X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=a096816027cd67abdd8d8e139ea0ead703203186;hb=41586185b43962c1ffb3f82e93066a480254aa17;hp=45359784b8682812c04c79d8b7d56e17a01a3922;hpb=635998cfe030da5f3dbec42a6daa3ca82fa5c871;p=samtools.git

diff --git a/ChangeLog b/ChangeLog
index 4535978..a096816 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,317 +1,640 @@
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-r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines
+r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/bam.h
-   M /branches/dev/samtools/bam_lpileup.c
-   M /branches/dev/samtools/bamtk.c
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-18
- * fixed a bug in bam_lpileup.c: segment start and end are not correctly recognized
+ * samtools-0.1.3-6 (r244)
+ * fixed segfault for unmapped reads
 
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-r103 | lh3lh3 | 2009-01-18 16:34:03 +0000 (Sun, 18 Jan 2009) | 5 lines
+r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 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
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-17
- * 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
+ * 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
 
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-r102 | lh3lh3 | 2009-01-17 19:46:49 +0000 (Sat, 17 Jan 2009) | 2 lines
+r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
 Changed paths:
-   A /branches/dev/samtools/INSTALL
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
 
-Instruction for compilation
+ * samtools-0.1.3-4 (r242)
+ * fixed a memory leak
 
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-r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines
+r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 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
+   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
 
- * replaced HAVE_RAZF with _NO_RAZF
- * added Makefile.lite for people who have trouble with razf.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
 
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-r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines
+r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
 Changed paths:
-   M /branches/dev/samtools/bam_mate.c
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/misc/wgsim.c
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_aux.c
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-15
- * fixed another bug in fixmate: unmapped pair has non-zero isize
+ * 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
 
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-r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines
+r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/ChangeLog
-   M /branches/dev/samtools/bam_mate.c
-   M /branches/dev/samtools/bamtk.c
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/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
+ * samtools-0.1.3-1
+ * fixed a bug in pileup: the first read in a chromosome may not be printed
 
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-r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines
+r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bamtk.c
+   M /trunk/samtools/Makefile.lite
 
- * samtools-0.1.1-13
- * fixed the prior for hom indels (Richard pointed this out)
+a missing file in Makefile.lite
 
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-r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines
+r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 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
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-12
- * fixed a bug in sort
- * update source file graph and copyright information
+Release samtools-0.1.3
 
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-r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines
+r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/glf.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
 
-fixed a typo
+ * samtools-0.1.2-28
+ * make samtools more robust to weird input such as empty file
 
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-r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines
+r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/glf.c
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/samtools.1
 
-added a main function for glf.c
+prepare for release 0.1.3
 
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-r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines
+r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 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
+   A /trunk/samtools/misc/blast2sam.pl
 
- * samtools-0.1.1-11
- * generate binary GLFv2
- * added glfview command to dump GLFv2 binary file
+convert NCBI-BLASTN to SAM
 
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-r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines
+r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/bam_rmdup.c
-   M /branches/dev/samtools/bamtk.c
-   M /branches/dev/samtools/glf.h
+   M /trunk/samtools/bam_lpileup.c
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-10
- * fixed several bugs in rmdup
- * prepare to generate GLF2
+ * samtools-0.1.2-27
+ * fixed a small memory leak in tview
 
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-r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines
+r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 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
+   M /trunk/samtools/bam_rmdup.c
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-9
- * implemented rmdup; NOT tested yet
+ * samtools-0.1.2-26
+ * fixed a bug in rmdup when there are unmapped reads
 
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-r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines
+r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/examples/00README.txt
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
 
-update README for typos
+proposed NEWS for the new release (have not yet)
 
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-r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines
+r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
 Changed paths:
-   M /branches/dev/samtools/examples/ex1.sam.gz
+   M /trunk/samtools/misc/samtools.pl
 
-update example
+ * 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
 
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-r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines
+r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 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
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/samtools.1
 
- * samtools-0.1.1-8
- * added fixmate command
+ * samtools-0.1.2-25
+ * change the pileup indel line to shows the number of alignments actually
+   containing indels
 
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-r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines
+r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bamtk.c
+   M /trunk/samtools/ChangeLog
 
- * samtools-0.1.1-7
- * change the reported indel position to the previous way
+update ChangeLog from "svn log"
 
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-r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines
+r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
 Changed paths:
-   M /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bamtk.c
+   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-0.1.1-6
- * addd glt output
- * allow to change indel calling parameters at the command line
+ * samtools-0.1.2-24
+ * in merge, gives a warning rather than error if the target sequence length is different
+ * allow empty header
 
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-r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines
+r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 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
+   M /trunk/samtools/bam.c
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-5
- * added two more flags
- * allowed to select reads shown in pileup with a mask
+ * samtools-0.1.2-23
+ * recognize '*' at the QUAL field
 
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-r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines
+r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/bam_index.c
-   M /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bamtk.c
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/kseq.h
 
