From: Heng Li Date: Fri, 9 Mar 2012 02:47:29 +0000 (+0000) Subject: Removed SVN ChangeLog; merged my private github Log to ChangeLog.old X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=6a5b7e3a825486f11aed798ebe0790c6d3196625 Removed SVN ChangeLog; merged my private github Log to ChangeLog.old --- diff --git a/ChangeLog b/ChangeLog deleted file mode 100644 index a471838..0000000 --- a/ChangeLog +++ /dev/null @@ -1,5948 +0,0 @@ ------------------------------------------------------------------------- -r925 | lh3lh3 | 2011-02-28 15:45:17 -0500 (Mon, 28 Feb 2011) | 2 lines -Changed paths: - M /trunk/samtools/phase.c - -minor changes to a heuristic rule - ------------------------------------------------------------------------- -r924 | lh3lh3 | 2011-02-28 15:24:04 -0500 (Mon, 28 Feb 2011) | 4 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bcftools/vcfutils.pl - M /trunk/samtools/phase.c - - * 0.1.12-r924:126 - * fixed a bug in phase (due to recent changes) - * fixed a bug in vcf2fq - ------------------------------------------------------------------------- -r923 | lh3lh3 | 2011-02-28 12:57:39 -0500 (Mon, 28 Feb 2011) | 5 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/phase.c - - * put version number in bam.h - * write version to BCF - * in phase, change the default -q to 37 - * output a little more information during phasing - ------------------------------------------------------------------------- -r922 | lh3lh3 | 2011-02-25 16:40:09 -0500 (Fri, 25 Feb 2011) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.tex - M /trunk/samtools/bcftools/bcf2qcall.c - M /trunk/samtools/bcftools/bcfutils.c - M /trunk/samtools/bcftools/ld.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/vcf.c - M /trunk/samtools/cut_target.c - - * change the order of PL/GL according to the latest VCF spec - * change the type of SP to int32_t - ------------------------------------------------------------------------- -r921 | lh3lh3 | 2011-02-25 14:40:56 -0500 (Fri, 25 Feb 2011) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.tex - -update the BCF spec - ------------------------------------------------------------------------- -r920 | lh3lh3 | 2011-02-25 00:59:27 -0500 (Fri, 25 Feb 2011) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - A /trunk/samtools/cut_target.c - M /trunk/samtools/errmod.h - M /trunk/samtools/faidx.c - M /trunk/samtools/khash.h - M /trunk/samtools/kstring.c - M /trunk/samtools/kstring.h - A /trunk/samtools/phase.c - M /trunk/samtools/samtools.1 - -added the phase command - ------------------------------------------------------------------------- -r918 | lh3lh3 | 2011-02-24 10:05:54 -0500 (Thu, 24 Feb 2011) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/prob1.h - -added "const" to bcf_p1_cal() - ------------------------------------------------------------------------- -r917 | lh3lh3 | 2011-02-24 09:36:30 -0500 (Thu, 24 Feb 2011) | 2 lines -Changed paths: - M /trunk/samtools/bam.c - -more meaningful BAM truncation message - ------------------------------------------------------------------------- -r916 | lh3lh3 | 2011-02-24 09:35:06 -0500 (Thu, 24 Feb 2011) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/vcf.c - - * automatically fix errors in GL - * output unrecognized FORMAT as "." - ------------------------------------------------------------------------- -r913 | lh3lh3 | 2011-02-10 22:59:47 -0500 (Thu, 10 Feb 2011) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/vcf.c - -finished VCF->BCF conversion - ------------------------------------------------------------------------- -r910 | petulda | 2011-02-03 03:13:48 -0500 (Thu, 03 Feb 2011) | 1 line -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - -Prevent division by zero ------------------------------------------------------------------------- -r909 | lh3lh3 | 2011-02-02 11:29:20 -0500 (Wed, 02 Feb 2011) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/call1.c - -fixed a typo in the VCF header - ------------------------------------------------------------------------- -r908 | lh3lh3 | 2011-02-02 11:28:24 -0500 (Wed, 02 Feb 2011) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam_index.c - - * fixed an out-of-boundary bug - * improved sorting order checking in index - ------------------------------------------------------------------------- -r907 | lh3lh3 | 2011-01-29 22:59:20 -0500 (Sat, 29 Jan 2011) | 4 lines -Changed paths: - M /trunk/samtools/INSTALL - M /trunk/samtools/bam_tview.c - M /trunk/samtools/knetfile.c - - * avoid a segfault when network connect fails - * update INSTALL - * fixed a bug in tview on big-endian by Nathan Weeks - ------------------------------------------------------------------------- -r903 | lh3lh3 | 2011-01-27 14:50:02 -0500 (Thu, 27 Jan 2011) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_md.c - - * fixed a rare memory issue in bam_md.c - * fixed a bug in indel calling related to unmapped and refskip reads - ------------------------------------------------------------------------- -r902 | lh3lh3 | 2011-01-23 21:46:18 -0500 (Sun, 23 Jan 2011) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/fet.c - -fixed two minor bugs in Fisher's exact test - ------------------------------------------------------------------------- -r899 | petulda | 2011-01-19 09:28:02 -0500 (Wed, 19 Jan 2011) | 1 line -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - -Skip sites with unknown ref ------------------------------------------------------------------------- -r898 | lh3lh3 | 2011-01-15 12:56:05 -0500 (Sat, 15 Jan 2011) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_md.c - -move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c - ------------------------------------------------------------------------- -r896 | lh3lh3 | 2011-01-06 10:52:15 -0500 (Thu, 06 Jan 2011) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/bcfutils.c - M /trunk/samtools/bcftools/call1.c - - * samtools-0.1.12-10 (r896) - * allow to exclude read groups in mpileup - ------------------------------------------------------------------------- -r895 | lh3lh3 | 2011-01-04 11:31:29 -0500 (Tue, 04 Jan 2011) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.tex - -sorry. It is SP not ST - ------------------------------------------------------------------------- -r894 | lh3lh3 | 2011-01-04 11:29:06 -0500 (Tue, 04 Jan 2011) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.tex - -added ST - ------------------------------------------------------------------------- -r893 | petulda | 2011-01-04 06:55:56 -0500 (Tue, 04 Jan 2011) | 1 line -Changed paths: - M /trunk/samtools/bcftools/call1.c - -Fixed a typo in read_samples ------------------------------------------------------------------------- -r892 | jmarshall | 2010-12-28 08:06:49 -0500 (Tue, 28 Dec 2010) | 9 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bcftools/Makefile - M /trunk/samtools/examples/Makefile - -System libraries go *after* user libraries in link commands, because -the user libraries may themselves have dependencies that are satisfied -by the system libraries. It's not rocket science! - -This makes a difference with some linkers; or with -static or --as-needed. - -The examples/Makefile fix is from Charles Plessy. -See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004 - ------------------------------------------------------------------------- -r891 | lh3lh3 | 2010-12-21 12:16:33 -0500 (Tue, 21 Dec 2010) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/bcfutils.c - M /trunk/samtools/bcftools/call1.c - - * samtools-0.1.12-9 (r891) - * allow to call SNPs from a subset of samples - ------------------------------------------------------------------------- -r889 | lh3lh3 | 2010-12-15 11:28:16 -0500 (Wed, 15 Dec 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.12-12 (r889) - * set mapQ as 20 if it equals 255 - ------------------------------------------------------------------------- -r888 | lh3lh3 | 2010-12-14 22:41:09 -0500 (Tue, 14 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - -When -B is applied to mpileup, still use paired reads only unless -A is flagged. - ------------------------------------------------------------------------- -r887 | lh3lh3 | 2010-12-14 22:37:05 -0500 (Tue, 14 Dec 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.12-6 (r887) - * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ. - ------------------------------------------------------------------------- -r886 | lh3lh3 | 2010-12-14 12:51:03 -0500 (Tue, 14 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - -(Arguably) improved the indel caller a tiny bit for lowCov data. - ------------------------------------------------------------------------- -r885 | petulda | 2010-12-14 04:55:46 -0500 (Tue, 14 Dec 2010) | 1 line -Changed paths: - M /trunk/samtools/bcftools/call1.c - -Fixed the VCF header to pass validation ------------------------------------------------------------------------- -r884 | lh3lh3 | 2010-12-12 23:02:19 -0500 (Sun, 12 Dec 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/vcfutils.pl - - * samtools-0.1.12-4 (r884) - * fixed a long-existing flaw in the INDEL calling model - ------------------------------------------------------------------------- -r883 | lh3lh3 | 2010-12-11 20:05:42 -0500 (Sat, 11 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcfutils.c - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/vcfutils.pl - -compute max SP and max GQ from sample genotypes - ------------------------------------------------------------------------- -r880 | lh3lh3 | 2010-12-10 10:50:54 -0500 (Fri, 10 Dec 2010) | 2 lines -Changed paths: - D /trunk/samtools/bcftools/bcf-fix.pl - -drop bcf-fix.pl as it is redundant by the latest changes - ------------------------------------------------------------------------- -r879 | lh3lh3 | 2010-12-10 10:50:29 -0500 (Fri, 10 Dec 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/vcf.c - - * fixed a minor issue in printing VCFs - * write bcftools specific INFO and FORMAT in the header - ------------------------------------------------------------------------- -r878 | lh3lh3 | 2010-12-10 10:09:14 -0500 (Fri, 10 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/bcfutils.c - M /trunk/samtools/bcftools/call1.c - -Make sure that the GT genotype field is the first - ------------------------------------------------------------------------- -r877 | lh3lh3 | 2010-12-08 17:27:05 -0500 (Wed, 08 Dec 2010) | 7 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.12-2 (r877) - - * allow to fine control the selection of indel candidates. The current - setting is okay for lowCov and highCov with ~100 samples, but it - skips too many indels for highCov with >250 samples. - - ------------------------------------------------------------------------- -r874 | lh3lh3 | 2010-12-07 22:40:35 -0500 (Tue, 07 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - -a spelling error.. - ------------------------------------------------------------------------- -r873 | lh3lh3 | 2010-12-07 22:39:57 -0500 (Tue, 07 Dec 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.12-1 (r873) - * added a switch to allow anomalous read pairs in calling - ------------------------------------------------------------------------- -r872 | lh3lh3 | 2010-12-07 14:43:54 -0500 (Tue, 07 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - -fixed a bug in vcf2fq - ------------------------------------------------------------------------- -r869 | lh3lh3 | 2010-12-05 01:18:06 -0500 (Sun, 05 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bamtk.c - -added a warning for the Windows version - ------------------------------------------------------------------------- -r868 | lh3lh3 | 2010-12-05 01:05:51 -0500 (Sun, 05 Dec 2010) | 4 lines -Changed paths: - M /trunk/samtools/bcftools/call1.c - -In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively. -According to the manual page, this change is valid. However, MinGW seems -to interpret "%lf" as "%Lf". - ------------------------------------------------------------------------- -r867 | lh3lh3 | 2010-12-05 00:35:43 -0500 (Sun, 05 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/Makefile.mingw - M /trunk/samtools/bam_aux.c - -bring back the windows support - ------------------------------------------------------------------------- -r866 | lh3lh3 | 2010-12-04 23:33:51 -0500 (Sat, 04 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_reheader.c - M /trunk/samtools/bcftools/vcfutils.pl - -Fixed a compiling error when knetfile is not used. - ------------------------------------------------------------------------- -r865 | lh3lh3 | 2010-12-04 00:13:22 -0500 (Sat, 04 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - -vcf->fastq - ------------------------------------------------------------------------- -r864 | lh3lh3 | 2010-12-03 17:12:30 -0500 (Fri, 03 Dec 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/prob1.h - - * remove "-f". Instead always compute consensus quality - * increase the upper limit of quality - ------------------------------------------------------------------------- -r863 | lh3lh3 | 2010-12-03 15:28:15 -0500 (Fri, 03 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - -more informative error message - ------------------------------------------------------------------------- -r862 | lh3lh3 | 2010-12-02 16:16:08 -0500 (Thu, 02 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/NEWS - M /trunk/samtools/bamtk.c - -Release samtools-0.1.12a - ------------------------------------------------------------------------- -r861 | lh3lh3 | 2010-12-02 15:55:06 -0500 (Thu, 02 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/call1.c - -a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect - ------------------------------------------------------------------------- -r859 | lh3lh3 | 2010-12-02 11:39:57 -0500 (Thu, 02 Dec 2010) | 2 lines -Changed paths: - M /trunk/samtools/NEWS - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - -Release samtools-0.1.12 - ------------------------------------------------------------------------- -r858 | lh3lh3 | 2010-12-02 11:24:41 -0500 (Thu, 02 Dec 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/bcf.c - - * samtools-0.1.11-1 (r858) - * fixed a bug in mpileup which causes segfaults - * bcftools: do not segfault when BCF contains errors - ------------------------------------------------------------------------- -r857 | lh3lh3 | 2010-11-30 23:52:50 -0500 (Tue, 30 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_index.c - -fixed a memory leak in bam_fetch() - ------------------------------------------------------------------------- -r856 | lh3lh3 | 2010-11-26 00:07:31 -0500 (Fri, 26 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bcftools/vcfutils.pl - - * fixed a memory violation - * added splitchr to vcfutils.pl - ------------------------------------------------------------------------- -r854 | lh3lh3 | 2010-11-23 09:05:08 -0500 (Tue, 23 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/ld.c - -fixed a typo/bug in r^2 computation - ------------------------------------------------------------------------- -r852 | lh3lh3 | 2010-11-21 22:20:20 -0500 (Sun, 21 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bamtk.c - -forget to change the version information - ------------------------------------------------------------------------- -r851 | lh3lh3 | 2010-11-21 22:16:52 -0500 (Sun, 21 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - M /trunk/samtools/bcftools/bcftools.1 - M /trunk/samtools/samtools.1 - -Release samtools-0.1.11 - ------------------------------------------------------------------------- -r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/prob1.h - - * samtools-0.1.10-9 (r844) - * added the "folded" or reference-free mode for variant calling - ------------------------------------------------------------------------- -r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/NEWS - M /trunk/samtools/bam_sort.c - -In merging, if -R is specified, do not abort if the sequence dictionary is different. - ------------------------------------------------------------------------- -r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines -Changed paths: - M /trunk/samtools/bam_sort.c - -When merging BAM headers, compare the list of target reference sequences -strictly (and fail/abort if there is a mismatch), but allow one list to be a -prefix of the other. (i.e., check that the lists are identical up until the -shorter runs out, and add the excess targets from the longer to the output.) - ------------------------------------------------------------------------- -r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.10 (r841) - * fixed a bug in pileup when the first CIGAR operation is D - * fixed a bug in view with range query - ------------------------------------------------------------------------- -r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.10-4 (r840) - - * drop the MNP caller. It is slow while does not diliver too much - benefit. Possibly I will work on it in future given more time. - - * there is a segfault in pileup - - * someone has reported segfault from view/index/sort - - ------------------------------------------------------------------------- -r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines -Changed paths: - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.10-6 (r839) - - * call MNPs without realignment because it seems to me that it is not - worthwhile to significantly slow down SNP calling. - - * the result looks quite different from the previous version. I have - work to do... - - ------------------------------------------------------------------------- -r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/knetfile.c - -Apply a patch by Rob Davis, which improves fault detection. - ------------------------------------------------------------------------- -r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - - * samtools-r836 - * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow) - ------------------------------------------------------------------------- -r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - - * modify the filtering rule: also filter SNPs around filtered indels - * added MNP filter - ------------------------------------------------------------------------- -r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.10-4 (r834) - * fixed a silly bug in printing MNP - * restrict to at most 1 alternative allele - ------------------------------------------------------------------------- -r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bamtk.c - -fixed a bug in printing MNPs - ------------------------------------------------------------------------- -r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - -minor change to how seqQ is applied - ------------------------------------------------------------------------- -r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.10 (r831) - * initial MNP caller - ------------------------------------------------------------------------- -r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - M /trunk/samtools/bamtk.c - -Release samtools-0.1.10 (r829) - ------------------------------------------------------------------------- -r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bamtk.c - -update version information: samtools-0.1.9-20 (r828) - ------------------------------------------------------------------------- -r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/call1.c - -bcftools: allow to skip indels - ------------------------------------------------------------------------- -r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_md.c - -remove ZQ if both BQ and ZQ are present - ------------------------------------------------------------------------- -r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - - * samtools-0.1.9-18 (r825) - * change the behaviour of calmd such that by default it does not change the base quality - ------------------------------------------------------------------------- -r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/samtools.1 - - * samtools-0.1.9-17 (r824) - * added command line options to change the default parameters in indel calling - * update the manual - ------------------------------------------------------------------------- -r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-r823 - * the BQ tag is now 64 shifted, not 33 shifted - ------------------------------------------------------------------------- -r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/vcfutils.pl - M /trunk/samtools/misc/samtools.pl - - * samtools-0.1.9-16 (r822) - * keep the raw depth because in indel calling, DP4 may be way off the true depth - ------------------------------------------------------------------------- -r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-15 (r821) - * calmd: write BQ - * skip realignment if BQ is present - ------------------------------------------------------------------------- -r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-14 (r820) - * penalize reads with excessive differences in indel calling - ------------------------------------------------------------------------- -r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-13 (r819) - * fixed a bug in pileup given refskip - ------------------------------------------------------------------------- -r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - - * samtools-r818 - * for indel calling, do two rounds of probabilistic realignments - ------------------------------------------------------------------------- -r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/vcfutils.pl - - * samtools-0.1.19-11 (r817) - * only initiate indel calling when 0.2% of reads contain a gap - ------------------------------------------------------------------------- -r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-10 (r816) - - * I know why the forward method fails. it is because of zero base - qualities. when that is fixed, the forward method seems to give - better results than Viterbi, as it should be. I am tired... - - ------------------------------------------------------------------------- -r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam2bcf_indel.c - -effectively revert to the viterbi version. The forward realignment gives too many false positives. - ------------------------------------------------------------------------- -r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-9 (r810) - * use forward, instead of viterbi, for realignment - * realignment is now quality aware - ------------------------------------------------------------------------- -r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/kprobaln.c - M /trunk/samtools/kprobaln.h - - * prepare to replace kaln with kprobaln in realignment - ------------------------------------------------------------------------- -r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - -fixed a typo - ------------------------------------------------------------------------- -r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.h - -use zlib for direct reading when BCF_LITE is in use - ------------------------------------------------------------------------- -r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - - * do not use reads containing too many mismatches for indel calling - * fixed a trivial bug in case of multi-allelic indels - ------------------------------------------------------------------------- -r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-8 (r809) - * fixed a bug in the indel caller - ------------------------------------------------------------------------- -r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - -minor change to makefile - ------------------------------------------------------------------------- -r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/vcfutils.pl - - * samtools-0.1.9-8 (r807) - * collect indel candidates only from specified platforms (@RG-PL) - * merge varFilter and filter4vcf in vcfutils.pl - ------------------------------------------------------------------------- -r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/prob1.h - -bcftools: compute equal-tail (Bayesian) credible interval - ------------------------------------------------------------------------- -r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - -added a double-hit filter to avoid overestimated indel likelihood - ------------------------------------------------------------------------- -r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-7 (r804) - * fixed a bug in the gap caller - ------------------------------------------------------------------------- -r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/prob1.c - - * samtools-0.1.9-6 (r803) - * mpileup: apply homopolymer correction when calculating GL, instead of before - * bcftools: apply a different prior to indels - ------------------------------------------------------------------------- -r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-5 (r802) - * relax tandem penalty. this will be made a command-line option in future. - ------------------------------------------------------------------------- -r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-4 (r801) - * fixed a minor issue in printing indel VCF - ------------------------------------------------------------------------- -r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bcftools/vcfutils.pl - -fixed another silly bug in mpileup's indel caller - ------------------------------------------------------------------------- -r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - -fixed a silly bug in the indel caller - ------------------------------------------------------------------------- -r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/sam_view.c - M /trunk/samtools/samtools.1 - -Incorporate patches by Marcel Martin for read counting. - ------------------------------------------------------------------------- -r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-2 (r797) - * mpileup: indel calling seems to be working - ------------------------------------------------------------------------- -r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/kaln.c - -indel calling is apparently working, but more information needs to be collected - ------------------------------------------------------------------------- -r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf_indel.c - -fixed a few bugs in the indel caller. Probably there are more. - ------------------------------------------------------------------------- -r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam.h - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - A /trunk/samtools/bam2bcf_indel.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/kaln.c - M /trunk/samtools/kaln.h - -prepare for the indel caller. It is not ready yet. - ------------------------------------------------------------------------- -r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam_plcmd.c - -Revert to r790. The recent changes are not good... - ------------------------------------------------------------------------- -r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam_plcmd.c - - * this revision is UNSTABLE - - * indel caller seems working, but it is very insensitive and has - several things I do not quite understand. - - ------------------------------------------------------------------------- -r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam_plcmd.c - -for backup. no effective changes - ------------------------------------------------------------------------- -r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - M /trunk/samtools/kprobaln.c - -fixed a minor problem in the example coming with kprobaln.c - ------------------------------------------------------------------------- -r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam_md.c - M /trunk/samtools/kaln.c - M /trunk/samtools/kaln.h - A /trunk/samtools/kprobaln.c - A /trunk/samtools/kprobaln.h - -Separate kaln and kprobaln as I am preparing further changes. At -present, the results should be identical to the previous. - - ------------------------------------------------------------------------- -r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line -Changed paths: - M /trunk/samtools/bam_plcmd.c - -Added -b option: read file names from a file ------------------------------------------------------------------------- -r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.9-2 (r787) - - * Allow to set a maximum per-sample depth to reduce memory. However, - BAQ computation is still applied to every read. The speed is not - improved. - - ------------------------------------------------------------------------- -r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/vcf.c - - * samtools-0.1.9-1 (r786) - * samtools: optionally perform exact test for each sample - ------------------------------------------------------------------------- -r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bcftools/bcf.c - -Optionally output "DP", the individual read depth - ------------------------------------------------------------------------- -r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/samtools.1 - -acknowledge Petr and John who have greatly contributed to the project. - ------------------------------------------------------------------------- -r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - -Release samtools-0.1.9 (r783) - ------------------------------------------------------------------------- -r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - -fixed a silly bug in pileup - ------------------------------------------------------------------------- -r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - - * samtools-0.1.8-22 (r781) - * made BAQ the default behavior of mpileup - * updated manual - * in merge, force to exit given inconsistent header when "-R" is not in use. - ------------------------------------------------------------------------- -r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.8-21 (r780) - * minor speedup to pileup - ------------------------------------------------------------------------- -r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/examples/toy.sam - -improve pileup a little bit - ------------------------------------------------------------------------- -r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.8-20 (r778) - * speed up pileup, although I do not know how much is the improvement - ------------------------------------------------------------------------- -r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_maqcns.