X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=12908c968c54e264baff1562e7cea623fb145dcb;hb=ac32543c12eac42f12e0c66b78c3d53211caeaab;hp=45359784b8682812c04c79d8b7d56e17a01a3922;hpb=635998cfe030da5f3dbec42a6daa3ca82fa5c871;p=samtools.git

diff --git a/ChangeLog b/ChangeLog
index 4535978..12908c9 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,320 +1,4280 @@
 ------------------------------------------------------------------------
-r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines
+r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 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_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.
 
- * 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
+r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 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_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-0.1.1-17
+ * samtools-0.1.3-8 (r251)
  * 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
+r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
 Changed paths:
-   A /branches/dev/samtools/INSTALL
+   A /trunk/samtools/AUTHORS
+   A /trunk/samtools/README
+   M /trunk/samtools/cleanup.sh
 
-Instruction for compilation
+added missing files
 
 ------------------------------------------------------------------------
-r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines
+r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 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.generic
+   M /trunk/samtools/Makefile.lite
+   M /trunk/samtools/configure.ac
+   M /trunk/samtools/misc/Makefile.generic
 
- * replaced HAVE_RAZF with _NO_RAZF
- * added Makefile.lite for people who have trouble with razf.c
+improve large file support in compilation
 
 ------------------------------------------------------------------------
-r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines
+r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 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/INSTALL
 
- * samtools-0.1.1-15
- * fixed another bug in fixmate: unmapped pair has non-zero isize
+update INSTALL
 
 ------------------------------------------------------------------------
-r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines
+r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/ChangeLog
-   M /branches/dev/samtools/bam_mate.c
-   M /branches/dev/samtools/bamtk.c
+   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
 
- * samtools-0.1.1-14
- * fixed a bug in fixmate: isize not equal to zero if two ends mapped to
-   different chr
+fixed various issues about the GNU building scripts
 
 ------------------------------------------------------------------------
-r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines
+r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
 Changed paths:
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bamtk.c
+   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-0.1.1-13
- * fixed the prior for hom indels (Richard pointed this out)
+ * samtools-0.1.3-6 (r244)
+ * fixed segfault for unmapped reads
 
 ------------------------------------------------------------------------
-r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines
+r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 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/bam.h
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-12
- * fixed a bug in sort
- * update source file graph and copyright information
+ * 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
 
 ------------------------------------------------------------------------
-r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines
+r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/glf.c
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
 
-fixed a typo
+ * 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
 
 ------------------------------------------------------------------------
-r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines
+r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
 Changed paths:
-   M /branches/dev/samtools/glf.c
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_aux.c
+   M /trunk/samtools/bamtk.c
 
-added a main function for glf.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
 
 ------------------------------------------------------------------------
-r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines
+r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 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
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-11
- * generate binary GLFv2
- * added glfview command to dump GLFv2 binary file
+ * samtools-0.1.3-1
+ * fixed a bug in pileup: the first read in a chromosome may not be printed
 
 ------------------------------------------------------------------------
-r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines
+r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 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/Makefile.lite
 
- * samtools-0.1.1-10
- * fixed several bugs in rmdup
- * prepare to generate GLF2
+a missing file in Makefile.lite
 
 ------------------------------------------------------------------------
-r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines
+r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 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/NEWS
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-9
- * implemented rmdup; NOT tested yet
+Release samtools-0.1.3
 
 ------------------------------------------------------------------------
-r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines
+r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/examples/00README.txt
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
 
-update README for typos
+ * samtools-0.1.2-28
+ * make samtools more robust to weird input such as empty file
 
 ------------------------------------------------------------------------
-r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines
+r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/examples/ex1.sam.gz
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/samtools.1
 
-update example
+prepare for release 0.1.3
 
 ------------------------------------------------------------------------
-r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines
+r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 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
+   A /trunk/samtools/misc/blast2sam.pl
 
- * samtools-0.1.1-8
- * added fixmate command
+convert NCBI-BLASTN to SAM
 
 ------------------------------------------------------------------------
-r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines
+r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bamtk.c
+   M /trunk/samtools/bam_lpileup.c
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-7
- * change the reported indel position to the previous way
+ * samtools-0.1.2-27
+ * fixed a small memory leak in tview
 
 ------------------------------------------------------------------------
-r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines
+r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/bam_plcmd.c
-   M /branches/dev/samtools/bamtk.c
+   M /trunk/samtools/bam_rmdup.c
+   M /trunk/samtools/bamtk.c
 
- * samtools-0.1.1-6
- * addd glt output
- * allow to change indel calling parameters at the command line
+ * samtools-0.1.2-26
+ * fixed a bug in rmdup when there are unmapped reads
 
 ------------------------------------------------------------------------
-r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines
+r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 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/ChangeLog
+   M /trunk/samtools/NEWS
 
- * samtools-0.1.1-5
- * added two more flags
- * allowed to select reads shown in pileup with a mask
+proposed NEWS for the new release (have not yet)
 