- * samtools-0.1.1-4
- * fixed a bug in indexing (linear index)
- * prepare to add glt output from pileup
+ * samtools-0.1.2-22
+ * the field separater is TAB only, now
 
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-r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines
+r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bamtk.c
+   M /trunk/samtools/examples/ex1.sam.gz
 
- * samtools-0.1.1-3
- * fixed a bug in outputing the coordinate of an indel
+ * fixed the problem in the example alignment due to the bug in fixmate
 
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-r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines
+r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bamtk.c
+   M /trunk/samtools/bam_mate.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/misc/soap2sam.pl
 
- * samtools-0.1.1-2
- * pileup: allows to output indel sites only
+ * samtools-0.1.2-21
+ * fixed a nasty bug in `fixmate'
 
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-r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines
+r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 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
+   M /trunk/samtools/misc/bowtie2sam.pl
+   M /trunk/samtools/misc/soap2sam.pl
+   M /trunk/samtools/misc/wgsim_eval.pl
 
- * samtools-0.1.1-1
- * implemented a Bayesian indel caller
+make the script robust to the bugs in SOAP-2.1.7
 
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-r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines
+r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/examples/00README.txt
-   D /branches/dev/samtools/examples/ex1.fa.fai
+   M /trunk/samtools/bam_stat.c
+   M /trunk/samtools/bamtk.c
 
-Let users generate ex1.fa.fai.
+ * samtools-0.1.2-20
+ * check if file is truncated in flagstat
 
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-r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines
+r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/misc/bowtie2sam.pl
+   M /trunk/samtools/bamtk.c
 
-make the bowtie converter works for "-k 2"
+ * samtools-0.1.2-19
+ * print the header if requested
 
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-r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines
+r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/misc/export2sam.pl
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
 
-fixed a bug for "QC" reads
+ * samtools-0.1.2-18
+ * fixed a minor bug reported by Nils Homer
 
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-r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines
+r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
 Changed paths:
-   A /branches/dev/samtools/misc/bowtie2sam.pl
-   M /branches/dev/samtools/misc/soap2sam.pl
+   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
 
- * soap2sam.pl: added NM tag
- * bowtie2sam.pl: converter for bowtie
+rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
 
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-r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines
+r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
 Changed paths:
-   A /branches/dev/samtools/misc/soap2sam.pl
+   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
 
-soap2sam.pl: convert soap output to SAM
+ * samtools-0.1.2-17
+ * incorporating Nils' changes
+ * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
 
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-r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines
+r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
 Changed paths:
-   M /branches/dev/samtools/misc/wgsim_eval.pl
+   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
 
- * wgsim_eval.pl-0.1.1
- * fixed a bug for a contig name like "NT_012345"
+ * 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.
 
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-r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines
+r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
 Changed paths:
-   A /branches/dev/samtools/misc/wgsim_eval.pl
+   M /trunk/samtools/misc/soap2sam.pl
 
- * evaluate alignment for reads generated by wgsim
+ * soap2sam.pl-0.1.2
+ * more robust to truncated soap output
 
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-r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines
+r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/misc/Makefile
-   M /branches/dev/samtools/misc/wgsim.c
+   M /trunk/samtools/Makefile.lite
 
-fixed compiling warnings for wgsim
+added bam_stat.o to Makefile.lite
 
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-r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines
+r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/bam_tview.c
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bamtk.c
 
-remove an unused variable (a compiler warning only)
+ * samtools-0.1.2-15
+ * generate RMS of mapQ instead of max mapQ
 
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-r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines
+r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/misc/Makefile
-   A /branches/dev/samtools/misc/wgsim.c
+   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
 
-wgsim: Paired-end reads simulator
+ * samtools-0.1.2-14
+ * implemented GLFv3
 
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-r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines
+r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bam_tview.c
+   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 11:24:16 +0000 (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 10:45:28 +0000 (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 10:39:09 +0000 (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 15:18:43 +0000 (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 19:43:57 +0000 (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 14:53:03 +0000 (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 14:02:57 +0000 (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 11:39:08 +0000 (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 22:23:27 +0000 (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 19:06:57 +0000 (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 10:49:55 +0000 (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 21:22:30 +0000 (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 09:54:45 +0000 (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 11:15:32 +0000 (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 10:30:29 +0000 (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 10:59:10 +0000 (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 10:43:11 +0000 (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 15:52:52 +0000 (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 10:12:15 +0000 (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 12:33:23 +0000 (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 13:31:12 +0000 (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 12:54:08 +0000 (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 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
+Changed paths:
+   A /trunk/samtools/misc/zoom2sam.pl
+
+convert ZOOM to SAM
+
+------------------------------------------------------------------------
+r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (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 20:57:39 +0000 (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 19:22:59 +0000 (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 15:36:48 +0000 (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 15:14:27 +0000 (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 21:42:15 +0000 (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 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
+Changed paths:
+   A /trunk/samtools (from /branches/dev/samtools:62)
 
-Move definition of bam_nt16_nt4_table so we can build without curses.
+Create trunk copy
 
 ------------------------------------------------------------------------
 r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines