+++ /dev/null
-------------------------------------------------------------------------
-r925 | lh3lh3 | 2011-02-28 15:45:17 -0500 (Mon, 28 Feb 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/phase.c
-
-minor changes to a heuristic rule
-
-------------------------------------------------------------------------
-r924 | lh3lh3 | 2011-02-28 15:24:04 -0500 (Mon, 28 Feb 2011) | 4 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bcftools/vcfutils.pl
- M /trunk/samtools/phase.c
-
- * 0.1.12-r924:126
- * fixed a bug in phase (due to recent changes)
- * fixed a bug in vcf2fq
-
-------------------------------------------------------------------------
-r923 | lh3lh3 | 2011-02-28 12:57:39 -0500 (Mon, 28 Feb 2011) | 5 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/phase.c
-
- * put version number in bam.h
- * write version to BCF
- * in phase, change the default -q to 37
- * output a little more information during phasing
-
-------------------------------------------------------------------------
-r922 | lh3lh3 | 2011-02-25 16:40:09 -0500 (Fri, 25 Feb 2011) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.tex
- M /trunk/samtools/bcftools/bcf2qcall.c
- M /trunk/samtools/bcftools/bcfutils.c
- M /trunk/samtools/bcftools/ld.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/vcf.c
- M /trunk/samtools/cut_target.c
-
- * change the order of PL/GL according to the latest VCF spec
- * change the type of SP to int32_t
-
-------------------------------------------------------------------------
-r921 | lh3lh3 | 2011-02-25 14:40:56 -0500 (Fri, 25 Feb 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.tex
-
-update the BCF spec
-
-------------------------------------------------------------------------
-r920 | lh3lh3 | 2011-02-25 00:59:27 -0500 (Fri, 25 Feb 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
- A /trunk/samtools/cut_target.c
- M /trunk/samtools/errmod.h
- M /trunk/samtools/faidx.c
- M /trunk/samtools/khash.h
- M /trunk/samtools/kstring.c
- M /trunk/samtools/kstring.h
- A /trunk/samtools/phase.c
- M /trunk/samtools/samtools.1
-
-added the phase command
-
-------------------------------------------------------------------------
-r918 | lh3lh3 | 2011-02-24 10:05:54 -0500 (Thu, 24 Feb 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/prob1.h
-
-added "const" to bcf_p1_cal()
-
-------------------------------------------------------------------------
-r917 | lh3lh3 | 2011-02-24 09:36:30 -0500 (Thu, 24 Feb 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/bam.c
-
-more meaningful BAM truncation message
-
-------------------------------------------------------------------------
-r916 | lh3lh3 | 2011-02-24 09:35:06 -0500 (Thu, 24 Feb 2011) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/vcf.c
-
- * automatically fix errors in GL
- * output unrecognized FORMAT as "."
-
-------------------------------------------------------------------------
-r913 | lh3lh3 | 2011-02-10 22:59:47 -0500 (Thu, 10 Feb 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/vcf.c
-
-finished VCF->BCF conversion
-
-------------------------------------------------------------------------
-r910 | petulda | 2011-02-03 03:13:48 -0500 (Thu, 03 Feb 2011) | 1 line
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
-Prevent division by zero
-------------------------------------------------------------------------
-r909 | lh3lh3 | 2011-02-02 11:29:20 -0500 (Wed, 02 Feb 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
-
-fixed a typo in the VCF header
-
-------------------------------------------------------------------------
-r908 | lh3lh3 | 2011-02-02 11:28:24 -0500 (Wed, 02 Feb 2011) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam_index.c
-
- * fixed an out-of-boundary bug
- * improved sorting order checking in index
-
-------------------------------------------------------------------------
-r907 | lh3lh3 | 2011-01-29 22:59:20 -0500 (Sat, 29 Jan 2011) | 4 lines
-Changed paths:
- M /trunk/samtools/INSTALL
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/knetfile.c
-
- * avoid a segfault when network connect fails
- * update INSTALL
- * fixed a bug in tview on big-endian by Nathan Weeks
-
-------------------------------------------------------------------------
-r903 | lh3lh3 | 2011-01-27 14:50:02 -0500 (Thu, 27 Jan 2011) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_md.c
-
- * fixed a rare memory issue in bam_md.c
- * fixed a bug in indel calling related to unmapped and refskip reads
-
-------------------------------------------------------------------------
-r902 | lh3lh3 | 2011-01-23 21:46:18 -0500 (Sun, 23 Jan 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/fet.c
-
-fixed two minor bugs in Fisher's exact test
-
-------------------------------------------------------------------------
-r899 | petulda | 2011-01-19 09:28:02 -0500 (Wed, 19 Jan 2011) | 1 line
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
-Skip sites with unknown ref
-------------------------------------------------------------------------
-r898 | lh3lh3 | 2011-01-15 12:56:05 -0500 (Sat, 15 Jan 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_md.c
-
-move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
-
-------------------------------------------------------------------------
-r896 | lh3lh3 | 2011-01-06 10:52:15 -0500 (Thu, 06 Jan 2011) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/bcfutils.c
- M /trunk/samtools/bcftools/call1.c
-
- * samtools-0.1.12-10 (r896)
- * allow to exclude read groups in mpileup
-
-------------------------------------------------------------------------
-r895 | lh3lh3 | 2011-01-04 11:31:29 -0500 (Tue, 04 Jan 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.tex
-
-sorry. It is SP not ST
-
-------------------------------------------------------------------------
-r894 | lh3lh3 | 2011-01-04 11:29:06 -0500 (Tue, 04 Jan 2011) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.tex
-
-added ST
-
-------------------------------------------------------------------------
-r893 | petulda | 2011-01-04 06:55:56 -0500 (Tue, 04 Jan 2011) | 1 line
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
-
-Fixed a typo in read_samples
-------------------------------------------------------------------------
-r892 | jmarshall | 2010-12-28 08:06:49 -0500 (Tue, 28 Dec 2010) | 9 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bcftools/Makefile
- M /trunk/samtools/examples/Makefile
-
-System libraries go *after* user libraries in link commands, because
-the user libraries may themselves have dependencies that are satisfied
-by the system libraries. It's not rocket science!
-
-This makes a difference with some linkers; or with -static or --as-needed.
-
-The examples/Makefile fix is from Charles Plessy.
-See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004
-
-------------------------------------------------------------------------
-r891 | lh3lh3 | 2010-12-21 12:16:33 -0500 (Tue, 21 Dec 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/bcfutils.c
- M /trunk/samtools/bcftools/call1.c
-
- * samtools-0.1.12-9 (r891)
- * allow to call SNPs from a subset of samples
-
-------------------------------------------------------------------------
-r889 | lh3lh3 | 2010-12-15 11:28:16 -0500 (Wed, 15 Dec 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.12-12 (r889)
- * set mapQ as 20 if it equals 255
-
-------------------------------------------------------------------------
-r888 | lh3lh3 | 2010-12-14 22:41:09 -0500 (Tue, 14 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
-When -B is applied to mpileup, still use paired reads only unless -A is flagged.
-
-------------------------------------------------------------------------
-r887 | lh3lh3 | 2010-12-14 22:37:05 -0500 (Tue, 14 Dec 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.12-6 (r887)
- * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.
-
-------------------------------------------------------------------------
-r886 | lh3lh3 | 2010-12-14 12:51:03 -0500 (Tue, 14 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
-
-(Arguably) improved the indel caller a tiny bit for lowCov data.
-
-------------------------------------------------------------------------
-r885 | petulda | 2010-12-14 04:55:46 -0500 (Tue, 14 Dec 2010) | 1 line
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
-
-Fixed the VCF header to pass validation
-------------------------------------------------------------------------
-r884 | lh3lh3 | 2010-12-12 23:02:19 -0500 (Sun, 12 Dec 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
- * samtools-0.1.12-4 (r884)
- * fixed a long-existing flaw in the INDEL calling model
-
-------------------------------------------------------------------------
-r883 | lh3lh3 | 2010-12-11 20:05:42 -0500 (Sat, 11 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcfutils.c
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
-compute max SP and max GQ from sample genotypes
-
-------------------------------------------------------------------------
-r880 | lh3lh3 | 2010-12-10 10:50:54 -0500 (Fri, 10 Dec 2010) | 2 lines
-Changed paths:
- D /trunk/samtools/bcftools/bcf-fix.pl
-
-drop bcf-fix.pl as it is redundant by the latest changes
-
-------------------------------------------------------------------------
-r879 | lh3lh3 | 2010-12-10 10:50:29 -0500 (Fri, 10 Dec 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/vcf.c
-
- * fixed a minor issue in printing VCFs
- * write bcftools specific INFO and FORMAT in the header
-
-------------------------------------------------------------------------
-r878 | lh3lh3 | 2010-12-10 10:09:14 -0500 (Fri, 10 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/bcfutils.c
- M /trunk/samtools/bcftools/call1.c
-
-Make sure that the GT genotype field is the first
-
-------------------------------------------------------------------------
-r877 | lh3lh3 | 2010-12-08 17:27:05 -0500 (Wed, 08 Dec 2010) | 7 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.12-2 (r877)
-
- * allow to fine control the selection of indel candidates. The current
- setting is okay for lowCov and highCov with ~100 samples, but it
- skips too many indels for highCov with >250 samples.
-
-
-------------------------------------------------------------------------
-r874 | lh3lh3 | 2010-12-07 22:40:35 -0500 (Tue, 07 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
-
-a spelling error..
-
-------------------------------------------------------------------------
-r873 | lh3lh3 | 2010-12-07 22:39:57 -0500 (Tue, 07 Dec 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.12-1 (r873)
- * added a switch to allow anomalous read pairs in calling
-
-------------------------------------------------------------------------
-r872 | lh3lh3 | 2010-12-07 14:43:54 -0500 (Tue, 07 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
-fixed a bug in vcf2fq
-
-------------------------------------------------------------------------
-r869 | lh3lh3 | 2010-12-05 01:18:06 -0500 (Sun, 05 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
-
-added a warning for the Windows version
-
-------------------------------------------------------------------------
-r868 | lh3lh3 | 2010-12-05 01:05:51 -0500 (Sun, 05 Dec 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
-
-In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
-According to the manual page, this change is valid. However, MinGW seems
-to interpret "%lf" as "%Lf".
-
-------------------------------------------------------------------------
-r867 | lh3lh3 | 2010-12-05 00:35:43 -0500 (Sun, 05 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile.mingw
- M /trunk/samtools/bam_aux.c
-
-bring back the windows support
-
-------------------------------------------------------------------------
-r866 | lh3lh3 | 2010-12-04 23:33:51 -0500 (Sat, 04 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_reheader.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
-Fixed a compiling error when knetfile is not used.
-
-------------------------------------------------------------------------
-r865 | lh3lh3 | 2010-12-04 00:13:22 -0500 (Sat, 04 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
-vcf->fastq
-
-------------------------------------------------------------------------
-r864 | lh3lh3 | 2010-12-03 17:12:30 -0500 (Fri, 03 Dec 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/prob1.h
-
- * remove "-f". Instead always compute consensus quality
- * increase the upper limit of quality
-
-------------------------------------------------------------------------
-r863 | lh3lh3 | 2010-12-03 15:28:15 -0500 (Fri, 03 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
-
-more informative error message
-
-------------------------------------------------------------------------
-r862 | lh3lh3 | 2010-12-02 16:16:08 -0500 (Thu, 02 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/NEWS
- M /trunk/samtools/bamtk.c
-
-Release samtools-0.1.12a
-
-------------------------------------------------------------------------
-r861 | lh3lh3 | 2010-12-02 15:55:06 -0500 (Thu, 02 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
-
-a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
-
-------------------------------------------------------------------------
-r859 | lh3lh3 | 2010-12-02 11:39:57 -0500 (Thu, 02 Dec 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/NEWS
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
-
-Release samtools-0.1.12
-
-------------------------------------------------------------------------
-r858 | lh3lh3 | 2010-12-02 11:24:41 -0500 (Thu, 02 Dec 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/bcf.c
-
- * samtools-0.1.11-1 (r858)
- * fixed a bug in mpileup which causes segfaults
- * bcftools: do not segfault when BCF contains errors
-
-------------------------------------------------------------------------
-r857 | lh3lh3 | 2010-11-30 23:52:50 -0500 (Tue, 30 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
-
-fixed a memory leak in bam_fetch()
-
-------------------------------------------------------------------------
-r856 | lh3lh3 | 2010-11-26 00:07:31 -0500 (Fri, 26 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
- * fixed a memory violation
- * added splitchr to vcfutils.pl
-
-------------------------------------------------------------------------
-r854 | lh3lh3 | 2010-11-23 09:05:08 -0500 (Tue, 23 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/ld.c
-
-fixed a typo/bug in r^2 computation
-
-------------------------------------------------------------------------
-r852 | lh3lh3 | 2010-11-21 22:20:20 -0500 (Sun, 21 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
-
-forget to change the version information
-
-------------------------------------------------------------------------
-r851 | lh3lh3 | 2010-11-21 22:16:52 -0500 (Sun, 21 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
- M /trunk/samtools/bcftools/bcftools.1
- M /trunk/samtools/samtools.1
-
-Release samtools-0.1.11
-
-------------------------------------------------------------------------
-r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/prob1.h
-
- * samtools-0.1.10-9 (r844)
- * added the "folded" or reference-free mode for variant calling
-
-------------------------------------------------------------------------
-r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/NEWS
- M /trunk/samtools/bam_sort.c
-
-In merging, if -R is specified, do not abort if the sequence dictionary is different.
-
-------------------------------------------------------------------------
-r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
-Changed paths:
- M /trunk/samtools/bam_sort.c
-
-When merging BAM headers, compare the list of target reference sequences
-strictly (and fail/abort if there is a mismatch), but allow one list to be a
-prefix of the other. (i.e., check that the lists are identical up until the
-shorter runs out, and add the excess targets from the longer to the output.)
-
-------------------------------------------------------------------------
-r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.10 (r841)
- * fixed a bug in pileup when the first CIGAR operation is D
- * fixed a bug in view with range query
-
-------------------------------------------------------------------------
-r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.10-4 (r840)
-
- * drop the MNP caller. It is slow while does not diliver too much
- benefit. Possibly I will work on it in future given more time.
-
- * there is a segfault in pileup
-
- * someone has reported segfault from view/index/sort
-
-
-------------------------------------------------------------------------
-r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.10-6 (r839)
-
- * call MNPs without realignment because it seems to me that it is not
- worthwhile to significantly slow down SNP calling.
-
- * the result looks quite different from the previous version. I have
- work to do...
-
-
-------------------------------------------------------------------------
-r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/knetfile.c
-
-Apply a patch by Rob Davis, which improves fault detection.
-
-------------------------------------------------------------------------
-r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
-
- * samtools-r836
- * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
-
-------------------------------------------------------------------------
-r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
- * modify the filtering rule: also filter SNPs around filtered indels
- * added MNP filter
-
-------------------------------------------------------------------------
-r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.10-4 (r834)
- * fixed a silly bug in printing MNP
- * restrict to at most 1 alternative allele
-
-------------------------------------------------------------------------
-r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bamtk.c
-
-fixed a bug in printing MNPs
-
-------------------------------------------------------------------------
-r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
-
-minor change to how seqQ is applied
-
-------------------------------------------------------------------------
-r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.10 (r831)
- * initial MNP caller
-
-------------------------------------------------------------------------
-r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
- M /trunk/samtools/bamtk.c
-
-Release samtools-0.1.10 (r829)
-
-------------------------------------------------------------------------
-r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
-
-update version information: samtools-0.1.9-20 (r828)
-
-------------------------------------------------------------------------
-r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
-
-bcftools: allow to skip indels
-
-------------------------------------------------------------------------
-r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
-
-remove ZQ if both BQ and ZQ are present
-
-------------------------------------------------------------------------
-r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
-
- * samtools-0.1.9-18 (r825)
- * change the behaviour of calmd such that by default it does not change the base quality
-
-------------------------------------------------------------------------
-r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/samtools.1
-
- * samtools-0.1.9-17 (r824)
- * added command line options to change the default parameters in indel calling
- * update the manual
-
-------------------------------------------------------------------------
-r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-r823
- * the BQ tag is now 64 shifted, not 33 shifted
-
-------------------------------------------------------------------------
-r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/vcfutils.pl
- M /trunk/samtools/misc/samtools.pl
-
- * samtools-0.1.9-16 (r822)
- * keep the raw depth because in indel calling, DP4 may be way off the true depth
-
-------------------------------------------------------------------------
-r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-15 (r821)
- * calmd: write BQ
- * skip realignment if BQ is present
-
-------------------------------------------------------------------------
-r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-14 (r820)
- * penalize reads with excessive differences in indel calling
-
-------------------------------------------------------------------------
-r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-13 (r819)
- * fixed a bug in pileup given refskip
-
-------------------------------------------------------------------------
-r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
-
- * samtools-r818
- * for indel calling, do two rounds of probabilistic realignments
-
-------------------------------------------------------------------------
-r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
- * samtools-0.1.19-11 (r817)
- * only initiate indel calling when 0.2% of reads contain a gap
-
-------------------------------------------------------------------------
-r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-10 (r816)
-
- * I know why the forward method fails. it is because of zero base
- qualities. when that is fixed, the forward method seems to give
- better results than Viterbi, as it should be. I am tired...
-
-
-------------------------------------------------------------------------
-r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam2bcf_indel.c
-
-effectively revert to the viterbi version. The forward realignment gives too many false positives.
-
-------------------------------------------------------------------------
-r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-9 (r810)
- * use forward, instead of viterbi, for realignment
- * realignment is now quality aware
-
-------------------------------------------------------------------------
-r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/kprobaln.c
- M /trunk/samtools/kprobaln.h
-
- * prepare to replace kaln with kprobaln in realignment
-
-------------------------------------------------------------------------
-r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
-
-fixed a typo
-
-------------------------------------------------------------------------
-r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.h
-
-use zlib for direct reading when BCF_LITE is in use
-
-------------------------------------------------------------------------
-r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
-
- * do not use reads containing too many mismatches for indel calling
- * fixed a trivial bug in case of multi-allelic indels
-
-------------------------------------------------------------------------
-r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-8 (r809)
- * fixed a bug in the indel caller
-
-------------------------------------------------------------------------
-r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
-
-minor change to makefile
-
-------------------------------------------------------------------------
-r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
- * samtools-0.1.9-8 (r807)
- * collect indel candidates only from specified platforms (@RG-PL)
- * merge varFilter and filter4vcf in vcfutils.pl
-
-------------------------------------------------------------------------
-r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/prob1.h
-
-bcftools: compute equal-tail (Bayesian) credible interval
-
-------------------------------------------------------------------------
-r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
-added a double-hit filter to avoid overestimated indel likelihood
-
-------------------------------------------------------------------------
-r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-7 (r804)
- * fixed a bug in the gap caller
-
-------------------------------------------------------------------------
-r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/prob1.c
-
- * samtools-0.1.9-6 (r803)
- * mpileup: apply homopolymer correction when calculating GL, instead of before
- * bcftools: apply a different prior to indels
-
-------------------------------------------------------------------------
-r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-5 (r802)
- * relax tandem penalty. this will be made a command-line option in future.
-
-------------------------------------------------------------------------
-r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-4 (r801)
- * fixed a minor issue in printing indel VCF
-
-------------------------------------------------------------------------
-r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
-fixed another silly bug in mpileup's indel caller
-
-------------------------------------------------------------------------
-r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
-
-fixed a silly bug in the indel caller
-
-------------------------------------------------------------------------
-r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/sam_view.c
- M /trunk/samtools/samtools.1
-
-Incorporate patches by Marcel Martin for read counting.
-
-------------------------------------------------------------------------
-r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-2 (r797)
- * mpileup: indel calling seems to be working
-
-------------------------------------------------------------------------
-r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/kaln.c
-
-indel calling is apparently working, but more information needs to be collected
-
-------------------------------------------------------------------------
-r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf_indel.c
-
-fixed a few bugs in the indel caller. Probably there are more.
-
-------------------------------------------------------------------------
-r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- A /trunk/samtools/bam2bcf_indel.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/kaln.c
- M /trunk/samtools/kaln.h
-
-prepare for the indel caller. It is not ready yet.
-
-------------------------------------------------------------------------
-r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam_plcmd.c
-
-Revert to r790. The recent changes are not good...
-
-------------------------------------------------------------------------
-r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam_plcmd.c
-
- * this revision is UNSTABLE
-
- * indel caller seems working, but it is very insensitive and has
- several things I do not quite understand.
-
-
-------------------------------------------------------------------------
-r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam_plcmd.c
-
-for backup. no effective changes
-
-------------------------------------------------------------------------
-r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
- M /trunk/samtools/kprobaln.c
-
-fixed a minor problem in the example coming with kprobaln.c
-
-------------------------------------------------------------------------
-r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/kaln.c
- M /trunk/samtools/kaln.h
- A /trunk/samtools/kprobaln.c
- A /trunk/samtools/kprobaln.h
-
-Separate kaln and kprobaln as I am preparing further changes. At
-present, the results should be identical to the previous.