 ------------------------------------------------------------------------
-r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines
+r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 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
+   M /trunk/samtools/misc/samtools.pl
 
- * samtools-0.1.1-4
- * fixed a bug in indexing (linear index)
- * prepare to add glt output from pileup
+ * 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
 
 ------------------------------------------------------------------------
-r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines
+r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
 Changed paths:
-   M /branches/dev/samtools/bam_plcmd.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-0.1.1-3
- * fixed a bug in outputing the coordinate of an indel
+ * samtools-0.1.2-25
+ * change the pileup indel line to shows the number of alignments actually
+   containing indels
 
 ------------------------------------------------------------------------
-r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines
+r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (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-0.1.1-2
- * pileup: allows to output indel sites only
+update ChangeLog from "svn log"
 
 ------------------------------------------------------------------------
-r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines
+r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 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/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-0.1.1-1
- * implemented a Bayesian indel caller
+ * samtools-0.1.2-24
+ * in merge, gives a warning rather than error if the target sequence length is different
+ * allow empty header
 
 ------------------------------------------------------------------------
-r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines
+r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 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.c
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
 
-Let users generate ex1.fa.fai.
+ * samtools-0.1.2-23
+ * recognize '*' at the QUAL field
 
 ------------------------------------------------------------------------
-r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines
+r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/misc/bowtie2sam.pl
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/kseq.h
 
-make the bowtie converter works for "-k 2"
+ * samtools-0.1.2-22
+ * the field separater is TAB only, now
 
 ------------------------------------------------------------------------
-r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines
+r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/misc/export2sam.pl
+   M /trunk/samtools/examples/ex1.sam.gz
 
-fixed a bug for "QC" reads
+ * fixed the problem in the example alignment due to the bug in fixmate
 
 ------------------------------------------------------------------------
-r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines
+r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
 Changed paths:
-   A /branches/dev/samtools/misc/bowtie2sam.pl
-   M /branches/dev/samtools/misc/soap2sam.pl
+   M /trunk/samtools/bam_mate.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/misc/soap2sam.pl
 
- * soap2sam.pl: added NM tag
- * bowtie2sam.pl: converter for bowtie
+ * samtools-0.1.2-21
+ * fixed a nasty bug in `fixmate'
 
 ------------------------------------------------------------------------
-r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines
+r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
 Changed paths:
-   A /branches/dev/samtools/misc/soap2sam.pl
+   M /trunk/samtools/misc/bowtie2sam.pl
+   M /trunk/samtools/misc/soap2sam.pl
+   M /trunk/samtools/misc/wgsim_eval.pl
 
-soap2sam.pl: convert soap output to SAM
+make the script robust to the bugs in SOAP-2.1.7
 
 ------------------------------------------------------------------------
-r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines
+r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/misc/wgsim_eval.pl
+   M /trunk/samtools/bam_stat.c
+   M /trunk/samtools/bamtk.c
 
- * wgsim_eval.pl-0.1.1
- * fixed a bug for a contig name like "NT_012345"
+ * samtools-0.1.2-20
+ * check if file is truncated in flagstat
 
 ------------------------------------------------------------------------
-r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines
+r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
 Changed paths:
-   A /branches/dev/samtools/misc/wgsim_eval.pl
+   M /trunk/samtools/bamtk.c
 
- * evaluate alignment for reads generated by wgsim
+ * samtools-0.1.2-19
+ * print the header if requested
 
 ------------------------------------------------------------------------
-r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines
+r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
 Changed paths:
-   M /branches/dev/samtools/misc/Makefile
-   M /branches/dev/samtools/misc/wgsim.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
 
-fixed compiling warnings for wgsim
+ * samtools-0.1.2-18
+ * fixed a minor bug reported by Nils Homer
 
 ------------------------------------------------------------------------
-r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines
+r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/bam_tview.c
+   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
 
-remove an unused variable (a compiler warning only)
+rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
 
 ------------------------------------------------------------------------
-r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines
+r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
 Changed paths:
-   M /branches/dev/samtools/misc/Makefile
-   A /branches/dev/samtools/misc/wgsim.c
+   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
 
-wgsim: Paired-end reads simulator
+ * soap2sam.pl-0.1.2
+ * more robust to truncated soap output
 
 ------------------------------------------------------------------------
-r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines
+r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
 Changed paths:
-   M /branches/dev/samtools/bam_maqcns.c
-   M /branches/dev/samtools/bam_tview.c
+   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)
 
-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
+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
@@ -323,7 +4283,7 @@ Changed paths:
 Release samtools-0.1.1
 
 ------------------------------------------------------------------------
-r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
+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
@@ -344,7 +4304,7 @@ Changed paths:
  * prepare to release 0.1.1
 
 ------------------------------------------------------------------------
-r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
+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
@@ -355,14 +4315,14 @@ Changed paths:
 example
 
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-r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
+r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
 Changed paths:
    M /branches/dev/samtools/ChangeLog
 
 update ChangeLog
 
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-r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
+r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
 Changed paths:
    M /branches/dev/samtools/misc/export2sam.pl
 