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/examples/Makefile - - * samtools-0.1.8-19 (r777) - * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior - ------------------------------------------------------------------------- -r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_md.c - -remove local realignment (probabilistic realignment is still there) - ------------------------------------------------------------------------- -r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines -Changed paths: - M /trunk/samtools/sam_view.c - -Add the relevant filename or region to error messages, and cause a failure -exit status where appropriate. Based on a patch provided by Marcel Martin. - ------------------------------------------------------------------------- -r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines -Changed paths: - M /trunk/samtools/examples/toy.sam - M /trunk/samtools/kaln.c - - * Minor code changes. No real effect. - * change quality to 30 in toy.sam - ------------------------------------------------------------------------- -r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/examples/toy.fa - M /trunk/samtools/examples/toy.sam - -added another toy example - ------------------------------------------------------------------------- -r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/ld.c - M /trunk/samtools/bcftools/vcfutils.pl - -improve the LD statistics - ------------------------------------------------------------------------- -r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/vcfutils.pl - - * a minor fix to the -L option - * add ldstats to vcfutils.pl - ------------------------------------------------------------------------- -r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - -a minor change - ------------------------------------------------------------------------- -r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - A /trunk/samtools/bcftools/ld.c - -forget to add the key file - ------------------------------------------------------------------------- -r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/vcfutils.pl - - * vcfutils.pl: fixed a typo in help message - * added APIs: bcf_append_info() and bcf_cpy() - * calculate adjacent LD - ------------------------------------------------------------------------- -r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - -added filter for samtools/bcftools genetated VCFs - ------------------------------------------------------------------------- -r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - M /trunk/samtools/kaln.c - - * removed a comment line in kaln.c - * vcfutils.pl fillac works when GT is not the first field - ------------------------------------------------------------------------- -r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line -Changed paths: - A /trunk/samtools/bcftools/bcf-fix.pl - -Convert VCF output of "bcftools view -bgcv" to a valid VCF file ------------------------------------------------------------------------- -r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - A /trunk/samtools/bcftools/bcftools.1 - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/samtools.1 - - * samtools-0.1.8-18 (r763) - * added bcftools manual page - * minor fix to mpileup and view command lines - ------------------------------------------------------------------------- -r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/vcfutils.pl - - * vcfutils.pl qstats: calculate marginal ts/tv - * allow to call genotypes at variant sites - ------------------------------------------------------------------------- -r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines -Changed paths: - M /trunk/samtools/kaln.c - M /trunk/samtools/misc/HmmGlocal.java - -I am changing the gap open probability back to 0.001. It seems that -being conservative here is a good thing... - ------------------------------------------------------------------------- -r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/kaln.c - A /trunk/samtools/misc/HmmGlocal.java - - * samtools-0.1.8-17 (r760) - * the default gap open penalty is too small (a typo) - * added comments on hmm_realn - * Java implementation - ------------------------------------------------------------------------- -r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bamtk.c - -mark samtools-0.1.8-16 (r759) - ------------------------------------------------------------------------- -r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/kaln.c - -round to the nearest integer - ------------------------------------------------------------------------- -r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines -Changed paths: - M /trunk/samtools/kaln.c - -I was trying to accelerate ka_prob_glocal() as this will be the -bottleneck. After an hour, the only gain is to change division to -multiplication. OK. I will stop. - ------------------------------------------------------------------------- -r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/kaln.c - -this is interesting. multiplication is much faster than division, at least on my Mac - ------------------------------------------------------------------------- -r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/kaln.c - -minor changes - ------------------------------------------------------------------------- -r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/kaln.c - -prob_realn() seems working! - ------------------------------------------------------------------------- -r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/kaln.c - -minor - ------------------------------------------------------------------------- -r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/kaln.c - M /trunk/samtools/kaln.h - -Convert phredQ to probabilities - ------------------------------------------------------------------------- -r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/kaln.c - M /trunk/samtools/kaln.h - -Implement the glocal HMM; discard the extention HMM - ------------------------------------------------------------------------- -r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/kaln.c - -improve numerical stability - ------------------------------------------------------------------------- -r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/kaln.c - -more comments - ------------------------------------------------------------------------- -r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/kaln.c - -fixed a bug in banded DP - ------------------------------------------------------------------------- -r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines -Changed paths: - M /trunk/samtools/kaln.c - - * fixed that weird issue. - * the banded version is NOT working - ------------------------------------------------------------------------- -r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/kaln.c - -More comments. This version seems working, but something is a little weird... - ------------------------------------------------------------------------- -r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines -Changed paths: - M /trunk/samtools/kaln.c - -A little code cleanup. Now the forward and backback algorithms give -nearly identical P(x), which means both are close to the correct -forms. However, I have only tested on toy examples. Minor errors in -the implementation may not be obvious. - - ------------------------------------------------------------------------- -r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bam_sort.c - M /trunk/samtools/kaln.c - M /trunk/samtools/kaln.h - -... - ------------------------------------------------------------------------- -r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines -Changed paths: - M /trunk/samtools/bam_sort.c - -Abort if merge -h's INH.SAM cannot be opened, just as we abort -if any of the IN#.BAM input files cannot be opened. - -Also propagate any error indication returned by bam_merge_core() -to samtools merge's exit status. - ------------------------------------------------------------------------- -r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines -Changed paths: - M /trunk/samtools/bam_index.c - -Use bam_validate1() to detect garbage records in the event of a corrupt -BAI index file that causes a bam_seek() to an invalid position. At most -one record (namely, the bam_iter_read terminator) is tested per bam_fetch() -call, so the cost is insignificant in the normal case. - ------------------------------------------------------------------------- -r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - -Add bam_validate1(). - ------------------------------------------------------------------------- -r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.8-15 (r379) - * allow to change capQ parameter in calmd - ------------------------------------------------------------------------- -r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/sam_view.c - -When bam_read1() returns an error (return value <= -2), propagate that error -to bam_iter_read()'s own return value. Similarly, also propagate it up to -bam_fetch()'s return value. Previously bam_fetch() always returned 0, and -callers ignored its return value anyway. With this change, 0 continues to -indicate success, while <= -2 (which can be written as < 0, as -1 is never -returned) indicates corrupted input. - -bam_iter_read() ought also to propagate errors returned by bam_seek(). - -main_samview() can now print an error message and fail when bam_fetch() -detects that a .bai index file is corrupted or otherwise does not correspond -to the .bam file it is being used with. - ------------------------------------------------------------------------- -r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_index.c - -0 is a successful return value from bam_read1(). (In practice, it never -returns 0 anyway; but all the other callers treat 0 as successful.) - ------------------------------------------------------------------------- -r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_index.c - M /trunk/samtools/bam_sort.c - - * merge files region-by-region. work on small examples but more tests are needed. - ------------------------------------------------------------------------- -r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - -improve qstats by checking the alleles as well - ------------------------------------------------------------------------- -r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - -convert UCSC SNP SQL dump to VCF - ------------------------------------------------------------------------- -r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - -hapmap2vcf convertor - ------------------------------------------------------------------------- -r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/vcf.c - - * added comments - * VCF->BCF is not possible without knowing the sequence dictionary before hand... - ------------------------------------------------------------------------- -r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/bcfutils.c - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/vcf.c - - * put n_smpl to "bcf1_t" to simplify API a little - ------------------------------------------------------------------------- -r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/index.c - -fixed a bug in indexing - ------------------------------------------------------------------------- -r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_pileup.c - - * fixed a bug in capQ - * valgrind identifies a use of uninitialised value, but I have not fixed it. - ------------------------------------------------------------------------- -r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines -Changed paths: - M /trunk/samtools/bgzip.c - M /trunk/samtools/razip.c - - * fixed a bug in razip: -c will delete the input file - * copy tabix/bgzip to here - ------------------------------------------------------------------------- -r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.8-14 (r727) - * allow to change the capQ parameter at the command line - ------------------------------------------------------------------------- -r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bcftools/vcfutils.pl - M /trunk/samtools/misc/samtools.pl - - * added varFilter to vcfutils.pl - * reimplement realn(). now it performs a local alignment - * added cap_mapQ() to cap mapping quality when there are many substitutions - ------------------------------------------------------------------------- -r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - A /trunk/samtools/bcftools/bcf2qcall.c - M /trunk/samtools/bcftools/call1.c - - * convert BCF to QCALL input - ------------------------------------------------------------------------- -r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_md.c - -dynamic band width in realignment - ------------------------------------------------------------------------- -r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_plcmd.c - -fixed a bug in realignment - ------------------------------------------------------------------------- -r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/prob1.c - -fixed a minor issue - ------------------------------------------------------------------------- -r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_md.c - -fixed a bug in realignment - ------------------------------------------------------------------------- -r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - -minor changes. It is BUGGY now! - ------------------------------------------------------------------------- -r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/kaln.c - M /trunk/samtools/kaln.h - - * aggressive gapped aligner is implemented in calmd. - * distinguish gap_open and gap_end_open in banded alignment - * make tview accepts alignment with heading and tailing D - ------------------------------------------------------------------------- -r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools - -Add svn:ignore properties for generated files that don't appear in "make all". - ------------------------------------------------------------------------- -r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines -Changed paths: - M /trunk/samtools - M /trunk/samtools/bcftools - M /trunk/samtools/misc - -Add svn:ignore properties listing the generated files. -(Except for *.o, which we'll assume is in global-ignores.) - ------------------------------------------------------------------------- -r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/sample.c - M /trunk/samtools/sample.h - - * samtools-0.1.8-13 (r715) - * fixed a bug in identifying SM across files - * bcftools: estimate heterozygosity - * bcftools: allow to skip sites without reference bases - ------------------------------------------------------------------------- -r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/prob1.h - -quite a lot changes to the contrast caller, but I still feel something is missing... - ------------------------------------------------------------------------- -r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/vcfutils.pl - - * changed 3.434 to 4.343 (typo!) - * fixed a bug in the contrast caller - * calculate heterozygosity - ------------------------------------------------------------------------- -r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/bcfutils.c - M /trunk/samtools/bcftools/call1.c - -SNP calling from the GL field - ------------------------------------------------------------------------- -r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcf.c - -fixed another problem - ------------------------------------------------------------------------- -r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/vcf.c - - * fixed bugs in parsing VCF - * parser now works with GT/GQ/DP/PL/GL - ------------------------------------------------------------------------- -r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - M /trunk/samtools/bcftools/prob1.c - -Do not compile _BCF_QUAD by default - ------------------------------------------------------------------------- -r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/bcfutils.c - M /trunk/samtools/bcftools/call1.c - -Write the correct ALT and PL in the SNP calling mode. - ------------------------------------------------------------------------- -r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfutils.pl - -more commands for my own uses - ------------------------------------------------------------------------- -r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines -Changed paths: - A /trunk/samtools/bcftools/vcfutils.pl - -Utilities for processing VCF - ------------------------------------------------------------------------- -r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/prob1.h - -preliminary contrast variant caller - ------------------------------------------------------------------------- -r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/call1.