-
-
-------------------------------------------------------------------------
-r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
-
-Added -b option: read file names from a file
-------------------------------------------------------------------------
-r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.9-2 (r787)
-
- * Allow to set a maximum per-sample depth to reduce memory. However,
- BAQ computation is still applied to every read. The speed is not
- improved.
-
-
-------------------------------------------------------------------------
-r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/vcf.c
-
- * samtools-0.1.9-1 (r786)
- * samtools: optionally perform exact test for each sample
-
-------------------------------------------------------------------------
-r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bcftools/bcf.c
-
-Optionally output "DP", the individual read depth
-
-------------------------------------------------------------------------
-r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/samtools.1
-
-acknowledge Petr and John who have greatly contributed to the project.
-
-------------------------------------------------------------------------
-r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
-
-Release samtools-0.1.9 (r783)
-
-------------------------------------------------------------------------
-r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
-
-fixed a silly bug in pileup
-
-------------------------------------------------------------------------
-r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
-
- * samtools-0.1.8-22 (r781)
- * made BAQ the default behavior of mpileup
- * updated manual
- * in merge, force to exit given inconsistent header when "-R" is not in use.
-
-------------------------------------------------------------------------
-r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-21 (r780)
- * minor speedup to pileup
-
-------------------------------------------------------------------------
-r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/examples/toy.sam
-
-improve pileup a little bit
-
-------------------------------------------------------------------------
-r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-20 (r778)
- * speed up pileup, although I do not know how much is the improvement
-
-------------------------------------------------------------------------
-r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_maqcns.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/examples/Makefile
-
- * samtools-0.1.8-19 (r777)
- * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
-
-------------------------------------------------------------------------
-r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
-
-remove local realignment (probabilistic realignment is still there)
-
-------------------------------------------------------------------------
-r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/sam_view.c
-
-Add the relevant filename or region to error messages, and cause a failure
-exit status where appropriate. Based on a patch provided by Marcel Martin.
-
-------------------------------------------------------------------------
-r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/examples/toy.sam
- M /trunk/samtools/kaln.c
-
- * Minor code changes. No real effect.
- * change quality to 30 in toy.sam
-
-------------------------------------------------------------------------
-r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/examples/toy.fa
- M /trunk/samtools/examples/toy.sam
-
-added another toy example
-
-------------------------------------------------------------------------
-r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/ld.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
-improve the LD statistics
-
-------------------------------------------------------------------------
-r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
- * a minor fix to the -L option
- * add ldstats to vcfutils.pl
-
-------------------------------------------------------------------------
-r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
-
-a minor change
-
-------------------------------------------------------------------------
-r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- A /trunk/samtools/bcftools/ld.c
-
-forget to add the key file
-
-------------------------------------------------------------------------
-r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
- * vcfutils.pl: fixed a typo in help message
- * added APIs: bcf_append_info() and bcf_cpy()
- * calculate adjacent LD
-
-------------------------------------------------------------------------
-r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
-added filter for samtools/bcftools genetated VCFs
-
-------------------------------------------------------------------------
-r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
- M /trunk/samtools/kaln.c
-
- * removed a comment line in kaln.c
- * vcfutils.pl fillac works when GT is not the first field
-
-------------------------------------------------------------------------
-r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
-Changed paths:
- A /trunk/samtools/bcftools/bcf-fix.pl
-
-Convert VCF output of "bcftools view -bgcv" to a valid VCF file
-------------------------------------------------------------------------
-r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- A /trunk/samtools/bcftools/bcftools.1
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/samtools.1
-
- * samtools-0.1.8-18 (r763)
- * added bcftools manual page
- * minor fix to mpileup and view command lines
-
-------------------------------------------------------------------------
-r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
- * vcfutils.pl qstats: calculate marginal ts/tv
- * allow to call genotypes at variant sites
-
-------------------------------------------------------------------------
-r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/kaln.c
- M /trunk/samtools/misc/HmmGlocal.java
-
-I am changing the gap open probability back to 0.001. It seems that
-being conservative here is a good thing...
-
-------------------------------------------------------------------------
-r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/kaln.c
- A /trunk/samtools/misc/HmmGlocal.java
-
- * samtools-0.1.8-17 (r760)
- * the default gap open penalty is too small (a typo)
- * added comments on hmm_realn
- * Java implementation
-
-------------------------------------------------------------------------
-r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
-
-mark samtools-0.1.8-16 (r759)
-
-------------------------------------------------------------------------
-r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
-round to the nearest integer
-
-------------------------------------------------------------------------
-r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
-I was trying to accelerate ka_prob_glocal() as this will be the
-bottleneck. After an hour, the only gain is to change division to
-multiplication. OK. I will stop.
-
-------------------------------------------------------------------------
-r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
-this is interesting. multiplication is much faster than division, at least on my Mac
-
-------------------------------------------------------------------------
-r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
-minor changes
-
-------------------------------------------------------------------------
-r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/kaln.c
-
-prob_realn() seems working!
-
-------------------------------------------------------------------------
-r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
-minor
-
-------------------------------------------------------------------------
-r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/kaln.c
- M /trunk/samtools/kaln.h
-
-Convert phredQ to probabilities
-
-------------------------------------------------------------------------
-r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/kaln.c
- M /trunk/samtools/kaln.h
-
-Implement the glocal HMM; discard the extention HMM
-
-------------------------------------------------------------------------
-r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
-improve numerical stability
-
-------------------------------------------------------------------------
-r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
-more comments
-
-------------------------------------------------------------------------
-r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
-fixed a bug in banded DP
-
-------------------------------------------------------------------------
-r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
- * fixed that weird issue.
- * the banded version is NOT working
-
-------------------------------------------------------------------------
-r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
-More comments. This version seems working, but something is a little weird...
-
-------------------------------------------------------------------------
-r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
-Changed paths:
- M /trunk/samtools/kaln.c
-
-A little code cleanup. Now the forward and backback algorithms give
-nearly identical P(x), which means both are close to the correct
-forms. However, I have only tested on toy examples. Minor errors in
-the implementation may not be obvious.
-
-
-------------------------------------------------------------------------
-r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/kaln.c
- M /trunk/samtools/kaln.h
-
-...
-
-------------------------------------------------------------------------
-r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
-Changed paths:
- M /trunk/samtools/bam_sort.c
-
-Abort if merge -h's INH.SAM cannot be opened, just as we abort
-if any of the IN#.BAM input files cannot be opened.
-
-Also propagate any error indication returned by bam_merge_core()
-to samtools merge's exit status.
-
-------------------------------------------------------------------------
-r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
-
-Use bam_validate1() to detect garbage records in the event of a corrupt
-BAI index file that causes a bam_seek() to an invalid position. At most
-one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
-call, so the cost is insignificant in the normal case.
-
-------------------------------------------------------------------------
-r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
-
-Add bam_validate1().
-
-------------------------------------------------------------------------
-r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-15 (r379)
- * allow to change capQ parameter in calmd
-
-------------------------------------------------------------------------
-r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/sam_view.c
-
-When bam_read1() returns an error (return value <= -2), propagate that error
-to bam_iter_read()'s own return value. Similarly, also propagate it up to
-bam_fetch()'s return value. Previously bam_fetch() always returned 0, and
-callers ignored its return value anyway. With this change, 0 continues to
-indicate success, while <= -2 (which can be written as < 0, as -1 is never
-returned) indicates corrupted input.
-
-bam_iter_read() ought also to propagate errors returned by bam_seek().
-
-main_samview() can now print an error message and fail when bam_fetch()
-detects that a .bai index file is corrupted or otherwise does not correspond
-to the .bam file it is being used with.
-
-------------------------------------------------------------------------
-r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
-
-0 is a successful return value from bam_read1(). (In practice, it never
-returns 0 anyway; but all the other callers treat 0 as successful.)
-
-------------------------------------------------------------------------
-r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bam_sort.c
-
- * merge files region-by-region. work on small examples but more tests are needed.
-
-------------------------------------------------------------------------
-r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
-improve qstats by checking the alleles as well
-
-------------------------------------------------------------------------
-r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
-convert UCSC SNP SQL dump to VCF
-
-------------------------------------------------------------------------
-r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
-hapmap2vcf convertor
-
-------------------------------------------------------------------------
-r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/vcf.c
-
- * added comments
- * VCF->BCF is not possible without knowing the sequence dictionary before hand...
-
-------------------------------------------------------------------------
-r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/bcfutils.c
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/vcf.c
-
- * put n_smpl to "bcf1_t" to simplify API a little
-
-------------------------------------------------------------------------
-r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/index.c
-
-fixed a bug in indexing
-
-------------------------------------------------------------------------
-r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_pileup.c
-
- * fixed a bug in capQ
- * valgrind identifies a use of uninitialised value, but I have not fixed it.
-
-------------------------------------------------------------------------
-r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bgzip.c
- M /trunk/samtools/razip.c
-
- * fixed a bug in razip: -c will delete the input file
- * copy tabix/bgzip to here
-
-------------------------------------------------------------------------
-r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-14 (r727)
- * allow to change the capQ parameter at the command line
-
-------------------------------------------------------------------------
-r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bcftools/vcfutils.pl
- M /trunk/samtools/misc/samtools.pl
-
- * added varFilter to vcfutils.pl
- * reimplement realn(). now it performs a local alignment
- * added cap_mapQ() to cap mapping quality when there are many substitutions
-
-------------------------------------------------------------------------
-r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- A /trunk/samtools/bcftools/bcf2qcall.c
- M /trunk/samtools/bcftools/call1.c
-
- * convert BCF to QCALL input
-
-------------------------------------------------------------------------
-r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
-
-dynamic band width in realignment
-
-------------------------------------------------------------------------
-r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_plcmd.c
-
-fixed a bug in realignment
-
-------------------------------------------------------------------------
-r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/prob1.c
-
-fixed a minor issue
-
-------------------------------------------------------------------------
-r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_md.c
-
-fixed a bug in realignment
-
-------------------------------------------------------------------------
-r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
-
-minor changes. It is BUGGY now!
-
-------------------------------------------------------------------------
-r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/kaln.c
- M /trunk/samtools/kaln.h
-
- * aggressive gapped aligner is implemented in calmd.
- * distinguish gap_open and gap_end_open in banded alignment
- * make tview accepts alignment with heading and tailing D
-
-------------------------------------------------------------------------
-r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools
-
-Add svn:ignore properties for generated files that don't appear in "make all".
-
-------------------------------------------------------------------------
-r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
-Changed paths:
- M /trunk/samtools
- M /trunk/samtools/bcftools
- M /trunk/samtools/misc
-
-Add svn:ignore properties listing the generated files.
-(Except for *.o, which we'll assume is in global-ignores.)
-
-------------------------------------------------------------------------
-r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/sample.c
- M /trunk/samtools/sample.h
-
- * samtools-0.1.8-13 (r715)
- * fixed a bug in identifying SM across files
- * bcftools: estimate heterozygosity
- * bcftools: allow to skip sites without reference bases
-
-------------------------------------------------------------------------
-r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/prob1.h
-
-quite a lot changes to the contrast caller, but I still feel something is missing...
-
-------------------------------------------------------------------------
-r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/vcfutils.pl
-
- * changed 3.434 to 4.343 (typo!)
- * fixed a bug in the contrast caller
- * calculate heterozygosity
-
-------------------------------------------------------------------------
-r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/bcfutils.c
- M /trunk/samtools/bcftools/call1.c
-
-SNP calling from the GL field
-
-------------------------------------------------------------------------
-r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcf.c
-
-fixed another problem
-
-------------------------------------------------------------------------
-r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/vcf.c
-
- * fixed bugs in parsing VCF
- * parser now works with GT/GQ/DP/PL/GL
-
-------------------------------------------------------------------------
-r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- M /trunk/samtools/bcftools/prob1.c
-
-Do not compile _BCF_QUAD by default
-
-------------------------------------------------------------------------
-r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/bcfutils.c
- M /trunk/samtools/bcftools/call1.c
-
-Write the correct ALT and PL in the SNP calling mode.
-
-------------------------------------------------------------------------
-r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfutils.pl
-
-more commands for my own uses
-
-------------------------------------------------------------------------
-r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
-Changed paths:
- A /trunk/samtools/bcftools/vcfutils.pl
-
-Utilities for processing VCF
-
-------------------------------------------------------------------------
-r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/prob1.h
-
-preliminary contrast variant caller
-
-------------------------------------------------------------------------
-r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/call1.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/prob1.h
-
-z' and z'' can be calculated
-
-------------------------------------------------------------------------
-r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
- M /trunk/samtools/bcftools/prob1.c
- D /trunk/samtools/bcftools/vcfout.c
-
- * rename vcfout.c as call1.c
- * prepare to add two-sample comparison
-
-------------------------------------------------------------------------
-r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfout.c
-
-fixed a bug in calculating the t statistics
-
-------------------------------------------------------------------------
-r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcftools/kfunc.c
- M /trunk/samtools/bcftools/vcfout.c
-
- * samtools-0.1.8-13 (r698)
- * perform one-tailed t-test for baseQ, mapQ and endDist
-
-------------------------------------------------------------------------
-r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/kfunc.c
-
-added regularized incomplete beta function
-
-------------------------------------------------------------------------
-r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_plcmd.c
-
-change the default correlation coefficient
-
-------------------------------------------------------------------------
-r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/vcfout.c
-
-print QUAL as floating numbers
-
-------------------------------------------------------------------------
-r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/examples/Makefile
- A /trunk/samtools/sample.c
- A /trunk/samtools/sample.h
-
- * samtools-0.1.8-12 (r692)
- * group data by samples in "mpileup -g"
-
-------------------------------------------------------------------------
-r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- D /trunk/samtools/bam_mcns.c
- D /trunk/samtools/bam_mcns.h
- M /trunk/samtools/bam_plcmd.c
-
-remove VCF output in mpileup
-
-------------------------------------------------------------------------
-r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
-
- * use the revised MAQ error model for mpileup
- * prepare to remove the independent model from mpileup
-
-------------------------------------------------------------------------
-r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_maqcns.h
- M /trunk/samtools/bam_plcmd.c
- A /trunk/samtools/errmod.c
- A /trunk/samtools/errmod.h
- M /trunk/samtools/ksort.h
-
-added revised MAQ error model
-
-------------------------------------------------------------------------
-r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/prob1.h
- M /trunk/samtools/bcftools/vcfout.c
-
-allow to read the prior from the error output. EM iteration is working.
-
-------------------------------------------------------------------------
-r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/main.c
- M /trunk/samtools/bcftools/vcf.c
-
- * write a little more VCF header
- * concatenate BCFs
-
-------------------------------------------------------------------------
-r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/bcf.tex
-
-use float for QUAL
-
-------------------------------------------------------------------------
-r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/prob1.c
-
-faster for large sample size (in principle)
-
-------------------------------------------------------------------------
-r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bcftools/prob1.c
-
- * a numerically stable method to calculate z_{jk}
- * currently slower than the old method but will be important for large sample size
- * in principle, we can speed up for large n, but have not tried
-
-------------------------------------------------------------------------
-r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfout.c
-
-fixed an issue in parsing integer
-
-------------------------------------------------------------------------
-r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
-
-do not print refname if file is converted from VCF
-
-------------------------------------------------------------------------
-r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcf.c
-
- * parse PL
- * fixed a bug in parsing VCF
-
-------------------------------------------------------------------------
-r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/bcfutils.c
- M /trunk/samtools/bcftools/main.c
- M /trunk/samtools/bcftools/vcf.c
- M /trunk/samtools/bcftools/vcfout.c
- M /trunk/samtools/bgzf.c
- M /trunk/samtools/kstring.c
-
- * fixed a bug in kstrtok@kstring.c
- * preliminary VCF parser (not parse everything for now)
- * improved view interface
-
-------------------------------------------------------------------------
-r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/vcfout.c
- M /trunk/samtools/kstring.c
- M /trunk/samtools/kstring.h
-
- * improved kstring (added kstrtok)
- * removed the limit on the format string length in bcftools
- * use kstrtok to parse format which fixed a bug in the old code
-
-------------------------------------------------------------------------
-r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
-Changed paths:
- A /trunk/samtools/bcftools/README
- M /trunk/samtools/bcftools/vcfout.c
-
-help messages
-
-------------------------------------------------------------------------
-r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcfout.c
-
-perform single-tail test for ED4
-
-------------------------------------------------------------------------
-r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- M /trunk/samtools/bcftools/kfunc.c
- M /trunk/samtools/bcftools/vcfout.c
-
- * test depth, end distance and HWE
-
-------------------------------------------------------------------------
-r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/kfunc.c
-
-reimplement incomplete gamma functions. no copy-paste
-
-------------------------------------------------------------------------
-r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bcftools/fet.c
- M /trunk/samtools/bcftools/prob1.c
- M /trunk/samtools/bcftools/prob1.h
- M /trunk/samtools/bcftools/vcfout.c
-
- * bcftools: add HWE (no testing for now)
- * record end dist in a 2x2 table, not avg, std any more
-
-------------------------------------------------------------------------
-r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
-Changed paths:
- A /trunk/samtools/bcftools/kfunc.c
-
- * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
- * Not using Numerical Recipe due to licensing issues
-
-------------------------------------------------------------------------
-r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
-Changed paths:
- A /trunk/samtools/bcftools/fet.c
-
-Fisher's exact test
-
-------------------------------------------------------------------------
-r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/examples/Makefile
-
- * samtools-0.1.8-11 (r672)
- * collect more stats for allele balance test in bcftools (not yet)
-
-------------------------------------------------------------------------
-r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/main.c
-
- * the code base is stablized again.
- * I will delay the vcf parser, which is quite complicated but with little value for now
-
-------------------------------------------------------------------------
-r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/examples/Makefile
-
-minor
-
-------------------------------------------------------------------------
-r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcftools/vcf.c
-
-unfinished vcf parser
-
-------------------------------------------------------------------------
-r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bcftools/Makefile
- M /trunk/samtools/bcftools/bcf.c
- M /trunk/samtools/bcftools/bcf.h
- M /trunk/samtools/bcftools/bcfutils.c
- M /trunk/samtools/bcftools/index.c
- M /trunk/samtools/bcftools/main.c
- A /trunk/samtools/bcftools/vcf.c
- M /trunk/samtools/bcftools/vcfout.c
-
- * added prelimiary VCF parser (not finished)
- * change struct a bit
-
-------------------------------------------------------------------------
-r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bcftools/bcf.c
-
- * allow to set min base q
- * fixed a bug in mpileup -u
-
-------------------------------------------------------------------------
-r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
-Changed paths:
- A /trunk/samtools/bcftools/bcf.tex
-
-spec
-
-------------------------------------------------------------------------
-r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/examples/Makefile
-
-added more examples
-
-------------------------------------------------------------------------
-r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bcftools/Makefile
-
-fixed compilation error
-
-------------------------------------------------------------------------
-r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- D /trunk/samtools/bcf.c
- D /trunk/samtools/bcf.h
- A /trunk/samtools/bcftools
- A /trunk/samtools/bcftools/Makefile
- A /trunk/samtools/bcftools/bcf.c
- A /trunk/samtools/bcftools/bcf.h
- A /trunk/samtools/bcftools/bcfutils.c
- A /trunk/samtools/bcftools/index.c
- A /trunk/samtools/bcftools/main.c
- A /trunk/samtools/bcftools/prob1.c
- A /trunk/samtools/bcftools/prob1.h
- A /trunk/samtools/bcftools/vcfout.c
-
-move bcftools to samtools
-
-------------------------------------------------------------------------
-r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
-
-fixed another minor bug
-
-------------------------------------------------------------------------
-r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bcf.c
-
- * samtools-0.1.8-10 (r658)
- * fixed a bug in bam2bcf when the reference is N
-
-------------------------------------------------------------------------
-r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
-
- * fixed a bug
- * treat ambiguous ref base as the fifth base
-
-------------------------------------------------------------------------
-r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/bcftools/bcf.c
- M /trunk/samtools/bcf.c
-
-missing a column in VCF output...
-
-------------------------------------------------------------------------
-r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcf.c
-
-fixed a memory leak
-
-------------------------------------------------------------------------
-r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bcf.c
-
-fixed a bug in bcf reader
-
-------------------------------------------------------------------------
-r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam2bcf.c
-
-fixed a bug
-
-------------------------------------------------------------------------
-r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam2bcf.c
- M /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-9 (r649)
- * lossless representation of PL in BCF output
-
-------------------------------------------------------------------------
-r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- A /trunk/samtools/bam2bcf.c
- A /trunk/samtools/bam2bcf.h
- M /trunk/samtools/bam_plcmd.c
- A /trunk/samtools/bcf.c
- A /trunk/samtools/bcf.h
-
-Generate binary VCF
-
-------------------------------------------------------------------------
-r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-8 (r644)
- * mpileup becomes a little stable again
- * the method is slightly different, but is more theoretically correct
- * snp calling is O(n^2) instead of O(n^3)
-
-------------------------------------------------------------------------
-r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
-
- * fixed a STUPID bug, which cost me a lot of time.
- * I am going to clean up mcns a little bit
-
-------------------------------------------------------------------------
-r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bam_mcns.h
- M /trunk/samtools/bam_plcmd.c
-
-supposedly this is THE correct implementation, but more testing is needed
-
-------------------------------------------------------------------------
-r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
-
-NOT ready yet. Going to make further changes...
