------------------------------------------------------------------------
-r451 | lh3lh3 | 2009-09-02 10:44:48 +0100 (Wed, 02 Sep 2009) | 4 lines
+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
* improved the help message a little bit
------------------------------------------------------------------------
-r450 | lh3lh3 | 2009-09-02 09:55:55 +0100 (Wed, 02 Sep 2009) | 3 lines
+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
* fixed a bug in bam_color.c (on behalf of Nils Homer)
------------------------------------------------------------------------
-r449 | lh3lh3 | 2009-08-29 20:36:41 +0100 (Sat, 29 Aug 2009) | 4 lines
+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
* in import, give a warning if the read is aligned but there is no CIGAR.
------------------------------------------------------------------------
-r448 | lh3lh3 | 2009-08-19 09:44:28 +0100 (Wed, 19 Aug 2009) | 3 lines
+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
* fixed an issue when the last CIGAR is I or D
------------------------------------------------------------------------
-r447 | lh3lh3 | 2009-08-17 09:34:57 +0100 (Mon, 17 Aug 2009) | 3 lines
+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
* fixed a bug in bam_aux_get(): 'A' is not checked
------------------------------------------------------------------------
-r446 | lh3lh3 | 2009-08-17 09:33:17 +0100 (Mon, 17 Aug 2009) | 2 lines
+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 10:02:36 +0100 (Tue, 11 Aug 2009) | 3 lines
+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
* bug in "merge -n"
------------------------------------------------------------------------
-r443 | lh3lh3 | 2009-08-11 09:29:11 +0100 (Tue, 11 Aug 2009) | 4 lines
+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
* parse CIGAR "=" and "X" as "M"
------------------------------------------------------------------------
-r442 | lh3lh3 | 2009-08-07 21:56:38 +0100 (Fri, 07 Aug 2009) | 4 lines
+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
* fixed a bug in detecting unsorted bam in pileup
------------------------------------------------------------------------
-r441 | bhandsaker | 2009-08-05 14:41:28 +0100 (Wed, 05 Aug 2009) | 2 lines
+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
Change copyright notices now that MIT has approved open source distribution.
------------------------------------------------------------------------
-r440 | lh3lh3 | 2009-08-05 10:44:24 +0100 (Wed, 05 Aug 2009) | 3 lines
+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
* in flagstats, do not report singletons if both ends are unmapped
------------------------------------------------------------------------
-r439 | lh3lh3 | 2009-08-04 22:16:51 +0100 (Tue, 04 Aug 2009) | 2 lines
+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 21:50:43 +0100 (Tue, 04 Aug 2009) | 2 lines
+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 09:13:24 +0100 (Tue, 04 Aug 2009) | 3 lines
+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
* fixed a typo
------------------------------------------------------------------------
-r434 | lh3lh3 | 2009-08-03 10:40:42 +0100 (Mon, 03 Aug 2009) | 3 lines
+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
* in tview, press 'r' to show read names rather than sequences
------------------------------------------------------------------------
-r433 | lh3lh3 | 2009-08-02 19:13:35 +0100 (Sun, 02 Aug 2009) | 3 lines
+r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
Changed paths:
M /trunk/samtools/knetfile.c
* anyway, MinGW seems to have problem with "%lld".
------------------------------------------------------------------------
-r432 | lh3lh3 | 2009-08-02 00:32:07 +0100 (Sun, 02 Aug 2009) | 5 lines
+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
* PDCurses support in Windows
------------------------------------------------------------------------
-r431 | lh3lh3 | 2009-08-01 23:34:54 +0100 (Sat, 01 Aug 2009) | 2 lines
+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 23:21:07 +0100 (Sat, 01 Aug 2009) | 2 lines
+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 22:41:19 +0100 (Sat, 01 Aug 2009) | 3 lines
+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
* knetfile.c is now compatible with mingw-winsock
------------------------------------------------------------------------
-r428 | lh3lh3 | 2009-08-01 00:39:07 +0100 (Sat, 01 Aug 2009) | 2 lines
+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 | 2009-08-01 00:30:54 +0100 (Sat, 01 Aug 2009) | 5 lines
+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
* zlib headers and Windows version of libz.a are included in win32/
------------------------------------------------------------------------
-r426 | lh3lh3 | 2009-07-31 23:32:09 +0100 (Fri, 31 Jul 2009) | 3 lines
+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
* fixed a bug caused by recent modifications. Sorry.
