (Fri, 21 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bgzf.c
+
+I think I have fixed the bug in bgzf
+
+------------------------------------------------------------------------
+r689 | lh3 | 2008-11-21 20:48:56 +0000 (Fri, 21 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bgzf.c
+
+bug fix by Bob
+
+------------------------------------------------------------------------
+r688 | lh3 | 2008-11-21 20:37:27 +0000 (Fri, 21 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+
+fixed a bug due to the name change in _IOLIB
+
+------------------------------------------------------------------------
+r687 | lh3 | 2008-11-21 14:42:56 +0000 (Fri, 21 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bgzf.c
+
+fix small things
+
+------------------------------------------------------------------------
+r686 | lh3 | 2008-11-21 14:37:59 +0000 (Fri, 21 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/bgzf.c
+   A /branches/prog/bam/bgzf.h
+   A /branches/prog/bam/bgzip.c
+
+Bob's BGZF format, although currently buggy
+
+------------------------------------------------------------------------
+r685 | lh3 | 2008-11-21 09:48:20 +0000 (Fri, 21 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bam-0.1.0-37
+ * improve interface a little bit
+
+------------------------------------------------------------------------
+r684 | lh3 | 2008-11-21 09:30:18 +0000 (Fri, 21 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bam-0.1.0-36
+ * improve the interface of tview, a little bit
+
+------------------------------------------------------------------------
+r683 | lh3 | 2008-11-20 22:33:54 +0000 (Thu, 20 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam_tview.c
+
+a little better viewer
+
+------------------------------------------------------------------------
+r682 | lh3 | 2008-11-20 22:27:01 +0000 (Thu, 20 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-35
+ * better viewer
+
+------------------------------------------------------------------------
+r681 | lh3 | 2008-11-20 20:51:16 +0000 (Thu, 20 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-34
+ * tview is now a component of bamtk
+
+------------------------------------------------------------------------
+r680 | lh3 | 2008-11-20 19:17:30 +0000 (Thu, 20 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/bam_tview.c
+
+text alignment viewer
+
+------------------------------------------------------------------------
+r679 | lh3 | 2008-11-20 19:17:15 +0000 (Thu, 20 Nov 2008) | 5 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_lpileup.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.1
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/faidx.c
+
+ * bamtk-0.1.0-33
+ * added routines to reset pileup bufferes
+ * fixed a bug in faidx
+ * add text alignment viewer
+
+------------------------------------------------------------------------
+r678 | lh3 | 2008-11-20 11:05:02 +0000 (Thu, 20 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   A /branches/prog/bam/bam_lpileup.c (from /branches/prog/bam/bam_tview.c:668)
+   D /branches/prog/bam/bam_tview.c
+
+rename tview as lpileup
+
+------------------------------------------------------------------------
+r677 | lh3 | 2008-11-20 10:08:52 +0000 (Thu, 20 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/razf.c
+
+fixed a bug in razf
+
+------------------------------------------------------------------------
+r676 | lh3 | 2008-11-19 22:52:20 +0000 (Wed, 19 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/faidx.h
+
+add documentations
+
+------------------------------------------------------------------------
+r674 | lh3 | 2008-11-19 21:39:17 +0000 (Wed, 19 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bamtk.1
+   M /branches/prog/bam/faidx.h
+
+update documentation
+
+------------------------------------------------------------------------
+r673 | lh3 | 2008-11-19 21:19:03 +0000 (Wed, 19 Nov 2008) | 2 lines
+Changed paths:
+   A /branches/prog/bam/bamtk.1
+
+add manual page
+
+------------------------------------------------------------------------
+r672 | lh3 | 2008-11-19 16:40:49 +0000 (Wed, 19 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/faidx.c
+
+ * bamtk-0.1.0-32
+ * make faidx more error resistant
+
+------------------------------------------------------------------------
+r671 | lh3 | 2008-11-19 16:09:55 +0000 (Wed, 19 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/faidx.h
+
+add index
+
+------------------------------------------------------------------------
+r670 | lh3 | 2008-11-19 16:02:39 +0000 (Wed, 19 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/faidx.c
+
+ * bamtk-0.1.0-31
+ * show reference sequence in pileup -v (not in the default pileup)
+
+------------------------------------------------------------------------
+r669 | lh3 | 2008-11-19 14:51:17 +0000 (Wed, 19 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bamtk.c
+   M /branches/prog/bam/faidx.c
+
+ * bamtk-0.1.0-30
+ * put faidx in bamtk and remove faidx_main.c
+
+------------------------------------------------------------------------
+r668 | lh3 | 2008-11-19 14:15:05 +0000 (Wed, 19 Nov 2008) | 4 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+   A /branches/prog/bam/faidx.c
+   A /branches/prog/bam/faidx.h
+   M /branches/prog/bam/razf.c
+
+ * bamtk-0.1.0-29
+ * fixed a bug in tview.c
+ * prepare to add faidx
+
+------------------------------------------------------------------------
+r667 | lh3 | 2008-11-19 10:20:45 +0000 (Wed, 19 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/razf.c
+   M /branches/prog/bam/razf.h
+
+gzip-compatible razf
+
+------------------------------------------------------------------------
+r664 | lh3 | 2008-11-18 12:50:23 +0000 (Tue, 18 Nov 2008) | 5 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-28
+ * fetch: fixed a bug at an array boundary
+ * fetch: fixed a bug when the whole chromosome is retrieved
+ * add linear index
+
+------------------------------------------------------------------------
+r663 | lh3 | 2008-11-17 21:29:22 +0000 (Mon, 17 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-27
+ * put l_qseq into core and move l_aux to bam1_t
+
+------------------------------------------------------------------------
+r662 | lh3 | 2008-11-17 20:55:16 +0000 (Mon, 17 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam.c
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_import.c
+   M /branches/prog/bam/bam_index.c
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-26
+ * save seq and qual separately
+
+------------------------------------------------------------------------
+r661 | lh3 | 2008-11-17 13:09:37 +0000 (Mon, 17 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+
+little
+
+------------------------------------------------------------------------
+r660 | lh3 | 2008-11-17 13:06:14 +0000 (Mon, 17 Nov 2008) | 2 lines
+Changed paths:
+   M /branches/prog/bam/bam.h
+
+more documentations
+
+------------------------------------------------------------------------
+r659 | lh3 | 2008-11-17 12:55:08 +0000 (Mon, 17 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bamtk.c
+
+ * bamtk-0.1.0-25
+ * make tview work for TAM
+
+------------------------------------------------------------------------
+r658 | lh3 | 2008-11-17 12:50:21 +0000 (Mon, 17 Nov 2008) | 3 lines
+Changed paths:
+   M /branches/prog/bam/Makefile
+   M /branches/prog/bam/bam.h
+   M /branches/prog/bam/bam_pileup.c
+   M /branches/prog/bam/bam_tview.c
+   M /branches/prog/bam/bamtk.c
+<