-
-------------------------------------------------------------------------
-r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-7 (r639)
- * fixed the reference allele assignment
-
-------------------------------------------------------------------------
-r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bam_mcns.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-6 (r638)
- * skip isnan/isinf in case of float underflow
- * added the flat prior
- * fixed an issue where there are no reads supporting the reference
-
-------------------------------------------------------------------------
-r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
-
-minor changes
-
-------------------------------------------------------------------------
-r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bam_mcns.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
-minor tweaks
-
-------------------------------------------------------------------------
-r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bam_mcns.h
- M /trunk/samtools/bam_plcmd.c
-
-posterior expectation FINALLY working. I am so tired...
-
-------------------------------------------------------------------------
-r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
-
-another minor fix to mpileup
-
-------------------------------------------------------------------------
-r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
-
-added the format column
-
-------------------------------------------------------------------------
-r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bam_mcns.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
-added an alternative prior
-
-------------------------------------------------------------------------
-r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bam_mcns.h
- M /trunk/samtools/bam_plcmd.c
-
-calculate posterior allele frequency
-
-------------------------------------------------------------------------
-r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-3 (r627)
- * multi-sample snp calling appears to work. More tests needed.
-
-------------------------------------------------------------------------
-r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bam_mcns.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bam_tview.c
-
- * preliminary multisample SNP caller.
- * something looks not so right, but it largely works
-
-------------------------------------------------------------------------
-r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_mcns.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.8-2 (r617)
- * allele frequency calculation apparently works...
-
-------------------------------------------------------------------------
-r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile
- A /trunk/samtools/bam_mcns.c
- A /trunk/samtools/bam_mcns.h
- M /trunk/samtools/bam_plcmd.c
-
- * added mutli-sample framework. It is not working, yet.
- * improved the mpileup interface
-
-------------------------------------------------------------------------
-r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/Makefile
-
- * samtools-0.1.8-1 (r615)
- * allow to get mpileup at required sites
-
-------------------------------------------------------------------------
-r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
-
-Release samtools-0.1.8
-
-------------------------------------------------------------------------
-r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/knetfile.c
-
-fixed a compiling issue for Windows
-
-------------------------------------------------------------------------
-r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_sort.c
-
-fixed a bug in sorting when output to stdout (by Peter Chines)
-
-------------------------------------------------------------------------
-r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/NEWS
- M /trunk/samtools/bam_plcmd.c
-
-change the command line option of pileup
-
-------------------------------------------------------------------------
-r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_pileup.c
- A /trunk/samtools/examples/toy.fa
- A /trunk/samtools/examples/toy.sam
-
-make pileup work with CIGAR with I/D at the beginning or in the end
-
-------------------------------------------------------------------------
-r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_maqcns.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bam_tview.c
-
- * make tview more friendly
- * a temporary remedy for an issue in indel calling
-
-------------------------------------------------------------------------
-r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-r607
- * improved the genotype accuracy for indels
- * use the SOAPsnp model for SNP calling by default.
-
-------------------------------------------------------------------------
-r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/Makefile
-
-removed a debugging example
-
-------------------------------------------------------------------------
-r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bamtk.c
-
- * samtools-.1.7-18 (r605)
- * fixed an issue when a deletion and mismatch occur at the same time
- and the base quality is higher than 40 (if -I40).
-
-------------------------------------------------------------------------
-r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/misc/Makefile
-
-fixed a minor bug in idxstats
-
-------------------------------------------------------------------------
-r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
-
-fixed a minor bug in indexing
-
-------------------------------------------------------------------------
-r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam.c
-
-change printf() to puts in exporting
-
-------------------------------------------------------------------------
-r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
-
-minor fix. No actual effect.
-
-------------------------------------------------------------------------
-r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
-
-added Makefile targets to compile shared/dynamic library
-
-------------------------------------------------------------------------
-r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-17 (r596)
- * also keep the number of coor-less reads in the index file
-
-------------------------------------------------------------------------
-r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-16 (r595)
- * write additional information to bam index
-
-------------------------------------------------------------------------
-r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
-
-fixed a bug for unmapped sequences in indexing
-
-------------------------------------------------------------------------
-r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/samtools.1
-
-rename iterf as iter
-
-------------------------------------------------------------------------
-r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-15 (r592)
- * fixed a few minor memory leaks in the new pileup code
- * improved the functionality of mpileup
-
-------------------------------------------------------------------------
-r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-14 (r591)
- * elementary multi-way pileup. More testing and more functionality to be done.
-
-------------------------------------------------------------------------
-r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-13 (r590)
- * added mpileup APIs. No compiling errors, but not tested at all. It is late.
-
-------------------------------------------------------------------------
-r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-12 (r589)
- * added iterator-like APIs for pileup
-
-------------------------------------------------------------------------
-r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-11 (r588)
- * ported a few improvements from tabix back to samtools
-
-------------------------------------------------------------------------
-r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-10 (r587)
- * added iterator interface for bam_fetch (ported back from tabix)
-
-------------------------------------------------------------------------
-r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile
- A /trunk/samtools/bam_reheader.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bgzf.c
-
- * samtools-0.1.7-9 (r586)
- * added "reheader" to replace the BAM header
-
-------------------------------------------------------------------------
-r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/kstring.h
-
- * samtools-0.1.7-8 (r585)
- * speed up "view"
-
-------------------------------------------------------------------------
-r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bgzf.c
- M /trunk/samtools/bgzf.h
- M /trunk/samtools/kstring.h
- M /trunk/samtools/misc/wgsim_eval.pl
-
- * samtools-0.1.7-7 (r584)
- * ported tabix BGZF to samtools
- * flush BGZF after writing the BAM header and between alignment boundaries
-
-------------------------------------------------------------------------
-r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
-Changed paths:
- A /trunk/samtools/misc/varfilter.py
-
-Initial release on behalf of Aylwyn Scally
-------------------------------------------------------------------------
-r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
-Changed paths:
- M /trunk/samtools/samtools.1
-
-Added a note about the indels coordinates
-------------------------------------------------------------------------
-r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
-Changed paths:
- M /trunk/samtools/misc/sam2vcf.pl
-
-Added the possibility to print or not to print the reference allele
-------------------------------------------------------------------------
-r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
-Changed paths:
- M /trunk/samtools/sam_header.c
-
-More descriptive message for space separated tags
-------------------------------------------------------------------------
-r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
-Changed paths:
- M /trunk/samtools/misc/sam2vcf.pl
-
-Speedup with -i, no need to query the reference all the time
-------------------------------------------------------------------------
-r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
-Changed paths:
- M /trunk/samtools/sam_header.c
-
-Fixed the order of sequences in the header
-------------------------------------------------------------------------
-r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
-Changed paths:
- M /trunk/samtools/misc/sam2vcf.pl
-
-Added possibility to select indels only and fixed a bug in reporting homozygous indels.
-------------------------------------------------------------------------
-r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
-Changed paths:
- M /trunk/samtools/bam.c
-
-Improve the invalid 'BAM\1' magic number error message, and also print it
-when no bytes can be read from the alleged BAM file, e.g., in the common
-user error case when a SAM file has accidentally been supplied.
-
-------------------------------------------------------------------------
-r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
-Changed paths:
- M /trunk/samtools/AUTHORS
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/sam_header.c
-
-Improved efficiency of header parsing
-------------------------------------------------------------------------
-r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/export2sam.pl
-
-Updated export2sam.pl by Chris Saunders from Illumina.
-
-
-------------------------------------------------------------------------
-r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
-Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
-------------------------------------------------------------------------
-r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
-Changed paths:
- M /trunk/samtools/misc/sam2vcf.pl
-
-Print an error for pileups in simple format
-------------------------------------------------------------------------
-r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
-
-added a hidden option in pileup to output the base position (for Erin)
-
-------------------------------------------------------------------------
-r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
-Changed paths:
- M /trunk/samtools/misc/sam2vcf.pl
-
-Added possibility to specify a custom column title for the data column
-------------------------------------------------------------------------
-r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
-
-Added the -d option to limit maximum depth for indels.
-------------------------------------------------------------------------
-r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
-Changed paths:
- M /trunk/samtools/misc/sam2vcf.pl
-
-Added VCF header
-------------------------------------------------------------------------
-r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/samtools.pl
- M /trunk/samtools/misc/wgsim.c
-
- * samtools-0.1.7-6
- * fixed a bug in faidx
-
-------------------------------------------------------------------------
-r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
-Changed paths:
- M /trunk/samtools/faidx.c
-
-Put the right filename in the error message.
-
-------------------------------------------------------------------------
-r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-5 (r528)
- * further add new consensus generation strategy
-
-------------------------------------------------------------------------
-r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
-Changed paths:
- M /trunk/samtools/knetfile.c
-
-Fixed a bug in knet_seek
-------------------------------------------------------------------------
-r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
-Changed paths:
- M /trunk/samtools/misc/sam2vcf.pl
-
-Small fix in VCF format: dot for the empty INFO field
-------------------------------------------------------------------------
-r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
-Changed paths:
- M /trunk/samtools/sam_header.c
-
-Allow tabs in the CO header field
-------------------------------------------------------------------------
-r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/Makefile.mingw
-
-Depend on libbam.a rather than the phony target, so that samtools is not
-unnecessarily rebuilt every time. Also clean bgzip.
-
-------------------------------------------------------------------------
-r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/Makefile.mingw
-
-Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
-is defined. Also introduce $(KNETFILE_O) which can be set to empty to
-facilitate non-knet builds.
-
-------------------------------------------------------------------------
-r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.7-4 (r522)
- * fixed a bug in "view -r"
- * added a new option "view -R" to read required read groups from a file
-
-------------------------------------------------------------------------
-r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.7-3 (r521)
- * calmd: optionally mask matching bases as N
-
-------------------------------------------------------------------------
-r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/samtools.pl
-
- * samtools-0.1.7-2 (r520)
- * fixed a few issues with compilation in Windows (on behalf of John)
- * choose a random base as the consensus (for population genetics studies)
-
-------------------------------------------------------------------------
-r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
-Changed paths:
- M /trunk/samtools/Makefile
-
-Put libraries at the end, so they can resolve references from libbam.a
-as well, even with old-fashioned linkers.
-
-Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
-the freshly built library, not some other libbam.a lying around the system.
-
-------------------------------------------------------------------------
-r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/misc/Makefile
-
-Also clean *.exe (for Cygwin users using this makefile).
-
-------------------------------------------------------------------------
-r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
-
-Index files should be opened in binary mode, not text mode.
-
-------------------------------------------------------------------------
-r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
-Changed paths:
- A /trunk/samtools/examples/bam2bed.c
-
-another example program
-
-------------------------------------------------------------------------
-r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/wgsim_eval.pl
- M /trunk/samtools/sam.c
-
- * samtools-0.1.7-1 (r515)
- * report an error when .fai contains duplicated names, instead of segfault
-
-------------------------------------------------------------------------
-r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bam.c
-
-Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
-
-------------------------------------------------------------------------
-r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile.mingw
-
-Update Makefile.mingw for the same reason
-
-------------------------------------------------------------------------
-r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
-
-Fixed a bug in compiling razip
-
-------------------------------------------------------------------------
-r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
-
-Release samtools-0.1.7 (r510)
-
-------------------------------------------------------------------------
-r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-22 (r509)
- * forget to fix a similar problem in glfgen
-
-------------------------------------------------------------------------
-r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.6-21 (r508)
- * fixed a potential bug in the indel caller towards the end of a chromosome
-
-------------------------------------------------------------------------
-r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.6-19 (r494)
- * allow to convert Illumina quality (64 based) to the BAM quality
-
-------------------------------------------------------------------------
-r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam_header.c
-
- * samtools-0.1.6-18 (r493)
- * fixed the bugs due to improperly incorporating Petr's header parser
- * a little code clean up in sam_header.c
-
-------------------------------------------------------------------------
-r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
-Changed paths:
- M /trunk/samtools/sam_header.c
-
-Added sam_header_line_free call for sam_header_parse2
-------------------------------------------------------------------------
-r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/sam_view.c
-
- * BUGGY VERSION
- * fixed a minor bug
-
-------------------------------------------------------------------------
-r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/sam.c
-
- * BUGGY VERSION
- * improved the interface a bit
- * bug unfixed
-
-------------------------------------------------------------------------
-r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/sam_header.c
- M /trunk/samtools/sam_header.h
-
- * BUGGY VERSION. Please NOT use it.
- * Fixed a minor bug, but the major bug is still there.
-
-------------------------------------------------------------------------
-r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_rmdup.c
- M /trunk/samtools/bam_rmdupse.c
- M /trunk/samtools/kaln.c
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam_header.c
- M /trunk/samtools/sam_header.h
- M /trunk/samtools/sam_view.c
-
- * This revision is SERIOUSLY BUGGY. Please NOT use it.
- * Start to incorporate header parsing from Petr Danecek
-
-------------------------------------------------------------------------
-r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
-Changed paths:
- M /trunk/samtools/sam_header.c
- M /trunk/samtools/sam_header.h
-
-Now possible to merge multiple HeaderDict dictionaries
-------------------------------------------------------------------------
-r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
-Changed paths:
- M /trunk/samtools/sam_header.c
-
-
-------------------------------------------------------------------------
-r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
-Changed paths:
- A /trunk/samtools/sam_header.c
- A /trunk/samtools/sam_header.h
-
-
-------------------------------------------------------------------------
-r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_rmdupse.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/examples/Makefile
-
- * samtools-0.1.6-17 (r484)
- * fixed a memory leak in rmdupse
- * fixed a bug in parsing @RG header lines
- * test rmdup in examples/
-
-------------------------------------------------------------------------
-r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_rmdup.c
- M /trunk/samtools/bam_rmdupse.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-16 (r483)
- * unify the interface of rmdup and rmdupse
- * a new bug found in rg2lib(). Have not been fixed yet.
-
-------------------------------------------------------------------------
-r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_rmdup.c
- M /trunk/samtools/bam_rmdupse.c
- M /trunk/samtools/bamtk.c
- A /trunk/samtools/klist.h
-
- * samtools-0.1.6-15 (r482)
- * rewrite rmdupse
- * rmdupse is now library aware
-
-------------------------------------------------------------------------
-r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_rmdup.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-14 (r480)
- * rmdup is now RG aware
-
-------------------------------------------------------------------------
-r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
-added a small unitity to parse SRA XML files
-
-------------------------------------------------------------------------
-r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_maqcns.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-13 (r479)
- * merge: optionally use file names as RG tags
-
-------------------------------------------------------------------------
-r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/kaln.c
-
- * samtools-0.1.6-12 (r478)
- * fixed a bug in the indel caller
-
-------------------------------------------------------------------------
-r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-11 (r477)
- * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
-
-------------------------------------------------------------------------
-r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
-Changed paths:
- A /trunk/samtools/misc/sam2vcf.pl
-
-Added the sam2vcf.pl script.
-------------------------------------------------------------------------
-r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bamtk.c
- A /trunk/samtools/kaln.c
- A /trunk/samtools/kaln.h
-
-Unfinished modification. Please do not use this revision...
-
-------------------------------------------------------------------------
-r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
-Changed paths:
- M /trunk/samtools/knetfile.c
-
-Removed the offending knet_seek message.
-------------------------------------------------------------------------
-r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
-Changed paths:
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/razf.c
-
-Bug fix - faidx on RAZF compressed files now working.
-------------------------------------------------------------------------
-r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/samtools.1
-
-Clarify the meaning of a region like "chr2:1,000,000".
-
-------------------------------------------------------------------------
-r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/novo2sam.pl
-
-Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
-
-------------------------------------------------------------------------
-r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile.mingw
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/knetfile.h
-
- * samtools-0.1.6-9 (r470)
- * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
-
-------------------------------------------------------------------------
-r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-9 (r469)
- * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
-
-------------------------------------------------------------------------
-r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/samtools.pl
-
- * samtools-0.1.6-7 (r468)
- * make merge stable
-
-------------------------------------------------------------------------
-r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
-Changed paths:
- M /trunk/samtools/bgzf.c
- M /trunk/samtools/bgzip.c
- M /trunk/samtools/razf.c
- M /trunk/samtools/razip.c
-
-Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
-------------------------------------------------------------------------
-r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-6 (r466)
- * do not crash calmd when some sequences are absent from the reference.
-
-------------------------------------------------------------------------
-r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/knetfile.c
-
-Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
-no way to seek on a pipe and the messages always appear.
-
-------------------------------------------------------------------------
-r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
-Changed paths:
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/razf.c
-
-A bug fix, "samtools view" is now working again.
-------------------------------------------------------------------------
-r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/faidx.c
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/knetfile.h
- M /trunk/samtools/razf.c
- M /trunk/samtools/razf.h
-
- * samtools-0.1.6-5 (r462)
- * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
-
-------------------------------------------------------------------------
-r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/samtools.1
-
-fixed a formatting issue
-
-------------------------------------------------------------------------
-r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-4 (r459)
- * make sort output the result to stdout when -o is in use
-
-------------------------------------------------------------------------
-r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/faidx.c
- M /trunk/samtools/faidx.h
- M /trunk/samtools/samtools.1
-
- * samtools-0.1.6-2 (r458)
- * added more interface to faidx (by Nils)
- * updated documentation
-
-------------------------------------------------------------------------
-r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.6-2 (r457)
- * get rid of three assert() in bam_sort.c
-
-------------------------------------------------------------------------
-r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/razf.c
-
-Return NULL from _razf_open() (and hence razf_open()/razf_open2())
-when opening the file fails.
-
-------------------------------------------------------------------------
-r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
- D /trunk/samtools/source.dot
-
-Release samtools-0.1.6
-
-------------------------------------------------------------------------
-r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_rmdup.c
- M /trunk/samtools/bam_rmdupse.c
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
-
- * samtools-0.1.5-34 (r451)
- * applied the patch by John
- * improved the help message a little bit
-
-------------------------------------------------------------------------
-r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_color.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-33 (r450)
- * fixed a bug in bam_color.c (on behalf of Nils Homer)
-
-------------------------------------------------------------------------
-r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/samtools.pl
-
- * samtools-0.1.5-32 (r449)
- * fillmd: fixed a bug in modifying MD/NM tags
- * in import, give a warning if the read is aligned but there is no CIGAR.
-
-------------------------------------------------------------------------
-r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/wgsim_eval.pl
-
- * samtools-0.1.5-31 (r448)
- * fixed an issue when the last CIGAR is I or D
-
-------------------------------------------------------------------------
-r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-30 (r447)
- * fixed a bug in bam_aux_get(): 'A' is not checked
-
-------------------------------------------------------------------------
-r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bamtk.c
-
- *
-
-------------------------------------------------------------------------
-r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-28 (r444)
- * bug in "merge -n"
-
-------------------------------------------------------------------------
-r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-27 (r443)
- * SEQ and QUAL can be "*"
- * parse CIGAR "=" and "X" as "M"
-
-------------------------------------------------------------------------
-r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/md5.c
- M /trunk/samtools/misc/md5.h
- M /trunk/samtools/misc/md5fa.c
-
- * samtools-0.1.5-26 (r442)
- * replace RSA Inc md5.* with ones under permissive lincense
- * fixed a bug in detecting unsorted bam in pileup
-
-------------------------------------------------------------------------
-r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bgzf.c
- M /trunk/samtools/bgzf.h
- M /trunk/samtools/bgzip.c
-
-Change copyright notices now that MIT has approved open source distribution.
-
-------------------------------------------------------------------------
-r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_stat.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-25 (r436)
- * in flagstats, do not report singletons if both ends are unmapped
-
-------------------------------------------------------------------------
-r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/maq2sam.c
-
-fixed a SERIOUS bug in setting 0x20 flag
-
-------------------------------------------------------------------------
-r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
-fixed two minor bugs (suggested by Tim M Storm)
-
-------------------------------------------------------------------------
-r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/samtools.pl
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-24 (r435)
- * fixed a typo
-
-------------------------------------------------------------------------
-r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-23 (r434)
- * in tview, press 'r' to show read names rather than sequences
-
-------------------------------------------------------------------------
-r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/knetfile.c
-
- * tried to fixed the buggy FTP random access in Windows. FAILED.
- * anyway, MinGW seems to have problem with "%lld".
-
-------------------------------------------------------------------------
-r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/Makefile.mingw
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/faidx.c
- M /trunk/samtools/razf.c
- A /trunk/samtools/win32/libcurses.a
- A /trunk/samtools/win32/xcurses.h
-
- * samtools-0.1.5-22 (r432)
- * faidx: fixed compitability issue with _WIN32
- * razf: fixed potential compitability issue with _WIN32
- * PDCurses support in Windows
-
-------------------------------------------------------------------------
-r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/win32/libz.a
-
-replace the GnuWin32 version of libz.a with my own build with MinGW.
-
-------------------------------------------------------------------------
-r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/knetfile.c
-
-add comments
-
-------------------------------------------------------------------------
-r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile.mingw
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/knetfile.h
-
- * samtools-0.1.5-21 (r428)
- * knetfile.c is now compatible with mingw-winsock
-
-------------------------------------------------------------------------
-r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile.mingw
-
-simplify MinGW Makefile
-
-------------------------------------------------------------------------
-r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
-Changed paths:
- A /trunk/samtools/Makefile.mingw
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
- A /trunk/samtools/win32
- A /trunk/samtools/win32/libz.a
- A /trunk/samtools/win32/zconf.h
- A /trunk/samtools/win32/zlib.h
-
- * samtools-0.1.5-20 (r427)
- * MinGW support. At least SAM<->BAM conversion is working. Other
- functionality are not tested at the moment.