------------------------------------------------------------------------
-r425 | lh3lh3 | 2009-07-31 23:23:51 +0100 (Fri, 31 Jul 2009) | 2 lines
+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 10:19:59 +0100 (Fri, 31 Jul 2009) | 5 lines
+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
* in tview, optionally allow to treat reference skip as deletion
------------------------------------------------------------------------
-r423 | lh3lh3 | 2009-07-30 22:00:36 +0100 (Thu, 30 Jul 2009) | 2 lines
+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 11:24:39 +0100 (Thu, 30 Jul 2009) | 6 lines
+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
* update ChangeLog
------------------------------------------------------------------------
-r421 | lh3lh3 | 2009-07-30 10:03:39 +0100 (Thu, 30 Jul 2009) | 3 lines
+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
* in view and pileup, load header from FASTA index if the input is SAM.
------------------------------------------------------------------------
-r420 | lh3lh3 | 2009-07-29 09:18:55 +0100 (Wed, 29 Jul 2009) | 2 lines
+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 09:52:33 +0100 (Tue, 28 Jul 2009) | 5 lines
+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
* add "unique" command to samtools.pl
------------------------------------------------------------------------
-r418 | lh3lh3 | 2009-07-24 14:04:19 +0100 (Fri, 24 Jul 2009) | 2 lines
+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 12:42:38 +0100 (Fri, 24 Jul 2009) | 3 lines
+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
* more help in "samtools view" due to the recent changes.
------------------------------------------------------------------------
-r416 | lh3lh3 | 2009-07-24 12:34:30 +0100 (Fri, 24 Jul 2009) | 3 lines
+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
* support import/export SAM with string tags
------------------------------------------------------------------------
-r415 | lh3lh3 | 2009-07-24 11:39:26 +0100 (Fri, 24 Jul 2009) | 3 lines
+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
* FLAG now can be in HEX
------------------------------------------------------------------------
-r414 | lh3lh3 | 2009-07-22 22:03:49 +0100 (Wed, 22 Jul 2009) | 2 lines
+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 22:19:40 +0100 (Tue, 21 Jul 2009) | 2 lines
+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 17:10:20 +0100 (Fri, 17 Jul 2009) | 2 lines
+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 15:29:21 +0100 (Fri, 17 Jul 2009) | 5 lines
+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
* bgzf.c: improved the compatibility with Windows headers
------------------------------------------------------------------------
-r407 | lh3lh3 | 2009-07-17 14:46:56 +0100 (Fri, 17 Jul 2009) | 5 lines
+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
* fillmd: cmd interface improvement
------------------------------------------------------------------------
-r406 | lh3lh3 | 2009-07-16 23:30:40 +0100 (Thu, 16 Jul 2009) | 2 lines
+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 23:30:11 +0100 (Thu, 16 Jul 2009) | 3 lines
+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
* improved the compatibility with PDCurses a little bit
------------------------------------------------------------------------
-r404 | lh3lh3 | 2009-07-16 23:23:52 +0100 (Thu, 16 Jul 2009) | 3 lines
+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
* compatible with PDCurses
------------------------------------------------------------------------
-r403 | lh3lh3 | 2009-07-16 22:39:39 +0100 (Thu, 16 Jul 2009) | 3 lines
+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
* fixed a bug in kseq.h for binary files (text files are fine)
------------------------------------------------------------------------
-r402 | lh3lh3 | 2009-07-16 11:49:53 +0100 (Thu, 16 Jul 2009) | 4 lines
+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
* improve portability to MinGW
------------------------------------------------------------------------
-r398 | lh3lh3 | 2009-07-13 10:21:36 +0100 (Mon, 13 Jul 2009) | 3 lines
+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)
* copy bam.h to bam-lite
------------------------------------------------------------------------
-r395 | lh3lh3 | 2009-07-13 10:12:57 +0100 (Mon, 13 Jul 2009) | 3 lines
+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
* added bam_pileup_file() and removed bam_lpileup_file()
------------------------------------------------------------------------
-r394 | lh3lh3 | 2009-07-13 00:35:10 +0100 (Mon, 13 Jul 2009) | 3 lines
+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
* http_proxy support in knetfile library (check http_proxy ENV)
------------------------------------------------------------------------
-r393 | lh3lh3 | 2009-07-12 23:57:07 +0100 (Sun, 12 Jul 2009) | 5 lines
+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
not seen the sideeffect so far.
------------------------------------------------------------------------
-r392 | lh3lh3 | 2009-07-12 18:50:55 +0100 (Sun, 12 Jul 2009) | 2 lines
+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 18:42:43 +0100 (Sun, 12 Jul 2009) | 3 lines
+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
* do not show a blank screen when no reads mapped
------------------------------------------------------------------------
-r390 | lh3lh3 | 2009-07-09 14:01:42 +0100 (Thu, 09 Jul 2009) | 4 lines
+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
* added bam_lite.c for light-weight BAM reading
------------------------------------------------------------------------
-r385 | lh3lh3 | 2009-07-07 16:53:29 +0100 (Tue, 07 Jul 2009) | 2 lines
+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 11:39:55 +0100 (Tue, 07 Jul 2009) | 2 lines
+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 11:20:06 +0100 (Tue, 07 Jul 2009) | 2 lines
+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
Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
------------------------------------------------------------------------
-r373 | lh3lh3 | 2009-07-07 10:26:57 +0100 (Tue, 07 Jul 2009) | 2 lines
+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
Release samtools-0.1.5
------------------------------------------------------------------------
-r372 | lh3lh3 | 2009-07-07 09:49:27 +0100 (Tue, 07 Jul 2009) | 3 lines
+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
* keep header text if "view -t" is used (by Gerton)
------------------------------------------------------------------------
-r371 | lh3lh3 | 2009-07-07 01:13:32 +0100 (Tue, 07 Jul 2009) | 2 lines
+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 22:24:34 +0100 (Thu, 02 Jul 2009) | 2 lines
+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 13:36:53 +0100 (Thu, 02 Jul 2009) | 4 lines
+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
* remove the debugging code in bam_aux_get() (Drat!)
------------------------------------------------------------------------
-r368 | lh3lh3 | 2009-07-02 11:32:26 +0100 (Thu, 02 Jul 2009) | 6 lines
+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
* small memory leak may be present on failure, though
------------------------------------------------------------------------
-r367 | lh3lh3 | 2009-06-30 16:18:42 +0100 (Tue, 30 Jun 2009) | 2 lines
+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
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-r366 | lh3lh3 | 2009-06-30 15:35:21 +0100 (Tue, 30 Jun 2009) | 2 lines
+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
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-r365 | lh3lh3 | 2009-06-30 14:04:30 +0100 (Tue, 30 Jun 2009) | 3 lines
+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
* download the BAM index file if it is not found in the current working directory.
------------------------------------------------------------------------
-r364 | lh3lh3 | 2009-06-30 12:39:07 +0100 (Tue, 30 Jun 2009) | 3 lines
+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
* knetfile: report error when the file is not present on FTP
------------------------------------------------------------------------
-r363 | lh3lh3 | 2009-06-29 23:23:32 +0100 (Mon, 29 Jun 2009) | 4 lines
+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
* bgzf: cache recent blocks (disabled by default)
------------------------------------------------------------------------
-r362 | lh3lh3 | 2009-06-25 21:04:34 +0100 (Thu, 25 Jun 2009) | 2 lines
+r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/bgzf.c
write changelog
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-r361 | lh3lh3 | 2009-06-25 21:03:10 +0100 (Thu, 25 Jun 2009) | 3 lines
+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
* if a file is given on FTP, search locally for the BAM index
------------------------------------------------------------------------
-r360 | lh3lh3 | 2009-06-25 20:44:52 +0100 (Thu, 25 Jun 2009) | 5 lines
+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
* support knetfile library in BGZF
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-r359 | lh3lh3 | 2009-06-25 17:10:55 +0100 (Thu, 25 Jun 2009) | 2 lines
+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 13:53:19 +0100 (Thu, 25 Jun 2009) | 2 lines
+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 13:52:03 +0100 (Thu, 25 Jun 2009) | 3 lines
+r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
Changed paths:
A /trunk/samtools/knetfile.c
* preliminary version
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-r354 | lh3lh3 | 2009-06-24 14:02:25 +0100 (Wed, 24 Jun 2009) | 3 lines
+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
* fixed a memory leak in bam_view1(), although samtools is not using this routine.
------------------------------------------------------------------------
-r351 | lh3lh3 | 2009-06-18 00:16:26 +0100 (Thu, 18 Jun 2009) | 4 lines
+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
* hope this does not introduce new bugs...
------------------------------------------------------------------------
-r350 | lh3lh3 | 2009-06-16 14:37:01 +0100 (Tue, 16 Jun 2009) | 3 lines
+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
* fixed a small memory leak in pileup, caused by recent modifications
------------------------------------------------------------------------
-r347 | lh3lh3 | 2009-06-13 21:20:49 +0100 (Sat, 13 Jun 2009) | 3 lines
+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
* added `-S' to pileup, similar to `view -S'
------------------------------------------------------------------------
-r346 | lh3lh3 | 2009-06-13 17:52:31 +0100 (Sat, 13 Jun 2009) | 3 lines
+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
* allow to select a read group at view command-line
------------------------------------------------------------------------
-r344 | lh3lh3 | 2009-06-13 14:06:24 +0100 (Sat, 13 Jun 2009) | 2 lines
+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
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-r343 | lh3lh3 | 2009-06-13 14:01:22 +0100 (Sat, 13 Jun 2009) | 2 lines
+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
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-r342 | lh3lh3 | 2009-06-13 13:58:48 +0100 (Sat, 13 Jun 2009) | 2 lines
+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 13:00:08 +0100 (Sat, 13 Jun 2009) | 6 lines
+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
* remove the support of -q in pileup
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-r340 | lh3lh3 | 2009-06-13 11:17:14 +0100 (Sat, 13 Jun 2009) | 6 lines
+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
* detect NCURSES in bam_tview.c
------------------------------------------------------------------------
-r339 | lh3lh3 | 2009-06-13 10:35:19 +0100 (Sat, 13 Jun 2009) | 2 lines
+r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/INSTALL
update INSTALL
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-r338 | lh3lh3 | 2009-06-13 00:15:24 +0100 (Sat, 13 Jun 2009) | 4 lines
+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
command line
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-r337 | lh3lh3 | 2009-06-12 21:25:50 +0100 (Fri, 12 Jun 2009) | 4 lines
+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
* "samtools view" support "-u" command-line option
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-r336 | lh3lh3 | 2009-06-12 17:20:12 +0100 (Fri, 12 Jun 2009) | 5 lines
+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
* on old version of zlib, writing is not available
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-r335 | lh3lh3 | 2009-06-12 16:47:33 +0100 (Fri, 12 Jun 2009) | 2 lines
+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...
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-r334 | lh3lh3 | 2009-06-12 15:43:36 +0100 (Fri, 12 Jun 2009) | 5 lines
+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
* this version works with the latest Bio::DB::Sam (20090612)
------------------------------------------------------------------------
-r333 | lh3lh3 | 2009-06-12 15:33:42 +0100 (Fri, 12 Jun 2009) | 2 lines
+r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/ChangeLog
update ChangeLog
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-r332 | lh3lh3 | 2009-06-12 15:21:21 +0100 (Fri, 12 Jun 2009) | 2 lines
+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
fixed minor things in Makefile
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-r331 | lh3lh3 | 2009-06-12 15:07:05 +0100 (Fri, 12 Jun 2009) | 4 lines
+r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
M /trunk/samtools/bamtk.c
changes in the Makefile building system.
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-r330 | lh3lh3 | 2009-06-12 15:03:38 +0100 (Fri, 12 Jun 2009) | 2 lines
+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...
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-r329 | lh3lh3 | 2009-06-12 14:52:21 +0100 (Fri, 12 Jun 2009) | 3 lines
+r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/novo2sam.pl
* this version works with indels
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-r328 | lh3lh3 | 2009-06-12 14:50:53 +0100 (Fri, 12 Jun 2009) | 3 lines
+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
* update INSTALL instruction
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-r327 | lh3lh3 | 2009-06-12 14:18:29 +0100 (Fri, 12 Jun 2009) | 4 lines
+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
* unfinished! (will be soon)
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-r326 | lh3lh3 | 2009-06-12 14:12:03 +0100 (Fri, 12 Jun 2009) | 2 lines
+r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
Unfinished
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-r325 | lh3lh3 | 2009-06-10 16:27:59 +0100 (Wed, 10 Jun 2009) | 3 lines
+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
* further avoid wrong consensus calls in repetitive regions.
------------------------------------------------------------------------
-r324 | lh3lh3 | 2009-06-10 15:56:17 +0100 (Wed, 10 Jun 2009) | 4 lines
+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
* allow filtering on mapQ at the pileup command line
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-r323 | lh3lh3 | 2009-06-10 10:04:21 +0100 (Wed, 10 Jun 2009) | 3 lines
+r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* indels and SNPs use different mapping quality threshold
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-r322 | lh3lh3 | 2009-06-10 10:03:22 +0100 (Wed, 10 Jun 2009) | 2 lines
+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
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-r321 | lh3lh3 | 2009-06-09 09:21:48 +0100 (Tue, 09 Jun 2009) | 2 lines
+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
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-r320 | lh3lh3 | 2009-06-08 14:32:51 +0100 (Mon, 08 Jun 2009) | 2 lines
+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
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-r319 | lh3lh3 | 2009-06-08 14:22:33 +0100 (Mon, 08 Jun 2009) | 4 lines
+r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* optionally print filtered variants
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-r318 | lh3lh3 | 2009-06-08 14:14:26 +0100 (Mon, 08 Jun 2009) | 3 lines
+r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* combine snpFilter and indelFilter
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-r317 | lh3lh3 | 2009-06-08 11:31:42 +0100 (Mon, 08 Jun 2009) | 3 lines
+r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* change a default parameter
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-r316 | lh3lh3 | 2009-06-08 11:11:06 +0100 (Mon, 08 Jun 2009) | 5 lines
+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
* pileup: allow to output variant sites only
------------------------------------------------------------------------
-r312 | lh3lh3 | 2009-06-04 13:01:10 +0100 (Thu, 04 Jun 2009) | 3 lines
+r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* added pileup2fq
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-r311 | lh3lh3 | 2009-06-03 09:40:40 +0100 (Wed, 03 Jun 2009) | 2 lines
+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
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-r310 | lh3lh3 | 2009-06-01 14:35:13 +0100 (Mon, 01 Jun 2009) | 3 lines
+r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* fixed a typo
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-r309 | lh3lh3 | 2009-06-01 14:04:39 +0100 (Mon, 01 Jun 2009) | 3 lines
+r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
* snpFilter
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-r306 | lh3lh3 | 2009-05-28 11:49:35 +0100 (Thu, 28 May 2009) | 3 lines
+r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
Changed paths:
M /trunk/samtools/bgzf.c
* suggested by {kdj,jm18}@sanger.ac.uk
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-r305 | lh3lh3 | 2009-05-28 11:16:08 +0100 (Thu, 28 May 2009) | 2 lines
+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.
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-r304 | lh3lh3 | 2009-05-28 11:08:49 +0100 (Thu, 28 May 2009) | 3 lines
+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
* fixed a minor bug in printing headers
------------------------------------------------------------------------
-r297 | lh3lh3 | 2009-05-21 16:06:16 +0100 (Thu, 21 May 2009) | 2 lines
+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
Release samtools-0.1.4
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-r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
+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
* another similar bug in the indel caller
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-r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
+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
* fixed a critical bug in the indel caller
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-r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
+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
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-r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
+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
* open tview in the dot-view mode by default
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-r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
+r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
Changed paths:
M /trunk/samtools/samtools.1
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-r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
+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
* declare bam_aux_get_core() in bam.h
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-r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
+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
* As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
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-r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
+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
backward compatibility with Bio::DB::Sam
------------------------------------------------------------------------
-r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
+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
* rmdupse: do not remove unmapped reads
------------------------------------------------------------------------
-r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
+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 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
+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
* added 'rmdupse' command
------------------------------------------------------------------------
-r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
+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
* in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
------------------------------------------------------------------------
-r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
+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
* report an error if a non-* reference is present while @SQ is absent
------------------------------------------------------------------------
-r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
+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
* make samopen() recognize @SQ header lines
------------------------------------------------------------------------
-r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 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
* report error for file I/O error
------------------------------------------------------------------------
-r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
+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 14:52:25 +0100 (Tue, 05 May 2009) | 3 lines
+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
* use the new I/O interface in pileup
------------------------------------------------------------------------
-r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
+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
* unify the interface to BAM and SAM I/O
------------------------------------------------------------------------
-r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
+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
* allow hex with "pileup -m"
------------------------------------------------------------------------
-r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
+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
* I do not know if this also fixes the bug causing assertion failure in the tview
------------------------------------------------------------------------
-r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
+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
* fixed a bug when there are reads without coordinates
------------------------------------------------------------------------
-r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
+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
added missing files
------------------------------------------------------------------------
-r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
+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
improve large file support in compilation
------------------------------------------------------------------------
-r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
+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 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
+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
fixed various issues about the GNU building scripts
------------------------------------------------------------------------
-r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
+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
* enhanced support of displaying color-space reads
------------------------------------------------------------------------
-r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
+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
* fixed segfault for unmapped reads
------------------------------------------------------------------------
-r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
+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
* consensus calling now works with "=", but indel calling not
------------------------------------------------------------------------
-r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
+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
* fixed a memory leak
------------------------------------------------------------------------
-r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
+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
* the plain pileup now support "=" bases, but consensus calling and glfgen may fail
------------------------------------------------------------------------
-r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
+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
* added tagview for testing bam_aux
------------------------------------------------------------------------
-r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
+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
* fixed a bug in pileup: the first read in a chromosome may not be printed
------------------------------------------------------------------------
-r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
+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 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
+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 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
+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
* make samtools more robust to weird input such as empty file
------------------------------------------------------------------------
-r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
+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
prepare for release 0.1.3
------------------------------------------------------------------------
-r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
+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 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines
+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
* fixed a small memory leak in tview
------------------------------------------------------------------------
-r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines
+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
* fixed a bug in rmdup when there are unmapped reads
------------------------------------------------------------------------
-r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines
+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 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines
+r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
Changed paths:
M /trunk/samtools/misc/samtools.pl
on the new pileup indel line implemented in samtools-0.1.2-25
------------------------------------------------------------------------
-r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines
+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
containing indels
------------------------------------------------------------------------
-r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines
+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 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines
+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
* allow empty header
------------------------------------------------------------------------
-r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines
+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
* recognize '*' at the QUAL field
------------------------------------------------------------------------
-r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines
+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
* the field separater is TAB only, now
------------------------------------------------------------------------
-r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines
+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 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines
+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
* fixed a nasty bug in `fixmate'
------------------------------------------------------------------------
-r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines
+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
make the script robust to the bugs in SOAP-2.1.7
------------------------------------------------------------------------
-r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines
+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
* check if file is truncated in flagstat
------------------------------------------------------------------------
-r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines
+r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
Changed paths:
M /trunk/samtools/bamtk.c
* print the header if requested
------------------------------------------------------------------------
-r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines
+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
* fixed a minor bug reported by Nils Homer
------------------------------------------------------------------------
-r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines
+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
rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
------------------------------------------------------------------------
-r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines
+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)
* rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)
------------------------------------------------------------------------
-r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines
+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
* added my kstring library for a bit complex parsing of the position list.