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/prob1.h - -z' and z'' can be calculated - ------------------------------------------------------------------------- -r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699) - M /trunk/samtools/bcftools/prob1.c - D /trunk/samtools/bcftools/vcfout.c - - * rename vcfout.c as call1.c - * prepare to add two-sample comparison - ------------------------------------------------------------------------- -r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfout.c - -fixed a bug in calculating the t statistics - ------------------------------------------------------------------------- -r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcftools/kfunc.c - M /trunk/samtools/bcftools/vcfout.c - - * samtools-0.1.8-13 (r698) - * perform one-tailed t-test for baseQ, mapQ and endDist - ------------------------------------------------------------------------- -r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/kfunc.c - -added regularized incomplete beta function - ------------------------------------------------------------------------- -r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_plcmd.c - -change the default correlation coefficient - ------------------------------------------------------------------------- -r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/vcfout.c - -print QUAL as floating numbers - ------------------------------------------------------------------------- -r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/examples/Makefile - A /trunk/samtools/sample.c - A /trunk/samtools/sample.h - - * samtools-0.1.8-12 (r692) - * group data by samples in "mpileup -g" - ------------------------------------------------------------------------- -r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - D /trunk/samtools/bam_mcns.c - D /trunk/samtools/bam_mcns.h - M /trunk/samtools/bam_plcmd.c - -remove VCF output in mpileup - ------------------------------------------------------------------------- -r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - - * use the revised MAQ error model for mpileup - * prepare to remove the independent model from mpileup - ------------------------------------------------------------------------- -r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_maqcns.h - M /trunk/samtools/bam_plcmd.c - A /trunk/samtools/errmod.c - A /trunk/samtools/errmod.h - M /trunk/samtools/ksort.h - -added revised MAQ error model - ------------------------------------------------------------------------- -r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/prob1.h - M /trunk/samtools/bcftools/vcfout.c - -allow to read the prior from the error output. EM iteration is working. - ------------------------------------------------------------------------- -r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/main.c - M /trunk/samtools/bcftools/vcf.c - - * write a little more VCF header - * concatenate BCFs - ------------------------------------------------------------------------- -r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/bcf.tex - -use float for QUAL - ------------------------------------------------------------------------- -r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/prob1.c - -faster for large sample size (in principle) - ------------------------------------------------------------------------- -r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines -Changed paths: - M /trunk/samtools/bcftools/prob1.c - - * a numerically stable method to calculate z_{jk} - * currently slower than the old method but will be important for large sample size - * in principle, we can speed up for large n, but have not tried - ------------------------------------------------------------------------- -r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfout.c - -fixed an issue in parsing integer - ------------------------------------------------------------------------- -r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - -do not print refname if file is converted from VCF - ------------------------------------------------------------------------- -r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/vcf.c - - * parse PL - * fixed a bug in parsing VCF - ------------------------------------------------------------------------- -r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/bcfutils.c - M /trunk/samtools/bcftools/main.c - M /trunk/samtools/bcftools/vcf.c - M /trunk/samtools/bcftools/vcfout.c - M /trunk/samtools/bgzf.c - M /trunk/samtools/kstring.c - - * fixed a bug in kstrtok@kstring.c - * preliminary VCF parser (not parse everything for now) - * improved view interface - ------------------------------------------------------------------------- -r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines -Changed paths: - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/vcfout.c - M /trunk/samtools/kstring.c - M /trunk/samtools/kstring.h - - * improved kstring (added kstrtok) - * removed the limit on the format string length in bcftools - * use kstrtok to parse format which fixed a bug in the old code - ------------------------------------------------------------------------- -r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines -Changed paths: - A /trunk/samtools/bcftools/README - M /trunk/samtools/bcftools/vcfout.c - -help messages - ------------------------------------------------------------------------- -r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcfout.c - -perform single-tail test for ED4 - ------------------------------------------------------------------------- -r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - M /trunk/samtools/bcftools/kfunc.c - M /trunk/samtools/bcftools/vcfout.c - - * test depth, end distance and HWE - ------------------------------------------------------------------------- -r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/kfunc.c - -reimplement incomplete gamma functions. no copy-paste - ------------------------------------------------------------------------- -r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bcftools/fet.c - M /trunk/samtools/bcftools/prob1.c - M /trunk/samtools/bcftools/prob1.h - M /trunk/samtools/bcftools/vcfout.c - - * bcftools: add HWE (no testing for now) - * record end dist in a 2x2 table, not avg, std any more - ------------------------------------------------------------------------- -r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines -Changed paths: - A /trunk/samtools/bcftools/kfunc.c - - * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma) - * Not using Numerical Recipe due to licensing issues - ------------------------------------------------------------------------- -r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines -Changed paths: - A /trunk/samtools/bcftools/fet.c - -Fisher's exact test - ------------------------------------------------------------------------- -r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bamtk.c - M /trunk/samtools/examples/Makefile - - * samtools-0.1.8-11 (r672) - * collect more stats for allele balance test in bcftools (not yet) - ------------------------------------------------------------------------- -r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/main.c - - * the code base is stablized again. - * I will delay the vcf parser, which is quite complicated but with little value for now - ------------------------------------------------------------------------- -r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/examples/Makefile - -minor - ------------------------------------------------------------------------- -r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcftools/vcf.c - -unfinished vcf parser - ------------------------------------------------------------------------- -r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bcftools/Makefile - M /trunk/samtools/bcftools/bcf.c - M /trunk/samtools/bcftools/bcf.h - M /trunk/samtools/bcftools/bcfutils.c - M /trunk/samtools/bcftools/index.c - M /trunk/samtools/bcftools/main.c - A /trunk/samtools/bcftools/vcf.c - M /trunk/samtools/bcftools/vcfout.c - - * added prelimiary VCF parser (not finished) - * change struct a bit - ------------------------------------------------------------------------- -r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bcftools/bcf.c - - * allow to set min base q - * fixed a bug in mpileup -u - ------------------------------------------------------------------------- -r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines -Changed paths: - A /trunk/samtools/bcftools/bcf.tex - -spec - ------------------------------------------------------------------------- -r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/examples/Makefile - -added more examples - ------------------------------------------------------------------------- -r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bcftools/Makefile - -fixed compilation error - ------------------------------------------------------------------------- -r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - D /trunk/samtools/bcf.c - D /trunk/samtools/bcf.h - A /trunk/samtools/bcftools - A /trunk/samtools/bcftools/Makefile - A /trunk/samtools/bcftools/bcf.c - A /trunk/samtools/bcftools/bcf.h - A /trunk/samtools/bcftools/bcfutils.c - A /trunk/samtools/bcftools/index.c - A /trunk/samtools/bcftools/main.c - A /trunk/samtools/bcftools/prob1.c - A /trunk/samtools/bcftools/prob1.h - A /trunk/samtools/bcftools/vcfout.c - -move bcftools to samtools - ------------------------------------------------------------------------- -r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - -fixed another minor bug - ------------------------------------------------------------------------- -r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/bcf.c - - * samtools-0.1.8-10 (r658) - * fixed a bug in bam2bcf when the reference is N - ------------------------------------------------------------------------- -r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - - * fixed a bug - * treat ambiguous ref base as the fifth base - ------------------------------------------------------------------------- -r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines -Changed paths: - M /trunk/bcftools/bcf.c - M /trunk/samtools/bcf.c - -missing a column in VCF output... - ------------------------------------------------------------------------- -r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcf.c - -fixed a memory leak - ------------------------------------------------------------------------- -r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bcf.c - -fixed a bug in bcf reader - ------------------------------------------------------------------------- -r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam2bcf.c - -fixed a bug - ------------------------------------------------------------------------- -r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam2bcf.c - M /trunk/samtools/bam2bcf.h - M /trunk/samtools/bamtk.c - - * samtools-0.1.8-9 (r649) - * lossless representation of PL in BCF output - ------------------------------------------------------------------------- -r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - A /trunk/samtools/bam2bcf.c - A /trunk/samtools/bam2bcf.h - M /trunk/samtools/bam_plcmd.c - A /trunk/samtools/bcf.c - A /trunk/samtools/bcf.h - -Generate binary VCF - ------------------------------------------------------------------------- -r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.8-8 (r644) - * mpileup becomes a little stable again - * the method is slightly different, but is more theoretically correct - * snp calling is O(n^2) instead of O(n^3) - ------------------------------------------------------------------------- -r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - - * fixed a STUPID bug, which cost me a lot of time. - * I am going to clean up mcns a little bit - ------------------------------------------------------------------------- -r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bam_mcns.h - M /trunk/samtools/bam_plcmd.c - -supposedly this is THE correct implementation, but more testing is needed - ------------------------------------------------------------------------- -r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - -NOT ready yet. Going to make further changes... - ------------------------------------------------------------------------- -r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.8-7 (r639) - * fixed the reference allele assignment - ------------------------------------------------------------------------- -r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bam_mcns.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.8-6 (r638) - * skip isnan/isinf in case of float underflow - * added the flat prior - * fixed an issue where there are no reads supporting the reference - ------------------------------------------------------------------------- -r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - -minor changes - ------------------------------------------------------------------------- -r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bam_mcns.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - -minor tweaks - ------------------------------------------------------------------------- -r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bam_mcns.h - M /trunk/samtools/bam_plcmd.c - -posterior expectation FINALLY working. I am so tired... - ------------------------------------------------------------------------- -r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - -another minor fix to mpileup - ------------------------------------------------------------------------- -r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - -added the format column - ------------------------------------------------------------------------- -r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bam_mcns.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - -added an alternative prior - ------------------------------------------------------------------------- -r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bam_mcns.h - M /trunk/samtools/bam_plcmd.c - -calculate posterior allele frequency - ------------------------------------------------------------------------- -r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.8-3 (r627) - * multi-sample snp calling appears to work. More tests needed. - ------------------------------------------------------------------------- -r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bam_mcns.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bam_tview.c - - * preliminary multisample SNP caller. - * something looks not so right, but it largely works - ------------------------------------------------------------------------- -r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_mcns.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.8-2 (r617) - * allele frequency calculation apparently works... - ------------------------------------------------------------------------- -r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines -Changed paths: - M /trunk/samtools/Makefile - A /trunk/samtools/bam_mcns.c - A /trunk/samtools/bam_mcns.h - M /trunk/samtools/bam_plcmd.c - - * added mutli-sample framework. It is not working, yet. - * improved the mpileup interface - ------------------------------------------------------------------------- -r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/Makefile - - * samtools-0.1.8-1 (r615) - * allow to get mpileup at required sites - ------------------------------------------------------------------------- -r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - -Release samtools-0.1.8 - ------------------------------------------------------------------------- -r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/knetfile.c - -fixed a compiling issue for Windows - ------------------------------------------------------------------------- -r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_sort.c - -fixed a bug in sorting when output to stdout (by Peter Chines) - ------------------------------------------------------------------------- -r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/NEWS - M /trunk/samtools/bam_plcmd.c - -change the command line option of pileup - ------------------------------------------------------------------------- -r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_pileup.c - A /trunk/samtools/examples/toy.fa - A /trunk/samtools/examples/toy.sam - -make pileup work with CIGAR with I/D at the beginning or in the end - ------------------------------------------------------------------------- -r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_maqcns.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bam_tview.c - - * make tview more friendly - * a temporary remedy for an issue in indel calling - ------------------------------------------------------------------------- -r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-r607 - * improved the genotype accuracy for indels - * use the SOAPsnp model for SNP calling by default. - ------------------------------------------------------------------------- -r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/misc/Makefile - -removed a debugging example - ------------------------------------------------------------------------- -r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bamtk.c - - * samtools-.1.7-18 (r605) - * fixed an issue when a deletion and mismatch occur at the same time - and the base quality is higher than 40 (if -I40). - ------------------------------------------------------------------------- -r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_index.c - M /trunk/samtools/misc/Makefile - -fixed a minor bug in idxstats - ------------------------------------------------------------------------- -r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_index.c - -fixed a minor bug in indexing - ------------------------------------------------------------------------- -r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam.c - -change printf() to puts in exporting - ------------------------------------------------------------------------- -r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines -Changed paths: - M /trunk/samtools/bamtk.c - -minor fix. No actual effect. - ------------------------------------------------------------------------- -r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - -added Makefile targets to compile shared/dynamic library - ------------------------------------------------------------------------- -r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-17 (r596) - * also keep the number of coor-less reads in the index file - ------------------------------------------------------------------------- -r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-16 (r595) - * write additional information to bam index - ------------------------------------------------------------------------- -r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_index.c - -fixed a bug for unmapped sequences in indexing - ------------------------------------------------------------------------- -r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_index.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/samtools.1 - -rename iterf as iter - ------------------------------------------------------------------------- -r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bam_index.c - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-15 (r592) - * fixed a few minor memory leaks in the new pileup code - * improved the functionality of mpileup - ------------------------------------------------------------------------- -r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-14 (r591) - * elementary multi-way pileup. More testing and more functionality to be done. - ------------------------------------------------------------------------- -r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-13 (r590) - * added mpileup APIs. No compiling errors, but not tested at all. It is late. - ------------------------------------------------------------------------- -r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-12 (r589) - * added iterator-like APIs for pileup - ------------------------------------------------------------------------- -r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-11 (r588) - * ported a few improvements from tabix back to samtools - ------------------------------------------------------------------------- -r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-10 (r587) - * added iterator interface for bam_fetch (ported back from tabix) - ------------------------------------------------------------------------- -r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines -Changed paths: - M /trunk/samtools/Makefile - A /trunk/samtools/bam_reheader.