- * zlib headers and Windows version of libz.a are included in win32/
-
-------------------------------------------------------------------------
-r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-19 (r426)
- * fixed a bug caused by recent modifications. Sorry.
-
-------------------------------------------------------------------------
-r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bgzf.c
-
-compatible with Windows binary files
-
-------------------------------------------------------------------------
-r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_maqcns.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/samtools.pl
-
- * samtools-0.1.5-18 (r423)
- * output additional information in pileup indel lines, for the purepose
- of debugging at the moment
- * in tview, optionally allow to treat reference skip as deletion
-
-------------------------------------------------------------------------
-r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
-Changed paths:
- A /trunk/samtools/misc/psl2sam.pl
-
-convert BLAT psl to SAM.
-
-------------------------------------------------------------------------
-r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bgzf.c
- M /trunk/samtools/bgzf.h
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-17 (r422)
- * fixed a but in knetfile.c when seek type is not SEEK_SET
- * write an empty BGZF block to every BGZF file
- * check BGZF EOF marker in bam_header_read()
- * update ChangeLog
-
-------------------------------------------------------------------------
-r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/samtools.pl
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam.h
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-16 (r421)
- * in view and pileup, load header from FASTA index if the input is SAM.
-
-------------------------------------------------------------------------
-r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/maq2sam.c
-
-do not set "read 1" if reads are not mapped in the PE mode of maq
-
-------------------------------------------------------------------------
-r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/samtools.pl
- M /trunk/samtools/misc/wgsim_eval.pl
-
- * samtools-0.1.5-15 (r419)
- * in sam_open(), return NULL when the file cannot be opened.
- * make wgsim_eval.pl more robust to imperfect SAM
- * add "unique" command to samtools.pl
-
-------------------------------------------------------------------------
-r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/wgsim_eval.pl
-
-skip @header lines in SAM
-
-------------------------------------------------------------------------
-r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-14 (r417)
- * more help in "samtools view" due to the recent changes.
-
-------------------------------------------------------------------------
-r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam.h
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-17 (r416)
- * support import/export SAM with string tags
-
-------------------------------------------------------------------------
-r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam.h
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.5-12 (r415)
- * FLAG now can be in HEX
-
-------------------------------------------------------------------------
-r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/kstring.h
-
-fixed a compiling error (thank Ken for fixing it)
-
-------------------------------------------------------------------------
-r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/kstring.c
- M /trunk/samtools/kstring.h
-
-Implemented Boyer-Moore search in the kstring library.
-
-------------------------------------------------------------------------
-r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
-
-do not include knetfile.h when _USE_KNETFILE is not defined
-
-------------------------------------------------------------------------
-r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bgzf.c
-
- * samtools-0.1.5-11 (r408)
- * force to overwirte existing MD if it is different from the one calculated
- from fillmd.
- * bgzf.c: improved the compatibility with Windows headers
-
-------------------------------------------------------------------------
-r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.h
-
- * samtools-0.1.5-10 (r407)
- * implemented bam_aux_del() to remove a tag
- * fillmd: generate the NM tag
- * fillmd: cmd interface improvement
-
-------------------------------------------------------------------------
-r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
-
-Sorry. The old Makefile is for PDCurses...
-
-------------------------------------------------------------------------
-r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-9 (r405)
- * improved the compatibility with PDCurses a little bit
-
-------------------------------------------------------------------------
-r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-8 (r404)
- * compatible with PDCurses
-
-------------------------------------------------------------------------
-r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/kseq.h
-
- * samtools-0.1.5-7 (r403)
- * fixed a bug in kseq.h for binary files (text files are fine)
-
-------------------------------------------------------------------------
-r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bgzf.c
-
- * samtools-0.1.5-6 (r402)
- * fixed compiling error when "-D_USE_NETFILE" is not applied
- * improve portability to MinGW
-
-------------------------------------------------------------------------
-r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
-Changed paths:
- A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
- A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
- D /trunk/samtools/bam_lite.c
-
- * move bam_lite.c to bam-lite
- * copy bam.h to bam-lite
-
-------------------------------------------------------------------------
-r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_lite.c
- M /trunk/samtools/bam_lpileup.c
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-5 (r395)
- * added bam_pileup_file() and removed bam_lpileup_file()
-
-------------------------------------------------------------------------
-r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/knetfile.h
-
- * samtools-0.1.5-4 (r394)
- * http_proxy support in knetfile library (check http_proxy ENV)
-
-------------------------------------------------------------------------
-r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/knetfile.h
-
- * samtools-0.1.5-3 (r393)
- * knetfile now supports HTTP (no proxy at the moment)
- * fixed a potential issue in knetfile on opening ordinary file, although I have
- not seen the sideeffect so far.
-
-------------------------------------------------------------------------
-r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/samtools.1
-
-Remove the warning in tview
-
-------------------------------------------------------------------------
-r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-2 (r391)
- * do not show a blank screen when no reads mapped
-
-------------------------------------------------------------------------
-r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam.h
- A /trunk/samtools/bam_lite.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.5-1 (r390)
- * removed useless _IOLIB in bam.h. This should cause no change at all.
- * added bam_lite.c for light-weight BAM reading
-
-------------------------------------------------------------------------
-r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/knetfile.c
-
-Release samtools-0.1.5c (fixed a bug in piping)
-
-------------------------------------------------------------------------
-r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
-
-Release samtools-0.1.5b (BUG! so embarrassing!)
-
-------------------------------------------------------------------------
-r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bamtk.c
-
-Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
-
-------------------------------------------------------------------------
-r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
-
-Release samtools-0.1.5
-
-------------------------------------------------------------------------
-r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
-
- * samtools-0.1.4-23 (r372)
- * keep header text if "view -t" is used (by Gerton)
-
-------------------------------------------------------------------------
-r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/samtools.1
-
-update documentation
-
-------------------------------------------------------------------------
-r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
-
-Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
-
-------------------------------------------------------------------------
-r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-22 (r369)
- * in pileup, optionally print E2 and U2
- * remove the debugging code in bam_aux_get() (Drat!)
-
-------------------------------------------------------------------------
-r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bam_lpileup.c
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bam_rmdup.c
- M /trunk/samtools/bam_stat.c
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/faidx.c
- M /trunk/samtools/faidx.h
- M /trunk/samtools/glf.c
-
- * samtools-0.1.4-21 (r368)
- * propagate errors rather than exit or complain assertion failure. Assertion
- should be only used for checking internal bugs, but not for external input
- inconsistency. I was just a bit lazy.
- * small memory leak may be present on failure, though
-
-------------------------------------------------------------------------
-r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/knetfile.c
-
-reduce the chance of blocking in FTP connection
-
-------------------------------------------------------------------------
-r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/knetfile.c
-
-minor changes to knetfile: invalid fd equals -1 rather than 0
-
-------------------------------------------------------------------------
-r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/knetfile.h
-
- * samtools-0.1.4-20 (r365)
- * download the BAM index file if it is not found in the current working directory.
-
-------------------------------------------------------------------------
-r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/knetfile.c
-
- * samtools-0.1.4-19 (r364)
- * knetfile: report error when the file is not present on FTP
-
-------------------------------------------------------------------------
-r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bgzf.c
- M /trunk/samtools/bgzf.h
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/knetfile.h
-
- * samtools-0.1.4-18 (r363)
- * knetfile: do not trigger network communication in FTP seek (lazy seek)
- * bgzf: cache recent blocks (disabled by default)
-
-------------------------------------------------------------------------
-r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bgzf.c
-
-write changelog
-
-------------------------------------------------------------------------
-r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-17 (r361)
- * if a file is given on FTP, search locally for the BAM index
-
-------------------------------------------------------------------------
-r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bgzf.c
- M /trunk/samtools/bgzf.h
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/knetfile.h
-
- * samtools-0.1.4-16 (r360)
- * report more information in index when the input is not sorted
- * change the behaviour of knet_seek() such that it returns 0 on success
- * support knetfile library in BGZF
-
-------------------------------------------------------------------------
-r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/knetfile.c
- M /trunk/samtools/knetfile.h
-
-fixed bugs in knetfile.*
-
-------------------------------------------------------------------------
-r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
-Changed paths:
- A /trunk/samtools/knetfile.h
-
-this is the header file
-
-------------------------------------------------------------------------
-r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
-Changed paths:
- A /trunk/samtools/knetfile.c
-
- * open a file at FTP
- * preliminary version
-
-------------------------------------------------------------------------
-r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-15 (r354)
- * fixed a memory leak in bam_view1(), although samtools is not using this routine.
-
-------------------------------------------------------------------------
-r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/faidx.c
-
- * samtools-0.1.4-13 (r351)
- * make faidx more tolerant to empty lines right before or after > lines
- * hope this does not introduce new bugs...
-
-------------------------------------------------------------------------
-r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-13 (r350)
- * fixed a small memory leak in pileup, caused by recent modifications
-
-------------------------------------------------------------------------
-r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.4-12 (r347)
- * added `-S' to pileup, similar to `view -S'
-
-------------------------------------------------------------------------
-r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam_view.c
- M /trunk/samtools/samtools.1
-
- * samtools-0.1.4-11 (r346)
- * allow to select a read group at view command-line
-
-------------------------------------------------------------------------
-r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/examples/calDepth.c
-
-added more comments
-
-------------------------------------------------------------------------
-r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/examples/calDepth.c
-
-nothing really
-
-------------------------------------------------------------------------
-r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/examples/Makefile
- A /trunk/samtools/examples/calDepth.c
-
-added an example of calculating read depth
-
-------------------------------------------------------------------------
-r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- A /trunk/samtools/bam_color.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam.h
-
- * samtools-0.1.4-10 (r341)
- * only include key APIs in libbam.a
- * move color-specific routines to bam_color.c
- * update documentations
- * remove the support of -q in pileup
-
-------------------------------------------------------------------------
-r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
-Changed paths:
- M /trunk/samtools/INSTALL
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/razf.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.4-9 (r340)
- * added a warning to razf.c if zlib<1.2.2.1
- * fixed a compilation warning
- * fixed a segfault caused by @RG parsing
- * detect NCURSES in bam_tview.c
-
-------------------------------------------------------------------------
-r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/INSTALL
-
-update INSTALL
-
-------------------------------------------------------------------------
-r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/kstring.h
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.4-8 (r338)
- * parse the @RG header lines and allow to choose library at the "samtools view"
- command line
-
-------------------------------------------------------------------------
-r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bgzf.c
- M /trunk/samtools/bgzf.h
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.4-7 (r337)
- * bgzf.c: support mode string "wu": uncompressed output
- * "samtools view" support "-u" command-line option
-
-------------------------------------------------------------------------
-r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/misc/Makefile
- M /trunk/samtools/razf.c
- M /trunk/samtools/razf.h
- M /trunk/samtools/razip.c
-
- * no changes to samtools itself
- * remove zlib source codes
- * make RAZF reading compatible with old version of zlib
- * on old version of zlib, writing is not available
-
-------------------------------------------------------------------------
-r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
-Changed paths:
- D /trunk/samtools/zlib
-
-remove zlib for simplification...
-
-------------------------------------------------------------------------
-r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-6 (r334)
- * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
- been implemented in that.
- * this version works with the latest Bio::DB::Sam (20090612)
-
-------------------------------------------------------------------------
-r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
-
-update ChangeLog
-
-------------------------------------------------------------------------
-r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/AUTHORS
- M /trunk/samtools/Makefile
- M /trunk/samtools/misc/Makefile
-
-fixed minor things in Makefile
-
-------------------------------------------------------------------------
-r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-5 (r3310
- * no change to samtools itself. Version number is increased to reflect the
- changes in the Makefile building system.
-
-------------------------------------------------------------------------
-r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/AUTHORS
- D /trunk/samtools/README
-
-update information...
-
-------------------------------------------------------------------------
-r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/novo2sam.pl
-
- * updated novoalign converter by Colin Hercus et al.
- * this version works with indels
-
-------------------------------------------------------------------------
-r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/INSTALL
- M /trunk/samtools/Makefile
- M /trunk/samtools/misc/Makefile
- M /trunk/samtools/zlib/Makefile
-
- * update Makefile
- * update INSTALL instruction
-
-------------------------------------------------------------------------
-r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
-Changed paths:
- A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
- D /trunk/samtools/Makefile.am
- D /trunk/samtools/Makefile.generic
- D /trunk/samtools/Makefile.lite
- D /trunk/samtools/autogen.sh
- D /trunk/samtools/cleanup.sh
- D /trunk/samtools/configure.ac
- A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
- D /trunk/samtools/misc/Makefile.am
- D /trunk/samtools/misc/Makefile.generic
- M /trunk/samtools/razf.c
- A /trunk/samtools/zlib
- A /trunk/samtools/zlib/Makefile
- A /trunk/samtools/zlib/adler32.c
- A /trunk/samtools/zlib/compress.c
- A /trunk/samtools/zlib/crc32.c
- A /trunk/samtools/zlib/crc32.h
- A /trunk/samtools/zlib/deflate.c
- A /trunk/samtools/zlib/deflate.h
- A /trunk/samtools/zlib/gzio.c
- A /trunk/samtools/zlib/infback.c
- A /trunk/samtools/zlib/inffast.c
- A /trunk/samtools/zlib/inffast.h
- A /trunk/samtools/zlib/inffixed.h
- A /trunk/samtools/zlib/inflate.c
- A /trunk/samtools/zlib/inflate.h
- A /trunk/samtools/zlib/inftrees.c
- A /trunk/samtools/zlib/inftrees.h
- A /trunk/samtools/zlib/trees.c
- A /trunk/samtools/zlib/trees.h
- A /trunk/samtools/zlib/uncompr.c
- A /trunk/samtools/zlib/zconf.h
- A /trunk/samtools/zlib/zlib.h
- A /trunk/samtools/zlib/zutil.c
- A /trunk/samtools/zlib/zutil.h
- D /trunk/samtools/zutil.h
-
- * added zlib-1.2.3 as razip requires that
- * prepare to changed back to the Makefile building system
- * unfinished! (will be soon)
-
-------------------------------------------------------------------------
-r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
-Unfinished
-
-------------------------------------------------------------------------
-r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.4-4 (r325)
- * further avoid wrong consensus calls in repetitive regions.
-
-------------------------------------------------------------------------
-r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam.h
-
- * samtools-0.1.4-3 (r324)
- * make maqcns generate the correct call in repetitive regions.
- * allow filtering on mapQ at the pileup command line
-
-------------------------------------------------------------------------
-r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.3.2 (r322)
- * indels and SNPs use different mapping quality threshold
-
-------------------------------------------------------------------------
-r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/export2sam.pl
-
-fixed a typo
-
-------------------------------------------------------------------------
-r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
-just typo. no real change
-
-------------------------------------------------------------------------
-r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
-a little bit code cleanup
-
-------------------------------------------------------------------------
-r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.3.1
- * change default parameters
- * optionally print filtered variants
-
-------------------------------------------------------------------------
-r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.3.0
- * combine snpFilter and indelFilter
-
-------------------------------------------------------------------------
-r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.2.3
- * change a default parameter
-
-------------------------------------------------------------------------
-r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_maqcns.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
-
- * samtools-0.1.4-2 (r316)
- * pileup: cap mapping quality at 60 (by default)
- * pileup: always calculate RMS mapq
- * pileup: allow to output variant sites only
-
-------------------------------------------------------------------------
-r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.2.2
- * added pileup2fq
-
-------------------------------------------------------------------------
-r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
- * in snpFilter, suppress non-SNP sites
-
-------------------------------------------------------------------------
-r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.2.1
- * fixed a typo
-
-------------------------------------------------------------------------
-r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.2.0
- * snpFilter
-
-------------------------------------------------------------------------
-r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bgzf.c
-
- * minor changes to bgzf: return NULL if fd == -1
- * suggested by {kdj,jm18}@sanger.ac.uk
-
-------------------------------------------------------------------------
-r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
-Changed paths:
- A /trunk/samtools/misc/interpolate_sam.pl
-
-Script for paired-end pileup, contributed by Stephen Montgomery.
-
-------------------------------------------------------------------------
-r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
-
- * samtools-0.1.4-1 (r304)
- * fixed a minor bug in printing headers
-
-------------------------------------------------------------------------
-r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/maq2sam.c
- M /trunk/samtools/samtools.1
-
-Release samtools-0.1.4
-
-------------------------------------------------------------------------
-r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-24 (r296)
- * another similar bug in the indel caller
-
-------------------------------------------------------------------------
-r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-23 (r295)
- * fixed a critical bug in the indel caller
-
-------------------------------------------------------------------------
-r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_stat.c
-
-added a missing header file
-
-------------------------------------------------------------------------
-r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-22 (r293)
- * open tview in the dot-view mode by default
-
-------------------------------------------------------------------------
-r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
-Changed paths:
- M /trunk/samtools/samtools.1
-
-Added a note to the manual. Currently SAMtools used unaligned words in
-several places. Although this does not cause bus errors to me, it may
-affect portability. Please see the "Bus error" wiki page for more
-information. Also thank James Bonfields for pointing this out.
-
-
-------------------------------------------------------------------------
-r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-21 (286)
- * declare bam_aux_get_core() in bam.h
-
-------------------------------------------------------------------------
-r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-20 (r276)
- * remove bam1_t::hash again. We need to modify the Perl API anyway to
- make it work with the latest SVN.
- * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
-
-------------------------------------------------------------------------
-r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam.h
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-19 (r275)
- * a minor change to the bam1_t struct: added back "void *hash" for the
- backward compatibility with Bio::DB::Sam
-
-------------------------------------------------------------------------
-r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_rmdupse.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-18 (r273)
- * rmdupse: do not remove unmapped reads
-
-------------------------------------------------------------------------
-r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_rmdupse.c
-
-change a parameter. It does nothing
-
-------------------------------------------------------------------------
-r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile.am
- M /trunk/samtools/Makefile.generic
- M /trunk/samtools/Makefile.lite
- A /trunk/samtools/bam_rmdupse.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/configure.ac
-
- * samtools-0.1.3-17 (r271)
- * added 'rmdupse' command
-
-------------------------------------------------------------------------
-r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.3-16 (r267)
- * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
-
-------------------------------------------------------------------------
-r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-15 (r266)
- * report an error if a non-* reference is present while @SQ is absent
-
-------------------------------------------------------------------------
-r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.3-14 (r262)
- * make samopen() recognize @SQ header lines
-
-------------------------------------------------------------------------
-r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bgzf.c
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam_view.c
-
- * samtools-0.1.3-13 (r260)
- * report error for file I/O error
-
-------------------------------------------------------------------------
-r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile.am
-
-update Makefile.am
-
-------------------------------------------------------------------------
-r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/sam.c
- M /trunk/samtools/sam.h
-
- * samtools-0.1.3-12 (r259)
- * use the new I/O interface in pileup
-
-------------------------------------------------------------------------
-r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile.generic
- M /trunk/samtools/Makefile.lite
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
- A /trunk/samtools/sam.c
- A /trunk/samtools/sam.h
- A /trunk/samtools/sam_view.c
-
- * samtools-0.1.3-11 (r258)
- * unify the interface to BAM and SAM I/O
-
-------------------------------------------------------------------------
-r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile.lite
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-10 (r257)
- * allow hex with "pileup -m"
-
-------------------------------------------------------------------------
-r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_lpileup.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-9 (r256)
- * fixed a bug in bam_lpileup.c
- * I do not know if this also fixes the bug causing assertion failure in the tview
-
-------------------------------------------------------------------------
-r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-8 (r251)
- * fixed a bug when there are reads without coordinates
-
-------------------------------------------------------------------------
-r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
-Changed paths:
- A /trunk/samtools/AUTHORS
- A /trunk/samtools/README
- M /trunk/samtools/cleanup.sh
-
-added missing files
-
-------------------------------------------------------------------------
-r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile.generic
- M /trunk/samtools/Makefile.lite
- M /trunk/samtools/configure.ac
- M /trunk/samtools/misc/Makefile.generic
-
-improve large file support in compilation
-
-------------------------------------------------------------------------
-r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/INSTALL
-
-update INSTALL
-
-------------------------------------------------------------------------
-r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile.am
- M /trunk/samtools/autogen.sh
- M /trunk/samtools/cleanup.sh
- M /trunk/samtools/configure.ac
- A /trunk/samtools/misc/Makefile.am
-
-fixed various issues about the GNU building scripts
-
-------------------------------------------------------------------------
-r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- D /trunk/samtools/Makefile
- A /trunk/samtools/Makefile.am
- A /trunk/samtools/Makefile.generic
- A /trunk/samtools/autogen.sh
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
- A /trunk/samtools/cleanup.sh
- A /trunk/samtools/configure.ac
- D /trunk/samtools/misc/Makefile
- A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
-
- * samtools-0.1.3-7 (r246)
- * incorporated revisions from Nils Homer
- * enhanced support of displaying color-space reads
-
-------------------------------------------------------------------------
-r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-6 (r244)
- * fixed segfault for unmapped reads
-
-------------------------------------------------------------------------
-r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-5 (r243)
- * fixed a long existing bug which may cause memory leak
- * check MD
- * consensus calling now works with "=", but indel calling not
-
-------------------------------------------------------------------------
-r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_md.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-4 (r242)
- * fixed a memory leak
-
-------------------------------------------------------------------------
-r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/Makefile.lite
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- A /trunk/samtools/bam_md.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-3 (r240)
- * generate MD tag
- * generate "=" bases
- * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
-
-------------------------------------------------------------------------
-r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_aux.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-2 (r239)
- * fixed bugs in bam_aux.c (these functions nevered used by samtools)
- * removed bam_aux_init()/bam_aux_destroy()
- * added tagview for testing bam_aux
-
-------------------------------------------------------------------------
-r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.3-1
- * fixed a bug in pileup: the first read in a chromosome may not be printed
-
-------------------------------------------------------------------------
-r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile.lite
-
-a missing file in Makefile.lite
-
-------------------------------------------------------------------------
-r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/NEWS
- M /trunk/samtools/bamtk.c
-
-Release samtools-0.1.3
-
-------------------------------------------------------------------------
-r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-28
- * make samtools more robust to weird input such as empty file
-
-------------------------------------------------------------------------
-r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
- M /trunk/samtools/samtools.1
-
-prepare for release 0.1.3
-
-------------------------------------------------------------------------
-r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
-Changed paths:
- A /trunk/samtools/misc/blast2sam.pl
-
-convert NCBI-BLASTN to SAM
-
-------------------------------------------------------------------------
-r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_lpileup.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-27
- * fixed a small memory leak in tview
-
-------------------------------------------------------------------------
-r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_rmdup.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-26
- * fixed a bug in rmdup when there are unmapped reads
-
-------------------------------------------------------------------------
-r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
-
-proposed NEWS for the new release (have not yet)
-
-------------------------------------------------------------------------
-r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/misc/samtools.pl
-
- * samtools.pl-0.1.1
- * improve indelFilter to avoid filtering true indels. The new filter relies
- on the new pileup indel line implemented in samtools-0.1.2-25
-
-------------------------------------------------------------------------
-r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
-
- * samtools-0.1.2-25
- * change the pileup indel line to shows the number of alignments actually
- containing indels
-
-------------------------------------------------------------------------
-r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
-
-update ChangeLog from "svn log"
-
-------------------------------------------------------------------------
-r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/kseq.h
-
- * samtools-0.1.2-24
- * in merge, gives a warning rather than error if the target sequence length is different
- * allow empty header
-
-------------------------------------------------------------------------
-r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-23
- * recognize '*' at the QUAL field
-
-------------------------------------------------------------------------
-r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/kseq.h
-
- * samtools-0.1.2-22
- * the field separater is TAB only, now
-
-------------------------------------------------------------------------
-r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/examples/ex1.sam.gz
-
- * fixed the problem in the example alignment due to the bug in fixmate
-
-------------------------------------------------------------------------
-r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_mate.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/soap2sam.pl
-
- * samtools-0.1.2-21
- * fixed a nasty bug in `fixmate'
-
-------------------------------------------------------------------------
-r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/bowtie2sam.pl
- M /trunk/samtools/misc/soap2sam.pl
- M /trunk/samtools/misc/wgsim_eval.pl
-
-make the script robust to the bugs in SOAP-2.1.7
-
-------------------------------------------------------------------------
-r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_stat.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-20
- * check if file is truncated in flagstat
-
-------------------------------------------------------------------------
-r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-19
- * print the header if requested
-
-------------------------------------------------------------------------
-r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-18
- * fixed a minor bug reported by Nils Homer
-
-------------------------------------------------------------------------
-r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
-Changed paths:
- A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
- D /trunk/samtools/Makefile.std
- A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
- D /trunk/samtools/misc/Makefile.std
-
-rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
-
-------------------------------------------------------------------------
-r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
-Changed paths:
- D /trunk/samtools/Makefile
- A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bam_tview.c
- M /trunk/samtools/bamtk.c
- D /trunk/samtools/misc/Makefile
- A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
- M /trunk/samtools/samtools.1
-
- * samtools-0.1.2-17
- * incorporating Nils' changes
- * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
-
-------------------------------------------------------------------------
-r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_maqcns.h
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/kseq.h
- A /trunk/samtools/kstring.c
- A /trunk/samtools/kstring.h
-
- * samtools-0.1.2-16
- * made pileup take a list of proposed indels. An insertion is N at the moment.
- * added my kstring library for a bit complex parsing of the position list.
-
-------------------------------------------------------------------------
-r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/soap2sam.pl
-
- * soap2sam.pl-0.1.2
- * more robust to truncated soap output
-
-------------------------------------------------------------------------
-r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile.lite
-
-added bam_stat.o to Makefile.lite
-
-------------------------------------------------------------------------
-r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-15
- * generate RMS of mapQ instead of max mapQ
-
-------------------------------------------------------------------------
-r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/glf.c
- M /trunk/samtools/glf.h
- M /trunk/samtools/misc/Makefile
-
- * samtools-0.1.2-14
- * implemented GLFv3
-
-------------------------------------------------------------------------
-r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-13
- * fixed a minor bug in displaying pileup
-
-------------------------------------------------------------------------
-r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-12
- * optionally print SAM header
-
-------------------------------------------------------------------------
-r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/glf.c
-
- * samtools-0.1.2-11
- * use "GLF\3" as the magic for GLFv3 files
-
-------------------------------------------------------------------------
-r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
-Changed paths:
- M /trunk/samtools/Makefile
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/glf.c
- M /trunk/samtools/glf.h
-
- * samtools-0.1.2-10
- * fixed a bug in import: core.bin is undefined for unmapped reads
- * this bug can be alleviated (not completely solved) in bam_index.c
- * update to GLFv3: pos is changed to offset for better compression
-
-------------------------------------------------------------------------
-r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/wgsim.c
-
- * wgsim-0.2.3
- * fixed a bug in simulating indels
-
-------------------------------------------------------------------------
-r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/misc/wgsim.c
-
- * wgsim-0.2.2
- * allow to print mismatch information as fastq comment. MAQ does
- not like long read names.
-
-------------------------------------------------------------------------
-r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/misc/wgsim.c
- M /trunk/samtools/misc/wgsim_eval.pl
-
- * wgsim-0.2.1
- * fixed a bug about color read coordinates
- * fixed a bug in read names
- * wgsim_eval.pl-0.1.3
- * make the script work with color reads
-
-------------------------------------------------------------------------
-r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/Makefile
- M /trunk/samtools/misc/wgsim.c
-
- * wgsim: added a note
-
-------------------------------------------------------------------------
-r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
-Changed paths:
- M /trunk/samtools/misc/wgsim.c
- M /trunk/samtools/misc/wgsim_eval.pl
-
- * wgsim-0.2.0
- * considerable code clean up
- * print number of substitutions/indels/errors on each read
- * potentially support SOLiD simulation, though not tested at the moment
- * wgsim_eval.pl-0.1.2
- * change in accordant with wgsim
-
-------------------------------------------------------------------------
-r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-9
- * fixed a bug in bam_fetch, caused by completely contained adjacent chunks
-
-------------------------------------------------------------------------
-r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bamtk.c
-
-Fix annoying segv when invalid region specified.
-
-------------------------------------------------------------------------
-r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
-Changed paths:
- D /trunk/samtools/misc/indel_filter.pl
- A /trunk/samtools/misc/samtools.pl
-
- * move indel_filter.pl to samtools.pl
-
-------------------------------------------------------------------------
-r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_mate.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-7
- * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
-
-------------------------------------------------------------------------
-r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_stat.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-7
- * fixed a minor bug in flagstat
-
-------------------------------------------------------------------------
-r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/misc/indel_filter.pl
-
- * samtools-0.1.2-6
- * improve indel caller by setting maximum window size
-
-------------------------------------------------------------------------
-r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bamtk.c
-
- * output max mapping quality in indel line
-
-------------------------------------------------------------------------
-r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/misc/maq2sam.c
-
-fixed a bug in generating tag AM
-
-------------------------------------------------------------------------
-r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bamtk.c
-
-fixed a potential memory problem in indexing
-
-------------------------------------------------------------------------
-r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/Makefile
-
-Pass LIBS to recursive targets to facilitate building at Broad.
-
-------------------------------------------------------------------------
-r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/bam_plcmd.c
- M /trunk/samtools/bam_stat.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-3
- * fixed a bug in generating GLFv2 for indels
- * improve flagstat report a little bit
-
-------------------------------------------------------------------------
-r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/Makefile
- A /trunk/samtools/bam_stat.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.2-1
- * added flagstat command
-
-------------------------------------------------------------------------
-r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/NEWS
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/samtools.1
-
-Release SAMtools-0.1.2
-
-------------------------------------------------------------------------
-r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
-Changed paths:
- A /trunk/samtools/misc/indel_filter.pl
-
-Script for filtering indel results
-
-------------------------------------------------------------------------
-r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
-Changed paths:
- A /trunk/samtools/misc/zoom2sam.pl
-
-convert ZOOM to SAM
-
-------------------------------------------------------------------------
-r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
-Changed paths:
- A /trunk/samtools/misc/novo2sam.pl
-
-add a script to convert novo alignment to SAM
-
-------------------------------------------------------------------------
-r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/ChangeLog
- M /trunk/samtools/ChangeLog.old
- M /trunk/samtools/samtools.1
-
-update documentation and ChangeLog
-
-------------------------------------------------------------------------
-r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
-
- * samtools-0.1.1-19
- * fixed a bug in "merge" command line
-
-------------------------------------------------------------------------
-r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/misc/Makefile
- A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
- M /trunk/samtools/misc/export2sam.pl
- A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
- A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
- A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)
-
- * merge from branches/dev/
- * all future development will happen here
-
-------------------------------------------------------------------------
-r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
-Changed paths:
- M /trunk/samtools/COPYING
- M /trunk/samtools/ChangeLog
- A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
- M /trunk/samtools/Makefile
- A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
- M /trunk/samtools/bam.c
- M /trunk/samtools/bam.h
- M /trunk/samtools/bam_import.c
- M /trunk/samtools/bam_index.c
- M /trunk/samtools/bam_lpileup.c
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_maqcns.h
- A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
- M /trunk/samtools/bam_pileup.c
- M /trunk/samtools/bam_plcmd.c
- A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
- M /trunk/samtools/bam_sort.c
- M /trunk/samtools/bamtk.c
- M /trunk/samtools/bgzf.h
- M /trunk/samtools/examples/00README.txt
- A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
- D /trunk/samtools/examples/ex1.fa.fai
- M /trunk/samtools/examples/ex1.sam.gz
- M /trunk/samtools/faidx.c
- A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
- M /trunk/samtools/glf.h
- M /trunk/samtools/misc/Makefile
- M /trunk/samtools/misc/maq2sam.c
- M /trunk/samtools/razf.c
- M /trunk/samtools/source.dot
-
- * Merge from branches/dev/
- * all future development will happen here at trunk/
-
-------------------------------------------------------------------------
-r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
-Changed paths:
- M /trunk/samtools/bam_maqcns.c
- M /trunk/samtools/bam_tview.c
-
-Fix problem with compiling without curses.
-
-------------------------------------------------------------------------
-r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
-Changed paths:
- A /trunk/samtools (from /branches/dev/samtools:62)
-
-Create trunk copy
-
-------------------------------------------------------------------------
-r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
-Changed paths:
- A /branches/dev/samtools/NEWS
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/samtools.1
-
-Release samtools-0.1.1
-
-------------------------------------------------------------------------
-r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
-Changed paths:
- M /branches/dev/samtools/bam_aux.c
- M /branches/dev/samtools/bam_index.c
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bam_tview.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/razf.c
- M /branches/dev/samtools/samtools.1
-
- * samtools-0.1.0-66
- * fixed a bug in razf.c: reset z_eof when razf_seek() is called
- * fixed a memory leak in parsing a region
- * changed pileup a little bit when -s is in use: output ^ and $
- * when a bam is not indexed, output more meaningful error message
- * fixed a bug in indexing for small alignment
- * fixed a bug in the viewer when we come to the end of a reference file
- * updated documentation
- * prepare to release 0.1.1
-
-------------------------------------------------------------------------
-r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
-Changed paths:
- A /branches/dev/samtools/examples
- A /branches/dev/samtools/examples/00README.txt
- A /branches/dev/samtools/examples/ex1.fa
- A /branches/dev/samtools/examples/ex1.fa.fai
- A /branches/dev/samtools/examples/ex1.sam.gz
-
-example
-
-------------------------------------------------------------------------
-r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/ChangeLog
-
-update ChangeLog
-
-------------------------------------------------------------------------
-r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/misc/export2sam.pl
-
- * added comments
- * fixed several bugs
-
-------------------------------------------------------------------------
-r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
-Changed paths:
- A /branches/dev/samtools/misc/export2sam.pl
-
-convert Export format to SAM; not thoroughly tested
-
-------------------------------------------------------------------------
-r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
-Changed paths:
- M /branches/dev/samtools/bam_import.c
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bam_tview.c
- M /branches/dev/samtools/bamtk.c
- A /branches/dev/samtools/source.dot
-
- * samtools-0.1.0-65
- * pileup: generate maq-like simple output
- * pileup: allow to output pileup at required sites
- * source.dot: source file relationship graph
- * tview: fixed a minor bug
-
-------------------------------------------------------------------------
-r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
-Changed paths:
- D /branches/dev/samtools/misc/all2sam.pl
-
-remove all2sam.pl
-
-------------------------------------------------------------------------
-r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
-Changed paths:
- A /branches/dev/samtools/COPYING
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/faidx.h
- M /branches/dev/samtools/khash.h
- M /branches/dev/samtools/kseq.h
- M /branches/dev/samtools/ksort.h
- M /branches/dev/samtools/samtools.1
-
-Added copyright information and a bit more documentation. No code change.
-
-------------------------------------------------------------------------
-r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam.c
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/bam_index.c
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-64
- * improved efficiency of the indel caller for spliced alignments
-
-------------------------------------------------------------------------
-r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam.c
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/bam_aux.c
- M /branches/dev/samtools/bam_index.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-63
- * a bit code cleanup: reduce the dependency between source files
-
-------------------------------------------------------------------------
-r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-62
- * fixed a memory leak
-
-------------------------------------------------------------------------
-r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/ChangeLog
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/samtools.1
-
-update documentation, ChangeLog and a comment
-
-------------------------------------------------------------------------
-r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
-Changed paths:
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bam_maqcns.h
- M /branches/dev/samtools/bam_pileup.c
- A /branches/dev/samtools/bam_plcmd.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/samtools.1
-
- * samtools-0.1.0-61
- * moved pileup command to a separate source file
- * added indel caller
- * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
- * updated documentation
-
-------------------------------------------------------------------------
-r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-60
- * fixed another bug in maqcns when there is a nearby deletion
-
-------------------------------------------------------------------------
-r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
-Changed paths:
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bam_pileup.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-59
- * pileup: outputing consensus is now optional
- * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
- I am not quite sure why the previous version may have problem.
-
-------------------------------------------------------------------------
-r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
-Changed paths:
- M /branches/dev/samtools/bam_pileup.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-58
- * add maq consensus to pileup. However, I will move this part to a new
- command as strictly speaking, consensus callin is not part of pileup,
- and imposing it would make it harder to generate for other language
- bindings.
-
-------------------------------------------------------------------------
-r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/bgzf.c
-
-Fix bug in tell() after reads that consume to the exact end of a block.
-
-------------------------------------------------------------------------
-r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/samtools.1
-
-update manual
-
-------------------------------------------------------------------------
-r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
-Changed paths:
- M /branches/dev/samtools/bam_import.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-57
- * fixed a bug in parser when there is auxiliary fields
- * made the parser a bit more robust
-
-------------------------------------------------------------------------
-r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
-Changed paths:
- M /branches/dev/samtools/bam_index.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/bgzf.c
-
- * samtools-0.1.0-56
- * fixed a bug in bgzf (only reading is affected)
- * fixed a typo in bam_index.c
- * in bam_index.c, check potential bugs in the underlying I/O library
-
-------------------------------------------------------------------------
-r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/samtools.1
-
-update manual
-
-------------------------------------------------------------------------
-r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
-Changed paths:
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/bam_pileup.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-55
- * tried to make pileup work with clipping (previously not), though NOT tested
- * removed -v from pileup
- * made pileup take the reference sequence
-
-------------------------------------------------------------------------
-r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
-Changed paths:
- M /branches/dev/samtools/bam_import.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/samtools.1
-
- * samtools-0.1.0-54
- * in parser, recognize "=", rather than ",", as a match
- * in parser, correctl parse "=" at the MRNM field.
-
-------------------------------------------------------------------------
-r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/misc/maq2sam.c
-
-fixed a bug in handling maq flag 64 and 192
-
-------------------------------------------------------------------------
-r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/misc/md5fa.c
-
-also calculate unordered md5sum check
-
-------------------------------------------------------------------------
-r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/misc/md5fa.c
-
-fixed a minor bug when there are space in the sequence
-
-------------------------------------------------------------------------
-r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/misc/md5fa.c
-
-fixed a potential memory leak
-
-------------------------------------------------------------------------
-r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/bam_import.c
- M /branches/dev/samtools/bam_index.c
- M /branches/dev/samtools/bamtk.c
-
- * fixed a bug in import: bin is wrongly calculated
-
-------------------------------------------------------------------------
-r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/misc/all2sam.pl
-
-nothing, really
-
-------------------------------------------------------------------------
-r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/kseq.h
- M /branches/dev/samtools/misc/Makefile
- A /branches/dev/samtools/misc/md5.c
- A /branches/dev/samtools/misc/md5.h
- A /branches/dev/samtools/misc/md5fa.c
-
- * fixed two warnings in kseq.h
- * added md5sum utilities
-
-------------------------------------------------------------------------
-r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
-Changed paths:
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/bam_import.c
- M /branches/dev/samtools/bamtk.c
- A /branches/dev/samtools/kseq.h
- D /branches/dev/samtools/kstream.h
-
- * samtools-0.1.0-52
- * replace kstream with kseq. kseq is a superset of kstream. I need the
- extra functions in kseq.h.
- * also compile stand-alone faidx
-
-------------------------------------------------------------------------
-r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/bam_sort.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-51
- * sorting by read names is available
-
-------------------------------------------------------------------------
-r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam.c
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/bam_import.c
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bam_pileup.c
- M /branches/dev/samtools/bam_sort.c
- M /branches/dev/samtools/bam_tview.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/misc/maq2sam.c
-
- * samtools-0.1.0-50
- * format change to meet the latest specification
-
-------------------------------------------------------------------------
-r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/misc/maq2sam.c
-
- * minor change in maqcns: special care when n==0
- * change maq2sam to meet the latest specification
-
-------------------------------------------------------------------------
-r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/razf.c
- M /branches/dev/samtools/razf.h
-
-considerable code clean up in razf
-
-------------------------------------------------------------------------
-r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/ChangeLog
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/faidx.c
-
-make RAZF optional in faidx.c
-
-------------------------------------------------------------------------
-r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/bam_aux.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/samtools.1
-
- * samtools-0.1.0-49
- * added routines for retrieving aux data, NOT TESTED YET!
-
-------------------------------------------------------------------------
-r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
-Changed paths:
- M /branches/dev/samtools/bam.c
- M /branches/dev/samtools/bam_import.c
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/bgzf.c
- M /branches/dev/samtools/samtools.1
-
- * samtools-0.1.0-48
- * bgzf: fixed a potential integer overflow on 32-it machines
- * maqcns: set the minimum combined quality as 0
- * supporting hex strings
-
-------------------------------------------------------------------------
-r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/bam_maqcns.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-47
- * fixed the bug in maqcns
-
-------------------------------------------------------------------------
-r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/bam.h
- A /branches/dev/samtools/bam_maqcns.c
- A /branches/dev/samtools/bam_maqcns.h
- M /branches/dev/samtools/bam_tview.c
- M /branches/dev/samtools/bamtk.c
- A /branches/dev/samtools/glf.h
-
- * samtools-0.1.0-46
- * add MAQ consensus caller, currently BUGGY!
-
-------------------------------------------------------------------------
-r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
-Changed paths:
- M /branches/dev/samtools/bam_pileup.c
- M /branches/dev/samtools/bam_tview.c
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-45
- * tview: display padded alignment (but not P operation)
- * better coordinates and reference sequence
-
-------------------------------------------------------------------------
-r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
-Changed paths:
- A /branches/dev/samtools/ChangeLog
-
-new ChangeLog
-
-------------------------------------------------------------------------
-r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
-Changed paths:
- D /branches/dev/samtools/ChangeLog
- A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
-
-Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
-the log of my personal SVN repository.