------------------------------------------------------------------------
-r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines
+r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/soap2sam.pl
* more robust to truncated soap output
------------------------------------------------------------------------
-r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines
+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 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines
+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
* generate RMS of mapQ instead of max mapQ
------------------------------------------------------------------------
-r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines
+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
* implemented GLFv3
------------------------------------------------------------------------
-r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines
+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
* fixed a minor bug in displaying pileup
------------------------------------------------------------------------
-r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines
+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
* optionally print SAM header
------------------------------------------------------------------------
-r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines
+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
* use "GLF\3" as the magic for GLFv3 files
------------------------------------------------------------------------
-r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines
+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
* update to GLFv3: pos is changed to offset for better compression
------------------------------------------------------------------------
-r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines
+r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
Changed paths:
M /trunk/samtools/misc/wgsim.c
* fixed a bug in simulating indels
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-r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines
+r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
Changed paths:
M /trunk/samtools/misc/wgsim.c
not like long read names.
------------------------------------------------------------------------
-r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines
+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
* make the script work with color reads
------------------------------------------------------------------------
-r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines
+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 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines
+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
* change in accordant with wgsim
------------------------------------------------------------------------
-r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines
+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
* fixed a bug in bam_fetch, caused by completely contained adjacent chunks
------------------------------------------------------------------------
-r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines
+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.
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-r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines
+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
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-r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines
+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
* fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
------------------------------------------------------------------------
-r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines
+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
* fixed a minor bug in flagstat
------------------------------------------------------------------------
-r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines
+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
* improve indel caller by setting maximum window size
------------------------------------------------------------------------
-r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines
+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
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-r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines
+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 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines
+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 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines
+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.
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-r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines
+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
* improve flagstat report a little bit
------------------------------------------------------------------------
-r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
+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
* added flagstat command
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-r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
+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
Release SAMtools-0.1.2
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-r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
+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
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-r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
+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
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-r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
+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
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-r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
+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
update documentation and ChangeLog
------------------------------------------------------------------------
-r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
+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
* fixed a bug in "merge" command line
------------------------------------------------------------------------
-r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
+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)
* all future development will happen here
------------------------------------------------------------------------
-r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
+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
* all future development will happen here at trunk/
------------------------------------------------------------------------
-r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
+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 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
+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
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-r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
+r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/NEWS
M /branches/dev/samtools/bamtk.c
Release samtools-0.1.1
------------------------------------------------------------------------
-r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
+r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
Changed paths:
M /branches/dev/samtools/bam_aux.c
M /branches/dev/samtools/bam_index.c
* prepare to release 0.1.1
------------------------------------------------------------------------
-r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
+r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/examples
A /branches/dev/samtools/examples/00README.txt
example
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-r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
+r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
update ChangeLog
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-r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
+r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/misc/export2sam.pl
* fixed several bugs
------------------------------------------------------------------------
-r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
+r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/misc/export2sam.pl
convert Export format to SAM; not thoroughly tested
------------------------------------------------------------------------
-r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
+r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_plcmd.c
* tview: fixed a minor bug
------------------------------------------------------------------------
-r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
+r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
Changed paths:
D /branches/dev/samtools/misc/all2sam.pl
remove all2sam.pl
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-r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
+r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/COPYING
M /branches/dev/samtools/bam.h
Added copyright information and a bit more documentation. No code change.
------------------------------------------------------------------------
-r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
+r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
* improved efficiency of the indel caller for spliced alignments
------------------------------------------------------------------------
-r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
+r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
* a bit code cleanup: reduce the dependency between source files
------------------------------------------------------------------------
-r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
+r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_plcmd.c
* fixed a memory leak
------------------------------------------------------------------------
-r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
+r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
M /branches/dev/samtools/bam.h
update documentation, ChangeLog and a comment
------------------------------------------------------------------------
-r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
+r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
* updated documentation
------------------------------------------------------------------------
-r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
+r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* fixed another bug in maqcns when there is a nearby deletion
------------------------------------------------------------------------
-r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
+r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bam_pileup.c
I am not quite sure why the previous version may have problem.
------------------------------------------------------------------------
-r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
+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
bindings.
------------------------------------------------------------------------
-r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
+r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bgzf.c
Fix bug in tell() after reads that consume to the exact end of a block.