@@ -370,14 +4330,14 @@ Changed paths:
  * fixed several bugs 
 
 ------------------------------------------------------------------------
-r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
+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
 
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-r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
+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
@@ -392,14 +4352,14 @@ Changed paths:
  * tview: fixed a minor bug
 
 ------------------------------------------------------------------------
-r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
+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
 
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-r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
+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
@@ -412,7 +4372,7 @@ Changed paths:
 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
+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
@@ -424,7 +4384,7 @@ Changed paths:
  * improved efficiency of the indel caller for spliced alignments
 
 ------------------------------------------------------------------------
-r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
+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
@@ -436,7 +4396,7 @@ Changed paths:
  * 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
+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
@@ -446,7 +4406,7 @@ Changed paths:
  * fixed a memory leak
 
 ------------------------------------------------------------------------
-r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
+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
@@ -455,7 +4415,7 @@ Changed paths:
 update documentation, ChangeLog and a comment
 
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-r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
+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
@@ -473,7 +4433,7 @@ Changed paths:
  * updated documentation
 
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-r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
+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
@@ -482,7 +4442,7 @@ Changed paths:
  * 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
+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
@@ -494,7 +4454,7 @@ Changed paths:
    I am not quite sure why the previous version may have problem.
 
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-r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
+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
@@ -506,21 +4466,21 @@ Changed paths:
    bindings.
 
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-r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
+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.
 
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-r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
+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
 
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-r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
+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
@@ -530,7 +4490,7 @@ Changed paths:
  * made the parser a bit more robust
 
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-r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
+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
@@ -542,14 +4502,14 @@ Changed paths:
  * in bam_index.c, check potential bugs in the underlying I/O library
 
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-r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
+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
 
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-r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
+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
@@ -561,7 +4521,7 @@ Changed paths:
  * made pileup take the reference sequence
 
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-r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
+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
@@ -572,35 +4532,35 @@ Changed paths:
  * in parser, correctl parse "=" at the MRNM field.
 
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-r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
+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
 
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-r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
+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
 
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-r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
+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
 
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-r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
+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
 
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-r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
+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
@@ -609,14 +4569,14 @@ Changed paths:
  * fixed a bug in import: bin is wrongly calculated
 
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-r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
+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
 
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-r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
+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
@@ -629,7 +4589,7 @@ Changed paths:
  * added md5sum utilities
 
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-r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
+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
@@ -643,7 +4603,7 @@ Changed paths:
  * also compile stand-alone faidx
 
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-r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
+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
@@ -653,7 +4613,7 @@ Changed paths:
  * sorting by read names is available
 
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-r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
+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
@@ -669,7 +4629,7 @@ Changed paths:
  * format change to meet the latest specification
 
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-r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
+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
@@ -678,7 +4638,7 @@ Changed paths:
  * change maq2sam to meet the latest specification
 
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-r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
+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
@@ -686,7 +4646,7 @@ Changed paths:
 considerable code clean up in razf
 
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-r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
+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
@@ -695,7 +4655,7 @@ Changed paths:
 make RAZF optional in faidx.c
 
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-r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
+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
@@ -707,7 +4667,7 @@ Changed paths:
  * added routines for retrieving aux data, NOT TESTED YET!
 
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-r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
+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
@@ -722,7 +4682,7 @@ Changed paths:
  * supporting hex strings
 
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-r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
+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
@@ -731,7 +4691,7 @@ Changed paths:
  * fixed the bug in maqcns
 
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-r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
+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
@@ -745,7 +4705,7 @@ Changed paths:
  * add MAQ consensus caller, currently BUGGY!
 
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-r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
+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
@@ -756,14 +4716,14 @@ Changed paths:
  * better coordinates and reference sequence
 
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-r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
+r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
 Changed paths:
    A /branches/dev/samtools/ChangeLog
 
 new ChangeLog
 
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-r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
+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)
@@ -772,7 +4732,7 @@ Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
 the log of my personal SVN repository.
 
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-r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
+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
@@ -785,7 +4745,7 @@ Changed paths:
  * use BGZF by default, now
 
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-r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
+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
@@ -796,14 +4756,14 @@ Changed paths:
  * give more warnings when the file is truncated (or due to bugs in I/O library)
 
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-r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
+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
 
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-r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
+r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
 Changed paths:
    M /branches/dev/samtools/bamtk.c
 
@@ -812,14 +4772,14 @@ Changed paths:
    also update the version number anyway to avoid confusion
 
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-r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
+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
 
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-r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
+r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
 Changed paths:
    M /branches/dev/samtools/razf.c
 
@@ -827,21 +4787,21 @@ fixed a potential bug in razf. However, it seems still buggy, just
 rarely happens, very rarely.
 
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-r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
+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
 
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-r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
+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
 
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-r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
+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
@@ -851,14 +4811,14 @@ Changed paths:
  * Jue has updated razf to realize Bob's scheme
 
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-r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
+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
 
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-r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
+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
@@ -894,7 +4854,7 @@ 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.
 
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-r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
+r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
 Changed paths:
    A /branches/dev/samtools