-
-------------------------------------------------------------------------
-r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
-Changed paths:
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/bgzf.c
-
- * samtools-0.1.0-44
- * declare fseeko and ftello as some Linux may not do this by default and
- missing these declarations will make bgzf buggy
- * get rid of some harmless warings
- * use BGZF by default, now
-
-------------------------------------------------------------------------
-r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
-Changed paths:
- M /branches/dev/samtools/bam_index.c
- M /branches/dev/samtools/bamtk.c
- M /branches/dev/samtools/razf.c
-
- * samtools-0.1.0-43
- * fixed a bug in razf_read()
- * give more warnings when the file is truncated (or due to bugs in I/O library)
-
-------------------------------------------------------------------------
-r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/bgzf.c
-
-fixed a bug in bgzf.c at the end of the file
-
-------------------------------------------------------------------------
-r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
-Changed paths:
- M /branches/dev/samtools/bamtk.c
-
- * samtools-0.1.0-42
- * a lot happened to RAZF, although samtools itself is untouched. Better
- also update the version number anyway to avoid confusion
-
-------------------------------------------------------------------------
-r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/razf.c
-
-a change from Jue, but I think it should not matter
-
-------------------------------------------------------------------------
-r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
-Changed paths:
- M /branches/dev/samtools/razf.c
-
-fixed a potential bug in razf. However, it seems still buggy, just
-rarely happens, very rarely.
-
-------------------------------------------------------------------------
-r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/razf.c
-
-fixed a bug in razf, with the help of Jue
-
-------------------------------------------------------------------------
-r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/bam_index.c
-
-remove a comment
-
-------------------------------------------------------------------------
-r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
-Changed paths:
- M /branches/dev/samtools/Makefile
- M /branches/dev/samtools/bam.h
- M /branches/dev/samtools/razf.c
- M /branches/dev/samtools/razf.h
-
- * Jue has updated razf to realize Bob's scheme
-
-------------------------------------------------------------------------
-r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
-Changed paths:
- A /branches/dev/samtools/samtools.1
-
-the manual page
-
-------------------------------------------------------------------------
-r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
-Changed paths:
- A /branches/dev/samtools/ChangeLog
- A /branches/dev/samtools/Makefile
- A /branches/dev/samtools/bam.c
- A /branches/dev/samtools/bam.h
- A /branches/dev/samtools/bam_aux.c
- A /branches/dev/samtools/bam_endian.h
- A /branches/dev/samtools/bam_import.c
- A /branches/dev/samtools/bam_index.c
- A /branches/dev/samtools/bam_lpileup.c
- A /branches/dev/samtools/bam_pileup.c
- A /branches/dev/samtools/bam_sort.c
- A /branches/dev/samtools/bam_tview.c
- A /branches/dev/samtools/bamtk.c
- A /branches/dev/samtools/bgzf.c
- A /branches/dev/samtools/bgzf.h
- A /branches/dev/samtools/bgzip.c
- A /branches/dev/samtools/faidx.c
- A /branches/dev/samtools/faidx.h
- A /branches/dev/samtools/khash.h
- A /branches/dev/samtools/ksort.h
- A /branches/dev/samtools/kstream.h
- A /branches/dev/samtools/misc
- A /branches/dev/samtools/misc/Makefile
- A /branches/dev/samtools/misc/all2sam.pl
- A /branches/dev/samtools/misc/maq2sam.c
- A /branches/dev/samtools/razf.c
- A /branches/dev/samtools/razf.h
- A /branches/dev/samtools/razip.c
- A /branches/dev/samtools/zutil.h
-
-The initial version of samtools, replicated from my local SVN repository.
-The current version is: 0.1.0-42. All future development will happen here.
-
-------------------------------------------------------------------------
-r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
-Changed paths:
- A /branches/dev/samtools
-
-samtools (C version)
-
-------------------------------------------------------------------------
+commit db2ad3e19068cbafde72ecde75d0638bbb3598ba
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 16 14:45:17 2012 -0500
+
+ removed downsample.c
+
+commit 6c55c576903992c6fef148fe3b606fbc8bd10655
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 16 14:45:06 2012 -0500
+
+ print to output
+
+commit db1044a34e6049c87eaa63c39ed6e56f03e7d4c1
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 16 14:39:34 2012 -0500
+
+ removed sample
+
+ Downsampling already exists in "view". View also keeps pairing while "sample" does not.
+
+commit ffdeed3e5d4a530bfdf6f9ba97fff0ba7add6cba
+Merge: 2daad7b accf026
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 16 14:22:15 2012 -0500
+
+ Merge branch 'master' of github.com:lh3/samtools
+
+commit accf0260fd1117e10047344345d40b31a9ec31bb
+Merge: 9134e0d c554160
+Author: Heng Li <lh3@me.com>
+Date: Thu Feb 16 11:21:14 2012 -0800
+
+ Merge pull request #8 from nh13/master
+
+ Patches
+
+commit c554160df16ec7748cfdda4c7b54c641be7b809f
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 14:06:52 2012 -0500
+
+ * more README.md work
+
+commit 2a81ffe349208d917666808fbc9f3041e0cb57de
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 14:06:10 2012 -0500
+
+ * more README work
+
+commit fb3125f732715f62cded8685a23a002a96ce009b
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 14:05:19 2012 -0500
+
+ * more README work
+
+commit 444d41002c37e1c3d0f9208b4a88126c47276386
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 14:02:13 2012 -0500
+
+ * updating README
+
+commit dec53cb1043fe7efadfde75fa2fd39b76de22e54
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 13:55:01 2012 -0500
+
+ updating the README for markdown syntax
+
+commit 798da18c346dca8ec6005582a0ddb1d5420b04ca
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 13:48:35 2012 -0500
+
+ adding a README with the current differences between this repository and
+ the official one
+
+commit 4d22d86c0f28636662f2144a88cd168e104c4275
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 13:35:03 2012 -0500
+
+ adding "samtools sample" to the main
+
+commit 893c25a37c21005dc42f45d45e9ad78ddc5f29bb
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 13:33:51 2012 -0500
+
+ * removing some compile flags to work with OS X
+
+commit 7ac22f72fdc32edd5c24af6baebfa7db5faf8e7b
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date: Thu Feb 16 10:47:14 2012 -0500
+
+ Check write filehandle after opening for write. tamw/tamr is a union type, so change is only semantic.
+
+ Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit fef53330416631690f60fdff42b6e43d764170dc
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date: Thu Feb 16 10:44:59 2012 -0500
+
+ Catch and report invalid BAM header, instead of segfaulting later on.
+
+ Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 5cc013fe4930bf9b6e7963aab1cd4a3c94f695bc
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date: Thu Feb 16 10:44:16 2012 -0500
+
+ Add downsample to examples.
+
+ Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit b3fa9e7071532905a81dc7aa48eadc24b8c8846b
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date: Thu Feb 16 10:43:48 2012 -0500
+
+ Adjust for leading hard clip on colorspace reads.
+
+ Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 1a9296c1389469d1c1db5b8069f0e11ffcc8abb2
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date: Thu Feb 16 10:42:52 2012 -0500
+
+ Add samtools sample command, contributed by Davide Cittaro <davide.cittaro@ifom-ieo-campus.it>.
+
+ Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 2a804f3379748aeba944f1dec306dd726ff3235e
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date: Thu Feb 16 10:42:07 2012 -0500
+
+ Add samtools qa command, contributed by Roman Valls Guimera <roman.valls.guimera@scilifelab.se>.
+
+ Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 0f3207fe8fd93e44d40fcf57204079c8c06d24a6
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date: Thu Feb 16 10:39:08 2012 -0500
+
+ Makefile cleanup - allow CC, CFLAGS, LDFLAGS to be passed on make command line. Use LDFLAGS in samtools compile.
+
+ Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 6e7df604025f6a86881bf7f4a16f30e15d31538a
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date: Thu Feb 16 10:31:15 2012 -0500
+
+ Allow max_mem for sort to be specified with units.
+
+ Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit f12ebcaf6e60d34180a27d70e09b743cef140b98
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date: Thu Feb 16 10:29:11 2012 -0500
+
+ Allow user defined [lowercase] tags in header elements.
+
+ Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 50b931fa3312dc109537a4260698ddecd0f06a05
+Author: Jonathan Manning <jonathan.manning@lifetech.com>
+Date: Thu Feb 16 10:27:11 2012 -0500
+
+ Check lowerbound in text entry box to avoid segfault in tview. Remove redundant call to bam_aux_get.
+
+ Signed-off-by: Nils Homer <nils.homer@lifetech.com>
+
+commit 5e729da5190949a813d20d329eab7ddb661816bd
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 10:31:48 2012 -0500
+
+ * fixing overflow/underflow in integer parsing
+
+commit fa50a4330b9abedaf07c26e13d31f05e57f1d319
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 10:30:40 2012 -0500
+
+ * updating help message for samtools depth
+
+commit 79e52c9624b6dd3bdfdf439f4b4bc6f774c230a4
+Author: Nils Homer <nils.homer@lifetech.com>
+Date: Thu Feb 16 10:29:32 2012 -0500
+
+ * adding support for outputting a circos histogram file in "samtools depth". Use
+ the "-c/-B" options.
+
+commit 2daad7b52daa86561c0fb65fe366691fad9f5ed3
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 16 09:31:57 2012 -0500
+
+ bugfix: wrong SP; missing DV in the VCF hdr
+
+commit 9134e0d5047c281ef3bd53da91771d4814a5131c
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 8 11:19:12 2012 -0500
+
+ missing support of DV
+
+commit 34ebf12078c1d1015a0b8b9a9221243a60b22893
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 8 11:08:56 2012 -0500
+
+ new BCF DV format: number of variant reads
+
+commit 9589d3312fa2d076f48bdd68e2a5edd419c8070c
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Jan 10 10:30:27 2012 -0500
+
+ scale depth to quality (hidden option)
+
+commit 704473e14668333ecaca5fb7b238af405c43e3b1
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Jan 10 10:18:17 2012 -0500
+
+ really nothing
+
+commit 01b307fd287962372bbf07461c88b54f41636817
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Dec 7 13:07:42 2011 -0500
+
+ added an example containing 'B'
+
+commit c678791f0451ceb9205c1ab5c52c84641863c99a
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Dec 3 12:10:30 2011 -0500
+
+ 'B' now moves backward w.r.t. the query
+
+commit 152119bc06a073933ca830e8e1407538e44626cc
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Dec 2 10:50:12 2011 -0500
+
+ better consensus; a little more robust
+
+commit 454da4754ac503edda5b1329b67757d797e46e07
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Dec 2 00:20:22 2011 -0500
+
+ in pileup call remove_B()
+
+commit ff2bcac1cc078ba1879f18c89cfae314439d7086
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Dec 2 00:17:32 2011 -0500
+
+ working on a few toy examples
+
+commit 745ca7260158d6df7897b52598033ffb055a9e4f
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Dec 1 22:55:39 2011 -0500
+
+ bam_remove_B(); not tested
+
+commit 07e4cdc7300abfcc82e03105b4689f95cab551cd
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Nov 10 12:58:55 2011 -0500
+
+ baseQ threshold on plain pipleup; removed -E
+
+commit 322ebf2082dfa91df44b3a996d26c85357e5d5a2
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Oct 19 09:28:04 2011 -0400
+
+ fixed two gcc warnings
+
+commit a632457b4c4adc50d833b56b5a5231feafaf8193
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Oct 4 10:13:23 2011 -0400
+
+ change size_t to uint32_t in bam_header_t
+
+ This may cause issues on 64-bit big-endian machines. Reported and fixed by Paolo Emilio Mazzon.
+
+commit af31bf5a78aea03baf6eb90fe50076549d499f6e
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Sep 26 20:17:57 2011 -0400
+
+ rename pad2unpad to depad
+
+commit 77b198b73dfad1048e5d1c5a64aa75ee7b90f596
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Sep 23 01:22:40 2011 -0400
+
+ convert padded BAM to unpadded BAM
+
+commit adb9e2342b7b7501d9527d3c23afab10469ae2c6
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Sep 7 11:40:50 2011 -0400
+
+ generate template cigar with "fixmate"
+
+commit 46e5ab445a0fe880216cbc0daf1225725b569d7a
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Sep 2 12:50:18 2011 -0400
+
+ update kseq.h to the latest version
+
+commit 68e9e4a73eb91405bb3e56bf0cdaf12d1b487abb
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Sep 2 12:44:45 2011 -0400
+
+ Release samtools-0.1.18
+
+commit aa06bdadb2d109a79f927f478102f96a1f5fd258
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Sep 2 12:14:17 2011 -0400
+
+ updated the revision number
+
+commit 267e1e1b6e54c0ab24f94cd9aee9cbd2d1923f9f
+Merge: 19ff1d3 aebab30
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Sep 2 12:13:08 2011 -0400
+
+ Merge https://github.com/lh3/samtools into reduce
+
+ Conflicts:
+ bam_md.c
+
+ Fixed a few typos in the merge
+
+commit aebab302399c24eaa6c5ab79d13d6bd5e2e9ea9a
+Merge: c2c63d0 da62663
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Sep 2 09:03:49 2011 -0700
+
+ Merge pull request #4 from peterjc/x_equals2
+
+ Implement basic support for =/X CIGAR operations
+
+commit 19ff1d3d7f47d7e61b121292aefe5a74bb8a18d2
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Aug 25 16:38:12 2011 -0400
+
+ reduce BAM size (experimental)
+
+commit da626630fd98fd4e07ceb4d58c5c9a42d312a85d
+Author: peterjc <p.j.a.cock@googlemail.com>
+Date: Mon Aug 22 06:58:08 2011 +0100
+
+ Support =/X CIGAR operations (treated like M)
+
+commit 461d8003529db77a4d5ecbd108312e868b051a3d
+Author: peterjc <p.j.a.cock@googlemail.com>
+Date: Mon Aug 22 05:52:56 2011 +0100
+
+ Define CIGAR equals and X operationss (7 and 8)
+
+commit c2c63d067113baab41f3bc35fb28f4f00578accb
+Merge: 7ab3ef3 9a0ed9a
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Aug 18 17:21:54 2011 -0700
+
+ Merge pull request #3 from peterjc/x_equals
+
+ Accept SAM files using = in CIGAR (treats X and = as M)
+
+commit 9a0ed9a6b85c7981465f459300208dbd93e3c6f5
+Author: peterjc <p.j.a.cock@googlemail.com>
+Date: Thu Aug 18 19:28:52 2011 +0100
+
+ Accept SAM files using = in CIGAR (treats X and = as M)
+
+commit 7ab3ef388c1eb34d7912fd70cc5656c955240263
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Aug 8 10:22:22 2011 -0400
+
+ bugfix: indexing takes huge memory
+
+ This happens when an unmapped mate has coordinate 1. Thank Joel Martin for the fix.
+
+commit a3f6738593e944354a8f75306687d8b3acf08bf1
+Merge: a8bdca9 bc67ea2
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Aug 8 09:52:26 2011 -0400
+
+ Merge branch 'master' of github.com:lh3/samtools
+
+commit bc67ea225da653f36a70b38382d6111dd494f659
+Author: Petr Danecek <pd3@sanger.ac.uk>
+Date: Thu Jul 28 20:03:16 2011 +0100
+
+ Variant Distance Bias
+
+commit deb578f0c49d0b7d8c3bc6be220b4d67e2e7dfdf
+Author: Petr Danecek <pd3@sanger.ac.uk>
+Date: Tue Jul 26 09:57:37 2011 +0100
+
+ If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but use the tag instead.
+
+commit a8bdca9cf482a637b89ee4f98469a93e0ab5e69b
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Jul 25 10:10:55 2011 -0400
+
+ bugfix: LRT2=nan
+
+commit 0afe33137d046a3e849eeb4a54590f27cbad4228
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Jul 22 21:55:38 2011 -0400
+
+ fixed a bug/typo
+
+commit 62d5849658c10222d40308c6b53ab4f99a448494
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Jul 15 16:04:19 2011 -0400
+
+ allow to set see in subsampling
+
+commit 5f46243824cc9435b167973e1d51e13128794ea1
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Jul 15 15:54:47 2011 -0400
+
+ support subsampling
+
+commit 5e55b6f34fc86cba7cf98d52ccaed405c3ffabbc
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Jul 15 15:53:38 2011 -0400
+
+ support indels
+
+commit f31c162926d6f43e8b60171789a258d02e1f9be5
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jul 7 17:02:33 2011 -0400
+
+ do not count indel with "view -Y"
+
+commit e412dae587883b4c17e5fbf4b7c33f38bfa8458a
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jul 7 00:35:25 2011 -0400
+
+ for WIN32 compatibility
+
+commit 70a52501bcfa63824749893a5ab8ed3c38e34958
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jul 7 00:32:46 2011 -0400
+
+ for WIN32 compatibility
+
+commit 00438f14ed5984f08e8f7645a9b95644a812f969
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jul 6 23:41:45 2011 -0400
+
+ fixed an uninitialized variable
+
+commit 7609c4a01059c326544b3d0142dfe9c4229d68c6
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jul 6 23:39:31 2011 -0400
+
+ fixed an uninitialized variable
+
+commit cec7189a412f80ccb068a73bd28528915c16b0bf
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jul 6 22:53:19 2011 -0400
+
+ Release samtools-0.1.17
+
+commit 93c06a249de3bb666029bf07b66de5e8e5e314fa
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jul 6 09:46:09 2011 -0400
+
+ bugfix: incorrect idxstats for the last seq
+
+ Again, this bug is caused by 3rd-party code for the sorting order checking.