------------------------------------------------------------------------
-r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
+r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/samtools.1
update manual
------------------------------------------------------------------------
-r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
+r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bamtk.c
* made the parser a bit more robust
------------------------------------------------------------------------
-r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
+r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
* in bam_index.c, check potential bugs in the underlying I/O library
------------------------------------------------------------------------
-r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
+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 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
+r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_pileup.c
* made pileup take the reference sequence
------------------------------------------------------------------------
-r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
+r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bamtk.c
* in parser, correctl parse "=" at the MRNM field.
------------------------------------------------------------------------
-r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
+r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/maq2sam.c
fixed a bug in handling maq flag 64 and 192
------------------------------------------------------------------------
-r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
+r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
also calculate unordered md5sum check
------------------------------------------------------------------------
-r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
+r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
fixed a minor bug when there are space in the sequence
------------------------------------------------------------------------
-r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
+r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/md5fa.c
fixed a potential memory leak
------------------------------------------------------------------------
-r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
+r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_import.c
M /branches/dev/samtools/bam_index.c
* fixed a bug in import: bin is wrongly calculated
------------------------------------------------------------------------
-r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
+r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/misc/all2sam.pl
nothing, really
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-r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
+r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/kseq.h
* added md5sum utilities
------------------------------------------------------------------------
-r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
+r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam_import.c
* also compile stand-alone faidx
------------------------------------------------------------------------
-r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
+r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.h
M /branches/dev/samtools/bam_sort.c
* sorting by read names is available
------------------------------------------------------------------------
-r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
+r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam.h
* format change to meet the latest specification
------------------------------------------------------------------------
-r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
+r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/misc/maq2sam.c
* change maq2sam to meet the latest specification
------------------------------------------------------------------------
-r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
+r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
M /branches/dev/samtools/razf.h
considerable code clean up in razf
------------------------------------------------------------------------
-r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
+r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/ChangeLog
M /branches/dev/samtools/Makefile
make RAZF optional in faidx.c
------------------------------------------------------------------------
-r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
+r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
* added routines for retrieving aux data, NOT TESTED YET!
------------------------------------------------------------------------
-r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
+r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
Changed paths:
M /branches/dev/samtools/bam.c
M /branches/dev/samtools/bam_import.c
* supporting hex strings
------------------------------------------------------------------------
-r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
+r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/bam_maqcns.c
M /branches/dev/samtools/bamtk.c
* fixed the bug in maqcns
------------------------------------------------------------------------
-r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
+r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
* add MAQ consensus caller, currently BUGGY!
------------------------------------------------------------------------
-r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
+r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_pileup.c
M /branches/dev/samtools/bam_tview.c
* better coordinates and reference sequence
------------------------------------------------------------------------
-r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
+r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/ChangeLog
new ChangeLog
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-r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
+r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
D /branches/dev/samtools/ChangeLog
A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)
the log of my personal SVN repository.
------------------------------------------------------------------------
-r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
+r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bamtk.c
* use BGZF by default, now
------------------------------------------------------------------------
-r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
+r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
M /branches/dev/samtools/bamtk.c
* give more warnings when the file is truncated (or due to bugs in I/O library)
------------------------------------------------------------------------
-r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
+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 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
+r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
M /branches/dev/samtools/bamtk.c
also update the version number anyway to avoid confusion
------------------------------------------------------------------------
-r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
+r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
a change from Jue, but I think it should not matter
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-r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
+r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
Changed paths:
M /branches/dev/samtools/razf.c
rarely happens, very rarely.
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-r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
+r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/razf.c
fixed a bug in razf, with the help of Jue
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-r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
+r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/bam_index.c
remove a comment
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-r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
+r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
M /branches/dev/samtools/Makefile
M /branches/dev/samtools/bam.h
* Jue has updated razf to realize Bob's scheme
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-r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
+r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools/samtools.1
the manual page
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-r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
+r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
Changed paths:
A /branches/dev/samtools/ChangeLog
A /branches/dev/samtools/Makefile
The current version is: 0.1.0-42. All future development will happen here.
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-r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
+r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
A /branches/dev/samtools
projects / samtools.git / blobdiff