+
+commit 84f6ca62db6e27b8c4c711e7b5f3ca704bf27b4f
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Jul 5 23:30:23 2011 -0400
+
+ output mapping quality in the old pileup format
+
+commit 362e05fd670886acaede69b864903d730b9db3ca
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Jul 5 21:59:22 2011 -0400
+
+ added a brief description of the VCF format
+
+commit e690a696468205e0cc4560016361c997660dd496
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Jul 5 16:23:10 2011 -0400
+
+ improved samtools manual page
+
+commit 362b4a1408ef3c32311d638aa8d85ce39c1c7b2d
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Jul 5 15:58:29 2011 -0400
+
+ merge bcftools.1 to samtools.1
+
+commit 643e0e61ba7266efbc9e5bfcb8e41f369ba2ce0a
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Jul 5 13:39:02 2011 -0400
+
+ mpileup: when region set, set reference properly
+
+commit 613e4d67624a94f62563935fbd5cc294df69605a
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Jul 4 23:29:02 2011 -0400
+
+ compute the min PL diff
+
+commit 5b7d5d3f52b97ca42c8500eede808dab88a46a53
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Jul 4 22:57:48 2011 -0400
+
+ rename trio.c to mut.c
+
+commit 84fe96ad64b0365ead93a4115d1684b9bebb98fc
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Jul 3 15:38:51 2011 -0400
+
+ added pair caller interface; not tested
+
+commit 2f2867b87b84c35319cc416d6173819d5c8a4e8c
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Jul 3 15:24:23 2011 -0400
+
+ inital implementation of a pair caller
+
+commit e97653cf2ad653c95886933c42a2b5492ccab5ff
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Jul 3 00:06:28 2011 -0400
+
+ convert bam to single-end fastq
+
+commit e8013e11f7a8db0a8d18c60d130169cca39bf2bd
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Jul 2 14:39:18 2011 -0400
+
+ improve BED parsing
+
+commit 1025714325fdc636aeee47a76db8dafbbbfde64b
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Jul 1 14:19:54 2011 -0400
+
+ update the manual page
+
+commit 8022d0039dff47b1c11b2421357d510c1f28ae15
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Jul 1 14:17:03 2011 -0400
+
+ output the best constrained genotypes in trio
+
+commit 18c87295e12f5bebafdcae00d52000fb94c8a566
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Jul 1 11:18:14 2011 -0400
+
+ added documentations for view -T
+
+commit daf7a8d96bd495296bf7c7d99cddb808a3ced7d5
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jun 30 22:45:20 2011 -0400
+
+ fixed a bug in writing SP
+
+commit e5c32bf9b28c6e3e861db88de56b5dbe11058b61
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jun 30 22:35:25 2011 -0400
+
+ optionally output read positions in mpileup
+
+commit 1008051155ec994c1901e18f3eb03ea32a62e5d7
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jun 30 22:17:25 2011 -0400
+
+ make faidx works with <2GB lines
+
+commit 2daebb63762425dd3074ddf71582ad189001e394
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jun 30 17:28:58 2011 -0400
+
+ fixed an issue in the trio caller and the indel caller
+
+commit 9fdd52cf0716fb342a94946433d564b28b230835
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jun 30 13:34:01 2011 -0400
+
+ Added trio caller; NOT tested yet
+
+commit ea22a8ed83625e9c82382b56acc42a2d9cfd17e5
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jun 30 11:42:29 2011 -0400
+
+ convert PL to 10-likelihood GL
+
+commit 10d7065267b0d12c2bfcb6c70204fb6944cd395d
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jun 30 10:49:05 2011 -0400
+
+ fix a compatibility issue with the new bcftools
+
+commit d340f01f609c61b719d38a6a55629a3fc899e1cd
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Jun 26 23:41:20 2011 -0400
+
+ allow to ignore RG
+
+commit d6321faf98ebfe899b9409fb23c90a4aa8c6b542
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Jun 5 23:05:21 2011 -0400
+
+ fixed a bug in SO checking due to a recent change
+
+commit bc995abf666d0c9ab4258f6c1b3518a45a89209f
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Jun 3 14:45:36 2011 -0400
+
+ update the version number
+
+commit 9e7cd83a08383858d008e0ccb2238a2b93831d6c
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Jun 3 14:43:12 2011 -0400
+
+ smarter way to parse a region string
+
+commit e58a90a0fde54053dac65352b34c13c3fea815fc
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jun 1 14:36:22 2011 -0400
+
+ output LRT2 instead of LRT1
+
+commit 08f78c9af3e5661f04f80bef424232de721dba03
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jun 1 14:02:28 2011 -0400
+
+ genotype test, but assuming 1-degree
+
+commit 587b852340d7e60f6f7cf474a92ef77aeab46018
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jun 1 12:55:19 2011 -0400
+
+ perform 2-degree test by default
+
+commit 3d38e403c5c830478b7eb157a484776997440501
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jun 1 12:44:34 2011 -0400
+
+ fixed a typo; but the result is still not good
+
+commit 06291624f7dcc57445676f3be25d0bc355dd7110
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jun 1 12:24:18 2011 -0400
+
+ fixed a typo
+
+commit 63b98aa33636b0d82a435bf49153c8c1502e7d42
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jun 1 12:23:37 2011 -0400
+
+ added HWE+F<0 filter
+
+commit 37d926e8999999b593d0637ab7dc379dbd3d6006
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed May 4 10:11:59 2011 -0400
+
+ improved sorting order checking in index
+
+ Patches from Jonathan Manning
+
+commit 1c2dc6762c5f7cd946046b53346513f2f9761dbf
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue May 3 23:09:05 2011 -0400
+
+ added r^2 estimate; added Brent's method
+
+commit c2d3bcd8f98e31668b5f1321222fbc6fd6336e75
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun May 1 23:45:23 2011 -0400
+
+ combine several utilites into vcfutils.lua
+
+commit be2e7362d7593ea4d03fb33cdb6af2aa096ca6c4
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Apr 27 21:09:22 2011 -0400
+
+ minor warning
+
+commit 683ef0443860813d743cf84fa86dda9bfaf5445a
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Apr 27 10:10:38 2011 -0400
+
+ added versioning
+
+commit ed72f25ec85671f7646dbc92fa7b5b1dda427f7d
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Apr 27 10:04:02 2011 -0400
+
+ Output ML allele count
+
+commit 2a9e36d2d6c405b2411ca47458f028ada8fe1000
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Apr 26 16:14:20 2011 -0400
+
+ use ar -s
+
+commit 7a4f54e6dbcd7c94acbb3f1050a93f94b8a07949
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Apr 23 01:22:31 2011 -0400
+
+ added another type of LRT
+
+commit b9c5e84762a4aacce3a3771b51ea80967c79a2e5
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 22 16:00:31 2011 -0400
+
+ added version
+
+commit 8fad6677c5952efd67391581d64e67e02e7f6e68
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 22 00:30:19 2011 -0400
+
+ remove the pileup command
+
+commit 3a962fb6ebf779de70f9e6effb2d8701a9aa3dd9
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Apr 21 23:10:45 2011 -0400
+
+ Release 0.1.16 (r963:234)
+
+commit b4d683cffbd98c43f05aff8610b37d63dd7e54aa
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Apr 21 12:44:44 2011 -0400
+
+ fixed a bug when coordinate-less reads are on the reverse strand
+
+commit c5ec45a128f409debc6a56a798024f53004037dc
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Apr 20 11:36:52 2011 -0400
+
+ added option '-f' to merge to avoid overwritting
+
+commit 68d431531370d24907c01a27f166f2341d7c4d35
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Apr 20 10:26:58 2011 -0400
+
+ do not print a warning
+
+commit 32922607e51ad2260c337eb022b9e4aedacb049f
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Apr 20 10:21:06 2011 -0400
+
+ Added ldpair to compute LD between requested pairs
+
+commit b8d6fa71b91678fa02338257e0707d1e5ca098dd
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Apr 17 21:51:43 2011 -0400
+
+ On a toy sample, type "B" seems to be accepted
+
+commit 0e7ee9a6bb4029184202aa6e6738105ba0c0510b
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Apr 17 21:21:20 2011 -0400
+
+ added type "B"; not tested yet
+
+commit a513dfad0ac0062b03871eb6ecf26cb8d18dc895
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Apr 17 19:25:54 2011 -0400
+
+ fixed a bug in bedidx.c: input BED not sorted
+
+commit de1e192bb0a8a762a54a6eee81d882fab01c3d32
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Apr 17 18:51:08 2011 -0400
+
+ by default, always perform posterior chi^2
+
+commit df6e0d1099895fc6cd7a19dc89fba95ed6654d35
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Apr 16 12:33:28 2011 -0400
+
+ added debugging
+
+commit 8ce52e024dc2ef361dbd5399c232163055057e70
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Apr 16 00:59:05 2011 -0400
+
+ avoid a segfault given wrong input
+
+commit e66b6684fc9a397f91ec29fdeecae9f8eb986a55
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 15 19:55:39 2011 -0400
+
+ do not segfault when there is no PL
+
+commit 9ce3c584ec0cebfa45576f2ef538df4dad2b7e55
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 15 11:59:55 2011 -0400
+
+ remove another unused part
+
+commit f53a051d68bf312ac8d5865210fae7a9808c0fb9
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 15 10:41:25 2011 -0400
+
+ print G3 if HWE is small
+
+commit 4b2c08bb86ca4ed4959e4cb77a28f7d6fc19f5c9
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 15 10:04:34 2011 -0400
+
+ fixed a bug
+
+ actually not fix, but hide it
+
+commit 088e13c32453fb533b7bb1c65a573f9b90a23625
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 15 09:48:47 2011 -0400
+
+ added LRT based permutation; not used though
+
+commit 1e3c2001afcb80b5eaa4c3f88df9da7b01b62524
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 15 09:28:55 2011 -0400
+
+ Perform posterior contrast for small LRT
+
+ Posterior contrast is much slower than LRT. Nonetheless, posterior P-value is
+ more robust to sequencing artifacts. Thus we may combine the two to achieve a
+ balance between speed and low FPR.
+
+commit 6f1b066270902198a7175ff6c1b05ebc8d1919be
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 15 01:36:06 2011 -0400
+
+ Added Brent's method
+
+commit 3d061e5db25b67b25f6ff87afe4162e121354232
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Apr 14 23:30:10 2011 -0400
+
+ fixed a typo in printing
+
+commit 7fd14ceb5990bb350b8e97346ef3537d80058def
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Apr 14 23:14:23 2011 -0400
+
+ fixed a stupid bug
+
+commit f5b2c3459ec098b3cafd9619b9077132516baf58
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Apr 14 22:42:35 2011 -0400
+
+ separate EM and posterior
+
+ Now, constrast is not performed unless -C is in use. EM can be invoked
+ independently with -e without computing the posterior.
+
+commit 9eefcac963697fae554789b11ae3cb2c23f224d0
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Apr 14 22:00:19 2011 -0400
+
+ further code cleanup; prepare to add EM interface
+
+commit c2cce52355262743711e4742b0c8542bfcab1cdd
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Apr 14 21:44:03 2011 -0400
+
+ drop EM from prob1
+
+commit 24016f04bd3bdffb7eeb50cb25854f5007feb70f
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Apr 14 21:08:33 2011 -0400
+
+ drop posterior LRT; prepare for clean up
+
+commit 3670d8bd88c3eb22873f0a80e2a5913f64ca8c9a
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Apr 14 20:57:43 2011 -0400
+
+ better initial values for LD
+
+commit d48a8873c060b18b57799cfe3a0e5496ba069457
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Apr 14 20:36:25 2011 -0400
+
+ finished EM
+
+commit b101f2db476188a950c23f5c1b6185fdb7f8f40b
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Apr 13 01:19:04 2011 -0400
+
+ genotype frequency estimate
+
+commit d79bdcbf6242ecfb8accba9ac9a22fbcbd543cf2
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Apr 13 00:37:22 2011 -0400
+
+ prepare for code clean up
+
+commit e0ce416abfc094f0c090957080b1404fd0edf752
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Apr 13 00:34:15 2011 -0400
+
+ rename ld.c to em.c
+
+commit 45ede3ad181f35c1be24bed5d75841e472357ab7
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Apr 13 00:22:10 2011 -0400
+
+ implemeted EM likelihood ratio test
+
+ The idea is learned from a brief chat with Rasmus Nielsen.
+
+commit 0454a346b60e42b75a2f742272089810279c7131
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Apr 12 15:45:52 2011 -0400
+
+ added likelihood-ratio test (idea from Nick)
+
+commit f6287c8646c690440a1554c8958e7268f4134dc2
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Apr 10 18:24:37 2011 -0400
+
+ Release samtools-0.1.15 (r949:203)
+
+commit de6023f38f4d652438557cf7a0ac6eec324e7416
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Apr 10 15:54:58 2011 -0400
+
+ improved help information
+
+commit d3b337f2b7eda1e6f8f5575a19d1b5ed55cae279
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Apr 9 16:28:01 2011 -0400
+
+ fixed a minor issue
+
+commit 82f6e4f49247e75fbd8ec08c285b8d3047b3d235
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Apr 9 15:49:04 2011 -0400
+
+ separate QC-pass and QC-fail reads
+
+commit 8362b4a255081ee7ca0a4ca2eabc8c76758b6863
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 8 17:45:19 2011 -0400
+
+ added verbose level
+
+commit f7bf419c290462be7d289249a4a6d28f825b4c93
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 8 16:08:14 2011 -0400
+
+ fixed a bug
+
+commit 890cbb1ac93b3004fb6cf42ff47195077dcfc8ad
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 8 16:00:37 2011 -0400
+
+ drop unrelated @RG when "-R" is in use
+
+commit a62dc929c950fb51311b705f5b5bfba8e3f704d7
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 8 16:00:14 2011 -0400
+
+ skip header validation
+
+commit 39da810e2c56c8f0eff1ab726600b41f26d3d8e9
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Apr 5 23:52:22 2011 -0400
+
+ change error message
+
+commit c0c50a34df250ef8a7a29b172058cd229be582b5
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Apr 5 23:50:46 2011 -0400
+
+ fixed a bug caused by recent modifications
+
+commit 25226e8c468404cb5e1b5272efcea57e4193c762
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Apr 5 13:31:19 2011 -0400
+
+ reduce the indel filtering window
+
+commit 5e18d7014437734f9dac9ab45a95e43ec2526101
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Apr 4 13:56:20 2011 -0400
+
+ only output hwe if it is small enough
+
+commit 614941fb7dd276de662e7820eb8c7bae871a18cc
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Apr 4 13:34:02 2011 -0400
+
+ added HWE back
+
+commit 7abe8825aa0bacccdeb38125934ae94d18f0ad4d
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Apr 4 12:46:24 2011 -0400
+
+ EM estimate of genotype frequency
+
+commit 2bfeff9c645d177416664f1cb811e85cac3ff9e3
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Apr 4 11:29:12 2011 -0400
+
+ minor
+
+commit 401e40647e7e3abbac6e4ec3d8bb68eb6f2d401b
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Apr 4 11:24:04 2011 -0400
+
+ Added genotype freq estimate and association test
+
+commit 6cc226df6e3b480f1bd6e763ce8ef47f785bbb74
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Apr 3 20:57:23 2011 -0400
+
+ minor changes
+
+commit 7e47a39630e812f09b80369f14606245976f687e
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 1 15:21:59 2011 -0400
+
+ print the grayscale
+
+commit 2f675d9c0dde3c166c99e335fa17c7873a5ae8d5
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 1 08:55:16 2011 -0400
+
+ change to comment
+
+commit 0592bb514994544ed84f51e509b233cf8821e0cf
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Apr 1 08:54:35 2011 -0400
+
+ added base quality filtering
+
+commit fc1b47e04a7b94f6362c45856cbeb89d9d0b5ca5
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Mar 31 23:31:14 2011 -0400
+
+ fixed a few typos in comments
+
+commit 60be79bc8f0d24656e5e8a329af7e9b5b91d4c8b
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Mar 31 23:13:23 2011 -0400
+
+ comments
+
+commit 2432864acc25ebe5cee4217dbb0120439077a7f8
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Mar 31 22:42:46 2011 -0400
+
+ added bam2depth.c, a demo program
+
+commit 39625f7c6bea9ccbfd9af0feb22348d52079f012
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Mar 31 16:37:22 2011 -0400
+
+ added bgzf_check_bgzf() (used by tabix)
+
+commit 6de6bd3fb67fd22753a5f07d4cc25bf94e1b5a8c
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Mar 31 16:37:08 2011 -0400
+
+ fixed a bug in bedidx.c
+
+commit 3b9e257d25b2e81eed1625bc5d2882ed486ef20e
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 30 13:27:15 2011 -0400
+
+ added bed support to bcftools
+
+commit 47bcce3d14ec4d205283b61e5e653803996c42e0
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 30 12:56:40 2011 -0400
+
+ Added BED support to "samtools view"
+
+commit a812386017faedfc86c0e6562adbb2138329cfeb
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 30 12:47:04 2011 -0400
+
+ support BED file
+
+commit 3052dddc929f1825e6e7f7f6f6724d9465d6cf9a
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Mar 28 15:51:55 2011 -0400
+
+ relax RG matching; proper mismatching message
+
+commit f86d60c8fe25785523f01fae1486d2a6df4ee6ef
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Mar 26 10:38:23 2011 -0400
+
+ Avoid reporting association when something unexpected, which I do not understand, happens.
+
+commit dd41e6b26fd9fe30218748b9a0a1f49bdb1862b9
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Mar 26 10:38:01 2011 -0400
+
+ Added -1 to merge
+
+commit 4a0364b0d7f87f1c88d71ec5857a1f1d40710681
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 23 16:56:55 2011 -0400
+
+ plot pairwise r^2
+
+commit 452629a711582e612bec22b3b082e234bd37039b
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 23 14:31:01 2011 -0400
+
+ pairwise LD; case-control AF2
+
+commit 52862951adcaecde26ba8f0d9c1897944640a674
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Mar 21 23:03:14 2011 -0400
+
+ Release samtools-0.1.14 (r933:170)
+
+commit 59a5a8ba8e2940f0e38238f9339f02c91a8a0ce4
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Mar 21 13:52:55 2011 -0400
+
+ optionally skip loci with too low sample coverage
+
+commit 6434264b5c69514d4fafe62cbd30b3bbaddc1d41
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Mar 19 14:38:25 2011 -0400
+
+ mpileup support Illumina1.3+ quality; skip non-variant sites when "view -v" is in use
+
+commit 5f59e01987e1d5eca7d6359cae64a9734b18beea
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Mar 18 17:19:18 2011 -0400
+
+ update version to r933:167
+
+commit 4d2c3c950910aa3d2c87760c3532e458fe01c0fa
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Mar 18 16:25:01 2011 -0400
+
+ added "-1" to the command-line help
+
+commit 55313a015a7bd6369cf5a66fed7fab2333201dc9
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Mar 18 16:22:12 2011 -0400
+
+ added the "cat" command (by Chris Saunders)
+
+commit b670272cadf3efa4dc456ac4c76104f73477d60d
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Mar 18 15:59:46 2011 -0400
+
+ support varying the compression level
+
+commit c5dd3c9ca5f75f880e52c8cd2beae983bcb8d3b1
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 16 14:33:45 2011 -0400
+
+ update the manual pages
+
+commit 12fb4b596dc51bccd154fc4bd0593442f7937a46
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 16 12:49:26 2011 -0400
+
+ update changelog
+
+commit e7fe4fd66e02d60a1ca7952ad1938809e77729a9
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 16 12:10:05 2011 -0400
+
+ do not call indels when the depth is very high
+
+commit 7455eeaa32b949bb3856f75810890aabf7cacb18
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 16 11:56:56 2011 -0400
+
+ code clean up
+
+commit 5f16679e54ced8e67a75d949f9175c50480b914e
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Mar 15 14:45:24 2011 -0400
+
+ when -s is specified, change the sample order
+
+commit 7ba95adee09d3b06a7eaf797d25efef837e592f5
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Mar 15 14:11:42 2011 -0400
+
+ compute the rank in permutation
+
+commit d219783cea7643fc7e10e1bd3a98e9b3165b4506
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Mar 13 21:35:13 2011 -0400
+
+ I have found a SERIOUS BUG!!!
+
+commit 8e20d04ecdac1a7788eef71c4bb91b8479cf7150
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Mar 13 17:04:04 2011 -0400
+
+ optionally shuffle samples in a BCF (debugging)
+
+commit fc7b261f181f2a411427bc9ee5d586c883ca9cdc
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Mar 11 09:34:20 2011 -0500
+
+ fixed a bug
+
+commit b3bbcc3d40994ae85705ab6fef9866ec8c142201
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Mar 10 20:25:59 2011 -0500
+
+ use mode instead of mean
+
+commit f1161262d137098a19143b5cb0de810e5db3243e
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Mar 10 20:09:16 2011 -0500
+
+ start from the mean instead of the mode
+
+commit 2ba56f5e99e90674855c4ffc8bf583340b932e1e
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Mar 10 17:13:34 2011 -0500
+
+ fixed an error in Chi^2 test
+
+commit b4ce7ae400290bc43dd287240479667f99b3b11e
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Mar 10 00:23:39 2011 -0500
+
+ minor
+
+commit 8487fa5d3a73a43443964e731ea2a4c873c9d4e5
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 9 21:33:19 2011 -0500
+
+ added -F to accept BCFs generated by old samtools
+
+commit fd51d2093f7fd775a7eaaeea57fa34716ab59ac2
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 9 17:39:09 2011 -0500
+
+ update version
+
+commit b6da54335df943015a998a934075331b467abb5b
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 9 17:37:14 2011 -0500
+
+ compute pseudo-chi2 probability
+
+commit 9f73cefdb8935421d872b989dd98fbc8e1295029
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 9 15:54:04 2011 -0500
+
+ remove a comment which is wrong
+
+commit b10b1e47ece522e97ab8ef23417bcb6454f8b9db
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 9 15:51:12 2011 -0500
+
+ clean up
+
+commit 353bfae2c6ff59205bd9223db04084cf7f507f01
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 9 15:45:29 2011 -0500
+
+ for backup
+
+commit 53915d1c6410c2537d18bfa8eb8c657a2233c35e
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 9 15:27:56 2011 -0500
+
+ having debugging code
+
+commit 0d0dbf66995b1511390d593981eae7b5d36fe17b
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Mar 9 14:58:23 2011 -0500
+
+ temporary backup
+
+commit 5b74a174a8b637dee43b7f30250df6fb96580e12
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Mar 8 15:46:11 2011 -0500
+
+ the output makes sense, but there may be a typo...
+
+commit d81ec654b6c0c1eef6b0625d96f14b3155cee7c6
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Mar 8 15:19:09 2011 -0500
+
+ added contrast2(); fixed a bug in haploid mode
+
+commit 0cfd896fad5f7737cca49efa94a11892dafcd812
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Mar 7 21:40:17 2011 -0500
+
+ fixed a bug in haploid genotyping
+
+commit ccd52155ef61273f2b42ad9c7b31ff1915f81b24
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Mar 5 18:10:35 2011 -0500
+
+ fixed a few bugs; still not fully working
+
+commit edc3af753f96f831968ae32f2e0f915b74f31e6e
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Mar 4 17:31:33 2011 -0500
+
+ drop HWE calculation
+
+commit 92dac194debb66ca0718c21c871822dda2dd5bc1
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Mar 4 17:28:35 2011 -0500
+
+ implemented hap/dipoind mode; probably BUGGY!
+
+commit 7f26804bc27937e36fdc967e5c76514653ea40f5
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Mar 4 16:01:27 2011 -0500
+
+ read ploidy
+
+commit e7b7213475b5e61a69aab77ffb02b4983c8e7678
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Mar 4 14:12:14 2011 -0500
+
+ added math notes
+
+commit 46023e2f21321da83fc8e83e9229757a4e821acb
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Mar 4 13:34:10 2011 -0500
+
+ update BCF spec
+
+commit 13190c49eeb006ad7013b7f1e9fc1b3beca3ae78
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Mar 1 14:45:19 2011 -0500
+
+ Release samtools-0.1.13 (r926:134)
+
+commit be8fabbb6001d9fd5263a70a3e21ed6dfe5a9837
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Mar 1 14:07:15 2011 -0500
+
+ prepare to finalize 0.1.13
+
+commit 1e8c753660978bed7e9289fe50becd596d9314bb
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Mar 1 09:40:17 2011 -0500
+
+ allow to change whether to drop ambiguous reads
+
+commit 412210bfdb46606023f2e4b9086f2787f0cf1c62
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 28 22:01:29 2011 -0500
+
+ revert to the old behavior of phase
+
+commit 46035589518cf84738de8666b866e2619457c1fb
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 28 16:46:23 2011 -0500
+
+ change version number
+
+commit 7f40c33e37fc16fcb0a375ce46ae1d09cafb6d50
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 28 16:37:42 2011 -0500
+
+ bugfix in indel calling: interger overflow
+
+commit 75849470efbe30042e5ddd516f9bcbe3b9bf6062
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 28 15:35:47 2011 -0500
+
+ fixed a typo
+
+commit 9e6fb569885f906fabaab7fc2f02eae82f4bd602
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 28 15:34:09 2011 -0500
+
+ minor changes to heuristic rules
+
+commit 30a799a91f5e2c10b761aa5437f902c6649fceb3
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 28 15:20:26 2011 -0500
+
+ fixed a bug in the latest change
+
+commit e21ba9df950ea37f5c1b35c2af9ba9a4e0bba02a
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 28 12:47:06 2011 -0500
+
+ put version in bam.h
+
+commit 918b14780c1dceb39c7010638ecd61c626e17166
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 28 12:00:38 2011 -0500
+
+ frag_t::phased==0 reads are dumped to chimera.bam
+
+commit 657293c7bdba3ac69f53cd1ffa2874ed8756475e
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 28 11:05:29 2011 -0500
+
+ change default -q to 37 (previously 40)
+
+commit 33d8d3bea76e466798ea322d68d34deb8d2dff06
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 28 10:39:57 2011 -0500
+
+ fixed a minor bug in BAM reading
+
+commit daa25d426d42465d76c7317c95772bbb36bb3f47
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Feb 26 21:07:24 2011 -0500
+
+ suppress gzopen64() warning
+
+commit 9cec4256eb9e7848d4711adb67b540659c141e32
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 22:14:52 2011 -0500
+
+ fixed a long existing bug in vcf2fq
+
+commit 304487c83067a733add71cbc3886fa8c49f7ef2a
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 16:37:40 2011 -0500
+
+ change version number
+
+commit 10ba6bf4f16692760f696f7b17f3719065786f77
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 16:34:08 2011 -0500
+
+ Change the order of PL; change SP to int32_t
+
+commit c5cc2a8036a9c3579fbfde651efec4f6763b0228
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 14:52:03 2011 -0500
+
+ claim X defined in the header
+
+commit 4ee8cb29f6092fd14a89f0cc5d3575112a204f39
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 14:40:24 2011 -0500
+
+ minor changes
+
+commit 00065e9336a2831dc53bee7da2f4719845be1a2a
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 11:39:06 2011 -0500
+
+ fixed an error in the BCF spec
+
+commit 1e2a73afcb72a02aa448718cb017c0438de89f90
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 11:36:40 2011 -0500
+
+ update BCF spec
+
+commit dbf8eedaa38a405cb2fba5b3952b85776f51d035
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 11:28:43 2011 -0500
+
+ update BCF spec
+
+commit eed1d91af9fad3c9d965333a55e623757f9c4e9d
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 09:51:39 2011 -0500
+
+ fixed a flaw in targetcut
+
+commit 59bc980bb832b92a8b0cc244cf106e6150e4db6f
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 00:54:35 2011 -0500
+
+ update manual page
+
+commit fcc4738c4abdca79e3de159e21208df1b98ac76c
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 00:45:39 2011 -0500
+
+ update version format
+
+commit 5748639ae542b7f6b853562edc2bb3faf43030e4
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 00:45:12 2011 -0500
+
+ update version number
+
+commit 06b44cc366cf27ce8976ee6a05810a0b3c48b56d
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 00:44:21 2011 -0500
+
+ update version number
+
+commit ab7f4529d12739ff66fd4c09af9d992ab59c53ef
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 25 00:42:55 2011 -0500
+
+ various help message
+
+commit a092e1f6f963272f8bb23616986ddaf604fd0f82
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 24 23:43:13 2011 -0500
+
+ disable unfinished functionality
+
+commit f00a78db72b14ee4c6689fc13f20ed31aeaecd40
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 24 10:04:56 2011 -0500
+
+ added "const" to bcf_p1_cal()
+
+commit 91049c4a8db3bf50dcc9d07506f22fa4ca5b5a96
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 23 11:53:47 2011 -0500
+
+ randomly allocate unphased reads
+
+commit f4405354a8d4cb3441141fa734573031059d7f57
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 22 15:36:07 2011 -0500
+
+ fixed a typo
+
+commit 3075e4dc5c7c9d954426aabda6a73fa788357100
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 22 15:33:40 2011 -0500
+
+ make output more informative
+
+commit 628cf3235e2815a40acf089fb1d3357be6437787
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 22 14:50:06 2011 -0500
+
+ change the scoring rule; change default k to 13
+
+commit f22fd99831e4b5c74f898719216f359dbe987bbf
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 22 14:45:15 2011 -0500
+
+ update scoring in masking
+
+commit 2f23547b81984555032aa0eefd064b8e07986fdc
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 22 14:37:17 2011 -0500
+
+ remove dropreg()
+
+commit 4d8b6b1f1f331ca9041983c66e34a857c3b8f1bb
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 22 13:10:16 2011 -0500
+
+ accept files from stdin
+
+commit 9b50c5038e6fc0185e29ca5b50fe0806a9a939b9
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 22 11:16:57 2011 -0500
+
+ fixed a bug in consensus generation
+
+commit 1332ab32fb788fdc81b2ba8653b905d106238fad
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 21 22:53:23 2011 -0500
+
+ print dropped fragments
+
+commit a288761b4ca1584e51076a71cbc4d72fe923dda1
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 21 22:37:04 2011 -0500
+
+ bugfix: singletons are not phased
+
+commit 683365f534c0223dea7d72532015ac16a45ba22b
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 21 17:27:10 2011 -0500
+
+ output singleton blocks
+
+commit 841a4609084d81f1bc81e0b00dd806002461e7d9
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 21 15:58:55 2011 -0500
+
+ fixed a bug; not working with -l right now
+
+commit fdd57ea31732b5516dc212d72174b60206952636
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 21 15:17:00 2011 -0500
+
+ skip mapQ==0 reads
+
+commit 4eb6ba75c23c1c9be5f76814fa1b93a2e304b2af
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 21 14:03:03 2011 -0500
+
+ print the "targetcut" command
+
+commit 0123d9559ba58b026c0dfd15bc26019a193cd21a
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 21 11:22:13 2011 -0500
+
+ allow to set the maximum depth
+
+commit 0f92eb248a4d06645b2c3d736a0faea8a7a9f731
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 21 09:56:41 2011 -0500
+
+ use a proper error model to call hets
+
+commit 587a01504af5aea6288740d121dccf48fb8a75f4
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 21 09:16:38 2011 -0500
+
+ phase is UNFINISHED; strip RG when merging
+
+commit 723bf3cd79e4f4a558373d4c707fa6b3db0fb357
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Feb 19 23:38:11 2011 -0500
+
+ use a proper model to compute consensus
+
+commit 891a6b02d4a9af2ed98fbaac4915bf1f0da4f6c8
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Feb 19 22:14:19 2011 -0500
+
+ added comment
+
+commit 8b55e0a581ecc9e4ba754d1f3c8784f3038b6e48
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 18 17:23:39 2011 -0500
+
+ change the output format
+
+commit 75c36e8c563eddd0a362ba3b38cf0aea21aafb1f
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 15 20:31:00 2011 -0500
+
+ fixed a bug in writing BAM
+
+commit bb0ce52f066cfebaa35a125d57b353bb717a5165
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 23:39:09 2011 -0500
+
+ skip uncovered; unknown alleles taken as X
+
+commit ba67f4d119c7d06907db3015d337d9a01a3fc9fe
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 23:21:19 2011 -0500
+
+ fixed a bug
+
+commit e4448d49e6129a5e1ee9c7f04f43612f12d6aad6
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 22:43:09 2011 -0500
+
+ prepare to read hets from a list; unfinished
+
+commit 129ea29c1f12177c0a7c3e21676f6210370fc59b
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 16:32:22 2011 -0500
+
+ updated khash.h to 0.2.5
+
+commit 15b44ed93bd949dffcf79ac8dbea6d9b7dfcb58c
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 16:15:04 2011 -0500
+
+ use the latest version of khash
+
+commit 486c05f06f44d981dfb2069bcb43e4b35fd8389c
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 15:04:40 2011 -0500
+
+ change the default -k to 11
+
+commit 07cf9d1e443d73cf053de38dd01671e3781f6e29
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 14:50:51 2011 -0500
+
+ sort fragments by vpos instead of by beg
+
+commit d0d3e7faabf5cbb7e5ff7b294f7e220da807c4c0
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 14:45:41 2011 -0500
+
+ shuffling the two haplotypes for better randomness
+
+commit 3be28eaf5f6033229aedf12ddb11a0084ba01cd8
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 14:09:17 2011 -0500
+
+ write chimeras to a separate BAM
+
+commit 80ccbc26f43918fe42be123cc1da9d3d7ce30816
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 13:54:13 2011 -0500
+
+ no mem leak/violation on small files; correctness is not checked
+
+commit 5c923867432fa14c26a19e3782e7f48d4080f6ac
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 14 13:50:25 2011 -0500
+
+ bam separation; at least not immediate segfault
+
+commit cea2643ec30a59735bf89b2f562b563bf7263e79
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Feb 13 23:24:11 2011 -0500
+
+ on the way to implement BAM separation; unfinished
+
+commit 964269cd15036a470ca89e43d0952201a0825671
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Feb 13 18:07:56 2011 -0500
+
+ keep singletons in the hash table
+
+commit 2d4aa649bd670d5e038a1acaefd33c5fe24ae0e8
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Feb 13 17:42:24 2011 -0500
+
+ Revert "prepare to add bam separation"
+
+ This reverts commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f.
+
+commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Feb 13 00:24:28 2011 -0500
+
+ prepare to add bam separation
+
+commit d211e652d93791d2e112d334added243ffe5fc3e
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Feb 12 18:50:20 2011 -0500
+
+ accelerate kstrtok
+
+commit 2d6af49d331ff5afe7b9e9b102e79d7d4512fdbe
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 11 21:08:21 2011 -0500
+
+ split unlinked blocks
+
+commit 68e4cd1b560b0a6fd4c77e5e51eadde9fda26ea4
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 11 10:47:58 2011 -0500
+
+ remove heading and tailing ambiguous positions
+
+commit d2b685141426a902ae76660c1fbe8020da150cf8
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 11 10:02:21 2011 -0500
+
+ code clean up for further features
+
+commit c6980e062d55928b59f287c03e599dd5a37ed509
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 11 08:00:08 2011 -0500
+
+ change /64 to >>6; the latter is faster
+
+commit 91635b9c2687f24d72ee6a8aad2050a79bb8400f
+Merge: 41d4df2 9a7e155
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 11 01:22:55 2011 -0500
+
+ Merge branch 'master' into devel
+
+commit 9a7e155cc591c1b6c9f7f9cb939364a6becb65b2
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 11 01:21:07 2011 -0500
+
+ output an unrecognized field as '.'; autofix GL/PL
+
+commit 41d4df2e9545e9abe97151cfe5d6c763f3d00db1
+Merge: c00c41c aacce0c
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 10 23:00:14 2011 -0500
+
+ Merge branch 'master' into devel
+
+commit aacce0ce7276f451e4fddf81832f9e5f7f65198b
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 10 22:57:53 2011 -0500
+
+ finished VCF->BCF conversion
+
+commit 0e875df643e41d848b709e2fa877de8ae53cdd4c
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 10 21:57:28 2011 -0500
+
+ fixed a bug in reading VCF files
+
+commit c00c41c2a5da69cccea64adb542a0b365e56b4fc
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 10 16:28:37 2011 -0500
+
+ suppres one-allele blocks
+
+commit 2e2354b673722e2f00d72970a043f80a66270da1
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 10 16:06:56 2011 -0500
+
+ fixed the bug in filtering
+
+commit d971e1fe24de4ecaf94055efffc5f641e2bdb563
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 10 12:24:23 2011 -0500
+
+ prepare to add filtering; buggy right now
+
+commit a0a5a3fbf504c3b02f7b9212e72315c1047cc249
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 10 11:55:02 2011 -0500
+
+ make masking optional
+
+commit 28db71ccd95054a5f8a47c2332794f8968f6a822
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 10 11:40:47 2011 -0500
+
+ routine to mask poorly called regions
+
+commit a3f6c439262bc10a4067860440f4d4dde9e0c515
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 9 17:18:33 2011 -0500
+
+ code clean up: remove globals
+
+commit 0b711978492f6ad39d459d78723c299468906818
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 9 16:52:54 2011 -0500
+
+ output more information
+
+commit f69d217ae5b691bf42ad07a97f29a7cc6456046f
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 9 16:11:54 2011 -0500
+
+ fixed another bug in flipping
+
+commit d47882d549337fbcc251597508a2c7faf1bb92e2
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 9 16:01:35 2011 -0500
+
+ fixed a stupid bug in flipping
+
+commit e33f89de499496537f5fbde396a66557f0353f1b
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 9 15:54:42 2011 -0500
+
+ fix chimeras; a little weird...
+
+commit 03d3c1d0b945245108ce0942d4772536a32212c7
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 9 13:27:35 2011 -0500
+
+ no effective change; prepare to fix chimera
+
+commit 6bc0a4676dd2252085a6e67bb06daa5ae05a554f
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 9 11:52:58 2011 -0500
+
+ better count output
+
+commit dcac515439d25f71125d6de8111da417776ab9ce
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 9 10:31:07 2011 -0500
+
+ prepare for another way of filtering
+
+commit ca7e4f1899b86d2e077994c789e8f69d699b3cd9
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 8 16:10:08 2011 -0500
+
+ fixed the bug; I can do better.
+
+commit 0733f77b98af121bdcb198cea6151d159831bb9c
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 8 15:55:38 2011 -0500
+
+ fixed two bugs; still not working...
+
+commit 80f18cba9ba73c9592380fc1ecd53c351d294782
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 8 15:42:58 2011 -0500
+
+ filter false SNPs; NOT working right now
+
+commit 69a66e2f96d5b102cd712ff1527a3802fa84c590
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 8 14:39:09 2011 -0500
+
+ write sequence in the SAM format for debugging
+
+commit b6f1c9d160822af2b713be206f37bd6dde00546a
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 7 11:51:21 2011 -0500
+
+ fixed two bugs
+
+commit 400aa5c06100af9c47cd5e4ce8b95b7deb84f54b
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 7 11:22:38 2011 -0500
+
+ Optionally apply BAQ
+
+commit 4c82e0e19682e424f5cdb8381364114c307b329e
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Feb 7 01:23:31 2011 -0500
+
+ improved output; the result makes sense at a glance
+
+commit dc7853a581ab24bcc496e96b123ccf637e32ed1d
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Feb 6 14:12:43 2011 -0500
+
+ process per linked block instead of per chr
+
+commit e867d9c6c2e61d9e748e78163e5481dca5697a36
+Author: Heng Li <lh3@live.co.uk>
+Date: Sun Feb 6 00:45:46 2011 -0500
+
+ DP seems to work on toy examples
+
+commit 445ad72fc43d4354d56f5f759790e8ae0be73d02
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Feb 5 01:24:42 2011 -0500
+
+ implemented backtrack; not tested
+
+commit ba38e180b9cd545956583b22e97e09b4bb12073e
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 4 23:55:23 2011 -0500
+
+ More "correct" DP; backtrack not implemented
+
+commit d69761fd9351273ccd37ea431b10509add91e7cf
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 4 17:22:31 2011 -0500
+
+ scratch of dynamic programming; unfinished...
+
+commit 769ffcb44e26e59300791658801d321559b33858
+Author: Heng Li <lh3@live.co.uk>
+Date: Fri Feb 4 16:29:55 2011 -0500
+
+ UNFINISHED commit.
+
+commit 9adab9591317c3467f3d8cdf2d19ec1f65d1b5b7
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 3 16:20:59 2011 -0500
+
+ another way of counting; can be even faster
+
+commit bbafbdc01ed1ceaab44927def1ad47c4c78aeb9c
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Feb 3 14:48:20 2011 -0500
+
+ for backup
+
+commit eba7446389cad62a19133bced1386a4334dcab79
+Merge: a44a98e f01a593
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 2 14:06:07 2011 -0500
+
+ Merge branch 'master' into devel
+
+commit f01a5930445b5fda7e6b5b813ed63c652160ada2
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 2 11:31:54 2011 -0500
+
+ Better truncation warning when EOF is absent
+
+commit dd3ee5ed26c8bbef4a62fa5b2bfb0a75833f2c31
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 2 10:38:28 2011 -0500
+
+ fixed a typo in BCF/VCF headers
+
+commit b9d1137c55f401387113d1ad8a387489afe741db
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Feb 2 09:13:44 2011 -0500
+
+ fixed an out-of-boundary bug (fixed by Roel Kluin)
+
+commit a44a98e16559b9672e8a3492c8f8c640074b7ee2
+Merge: ef68a14 d0443d5
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 1 21:54:48 2011 -0500
+
+ Merge branch 'master' into devel
+
+commit d0443d5c2f648e0f69bd4c56eaac7868e501c18b
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 1 17:31:52 2011 -0500
+
+ improved sorting order checking
+
+commit ef68a14fab91399b2ecd38345936c3d6e7391cf3
+Merge: 1e597b3 1a39a2e
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 1 15:12:37 2011 -0500
+
+ Merge branch 'master' into devel
+
+commit 1a39a2eb08a270e20a34a0983e8bed6ffb3e2008
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 1 15:12:14 2011 -0500
+
+ more precise error message
+
+commit e028e7a47c02232e06a9dd3009262c00dede1060
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 1 14:48:01 2011 -0500
+
+ improved sorting order validation in index
+
+commit 1e597b3356744e2b791b12c9187f91c8054511d5
+Author: Heng Li <lh3@live.co.uk>
+Date: Tue Feb 1 14:44:27 2011 -0500
+
+ testing only; not working
+
+commit 5753ace1e54228822d8ee95f69943f586e42f6e8
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Jan 31 17:37:08 2011 -0500
+
+ reduce the effect of seq errors at the cost of SN
+
+commit 6f239ce5e0abd47babee33174476d48b723260d8
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Jan 31 17:29:34 2011 -0500
+
+ added testing code
+
+commit 3db42fe22d27d61ab5735cd2308f73d93def8ebe
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Jan 31 14:33:21 2011 -0500
+
+ routine for phasing fosmid resequencing (incomplete)
+
+commit ed88f2797323229ae8f38fbcd107b231007956a8
+Author: Heng Li <lh3@live.co.uk>
+Date: Mon Jan 31 10:12:53 2011 -0500
+
+ SAM output
+
+commit abc6acae28dc4794f6422255f077cf370d34e414
+Merge: f1985a9 b133dbf
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Jan 29 22:56:10 2011 -0500
+
+ Merge branch 'master' into devel
+
+commit b133dbf82de4e8cea5eb56e5bbf0c4b3e9368fd5
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Jan 29 22:37:11 2011 -0500
+
+ fixed a bug in tview on big-endian by Nathan Weeks
+
+commit 9d3fdaef29f91e21dbfcb9ff0165b9573e7c1042
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Jan 29 22:24:00 2011 -0500
+
+ update INSTALL
+
+commit 9d074a38bde53961f96157b6fb3683b6dded38d7
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Jan 29 21:56:25 2011 -0500
+
+ avoid a segfault when network connect fails
+
+commit f1985a93f7455b3ea1b0ef9b959d50b896ccd620
+Author: Heng Li <lh3@live.co.uk>
+Date: Sat Jan 29 21:53:18 2011 -0500
+
+ fixed a bug about bit ordering
+
+commit d09797db6fef648a6823cbe718d67664660c6ebe
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jan 27 16:53:19 2011 -0500
+
+ point out there are 4 or fewer free parameters
+
+commit 5fd1717650ed68ab6c55d094d1648c16a054891a
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jan 27 16:09:18 2011 -0500
+
+ updated .gitignore
+
+commit fccb19fbe8f9de91f59d85bb49a248683dc6266c
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jan 27 16:08:14 2011 -0500
+
+ fixed a bug; better scoring
+
+commit b4dcb844bde3d09eedcd9f6832186ece60ae5afd
+Merge: ffc3e89 6f502de
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jan 27 14:50:30 2011 -0500
+
+ Merge branch 'master' into devel
+
+commit 6f502dec46b18dae4bb5b2319715d028b5e193d0
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jan 27 14:47:31 2011 -0500
+
+ skip unmapped and ref-skip reads in indel calling
+
+commit 3639f37dd8257b24560c35effcc3b6c16c3c1bcb
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jan 27 14:19:15 2011 -0500
+
+ fixed an out-of-boundary bug in rare cases
+
+commit ffc3e89678ab9052b84f403da1e43044b045e73f
+Author: Heng Li <lh3@live.co.uk>
+Date: Thu Jan 27 14:00:17 2011 -0500
+
+ targetcut can be compiled, though probably buggy
+
+commit f452b3ac51306865ddde31a8d715b155d4d3e6e6
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jan 26 18:58:43 2011 -0500
+
+ this is for a very special application...
+
+commit ca1451c6406c7ee757cb31349ea0b8de70db0656
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jan 26 18:48:09 2011 -0500
+
+ fixed compiling errors
+
+commit 085b87a7642865f17239fb6a436e626e25417838
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jan 26 18:45:09 2011 -0500
+
+ This script was put in a wrong place...
+
+commit 090d360828622520de60385af4928ce1aebe0e48
+Author: Heng Li <lh3@live.co.uk>
+Date: Wed Jan 26 18:33:58 2011 -0500
+
+ Imported from samtools-r902
------------------------------------------------------------------------
r108 | lh3lh3 | 2009-01-20 11:56:45 +0000 (Tue, 20 Jan 2009) | 2 lines
Changed paths:
projects / samtools.git / commitdiff