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bgzf.c - - * samtools-0.1.7-9 (r586) - * added "reheader" to replace the BAM header - ------------------------------------------------------------------------- -r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/kstring.h - - * samtools-0.1.7-8 (r585) - * speed up "view" - ------------------------------------------------------------------------- -r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bgzf.c - M /trunk/samtools/bgzf.h - M /trunk/samtools/kstring.h - M /trunk/samtools/misc/wgsim_eval.pl - - * samtools-0.1.7-7 (r584) - * ported tabix BGZF to samtools - * flush BGZF after writing the BAM header and between alignment boundaries - ------------------------------------------------------------------------- -r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line -Changed paths: - A /trunk/samtools/misc/varfilter.py - -Initial release on behalf of Aylwyn Scally ------------------------------------------------------------------------- -r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line -Changed paths: - M /trunk/samtools/samtools.1 - -Added a note about the indels coordinates ------------------------------------------------------------------------- -r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line -Changed paths: - M /trunk/samtools/misc/sam2vcf.pl - -Added the possibility to print or not to print the reference allele ------------------------------------------------------------------------- -r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line -Changed paths: - M /trunk/samtools/sam_header.c - -More descriptive message for space separated tags ------------------------------------------------------------------------- -r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line -Changed paths: - M /trunk/samtools/misc/sam2vcf.pl - -Speedup with -i, no need to query the reference all the time ------------------------------------------------------------------------- -r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line -Changed paths: - M /trunk/samtools/sam_header.c - -Fixed the order of sequences in the header ------------------------------------------------------------------------- -r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line -Changed paths: - M /trunk/samtools/misc/sam2vcf.pl - -Added possibility to select indels only and fixed a bug in reporting homozygous indels. ------------------------------------------------------------------------- -r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines -Changed paths: - M /trunk/samtools/bam.c - -Improve the invalid 'BAM\1' magic number error message, and also print it -when no bytes can be read from the alleged BAM file, e.g., in the common -user error case when a SAM file has accidentally been supplied. - ------------------------------------------------------------------------- -r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line -Changed paths: - M /trunk/samtools/AUTHORS - M /trunk/samtools/bam.h - M /trunk/samtools/bam_import.c - M /trunk/samtools/sam_header.c - -Improved efficiency of header parsing ------------------------------------------------------------------------- -r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines -Changed paths: - M /trunk/samtools/misc/export2sam.pl - -Updated export2sam.pl by Chris Saunders from Illumina. - - ------------------------------------------------------------------------- -r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line -Changed paths: - M /trunk/samtools/misc/samtools.pl - -Fixed filtering of SNPs near indels. Added min indel and SNP quality filter. ------------------------------------------------------------------------- -r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line -Changed paths: - M /trunk/samtools/misc/sam2vcf.pl - -Print an error for pileups in simple format ------------------------------------------------------------------------- -r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - -added a hidden option in pileup to output the base position (for Erin) - ------------------------------------------------------------------------- -r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line -Changed paths: - M /trunk/samtools/misc/sam2vcf.pl - -Added possibility to specify a custom column title for the data column ------------------------------------------------------------------------- -r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line -Changed paths: - M /trunk/samtools/bam_plcmd.c - -Added the -d option to limit maximum depth for indels. ------------------------------------------------------------------------- -r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line -Changed paths: - M /trunk/samtools/misc/sam2vcf.pl - -Added VCF header ------------------------------------------------------------------------- -r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/samtools.pl - M /trunk/samtools/misc/wgsim.c - - * samtools-0.1.7-6 - * fixed a bug in faidx - ------------------------------------------------------------------------- -r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines -Changed paths: - M /trunk/samtools/faidx.c - -Put the right filename in the error message. - ------------------------------------------------------------------------- -r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-5 (r528) - * further add new consensus generation strategy - ------------------------------------------------------------------------- -r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line -Changed paths: - M /trunk/samtools/knetfile.c - -Fixed a bug in knet_seek ------------------------------------------------------------------------- -r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line -Changed paths: - M /trunk/samtools/misc/sam2vcf.pl - -Small fix in VCF format: dot for the empty INFO field ------------------------------------------------------------------------- -r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line -Changed paths: - M /trunk/samtools/sam_header.c - -Allow tabs in the CO header field ------------------------------------------------------------------------- -r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/Makefile.mingw - -Depend on libbam.a rather than the phony target, so that samtools is not -unnecessarily rebuilt every time. Also clean bgzip. - ------------------------------------------------------------------------- -r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/Makefile.mingw - -Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE -is defined. Also introduce $(KNETFILE_O) which can be set to empty to -facilitate non-knet builds. - ------------------------------------------------------------------------- -r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.7-4 (r522) - * fixed a bug in "view -r" - * added a new option "view -R" to read required read groups from a file - ------------------------------------------------------------------------- -r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.7-3 (r521) - * calmd: optionally mask matching bases as N - ------------------------------------------------------------------------- -r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/samtools.pl - - * samtools-0.1.7-2 (r520) - * fixed a few issues with compilation in Windows (on behalf of John) - * choose a random base as the consensus (for population genetics studies) - ------------------------------------------------------------------------- -r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines -Changed paths: - M /trunk/samtools/Makefile - -Put libraries at the end, so they can resolve references from libbam.a -as well, even with old-fashioned linkers. - -Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get -the freshly built library, not some other libbam.a lying around the system. - ------------------------------------------------------------------------- -r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/misc/Makefile - -Also clean *.exe (for Cygwin users using this makefile). - ------------------------------------------------------------------------- -r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines -Changed paths: - M /trunk/samtools/bam_index.c - -Index files should be opened in binary mode, not text mode. - ------------------------------------------------------------------------- -r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines -Changed paths: - A /trunk/samtools/examples/bam2bed.c - -another example program - ------------------------------------------------------------------------- -r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/wgsim_eval.pl - M /trunk/samtools/sam.c - - * samtools-0.1.7-1 (r515) - * report an error when .fai contains duplicated names, instead of segfault - ------------------------------------------------------------------------- -r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines -Changed paths: - M /trunk/samtools/bam.c - -Format 'c'-encoded auxiliary fields correctly, as *signed* integers. - ------------------------------------------------------------------------- -r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile.mingw - -Update Makefile.mingw for the same reason - ------------------------------------------------------------------------- -r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - -Fixed a bug in compiling razip - ------------------------------------------------------------------------- -r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - -Release samtools-0.1.7 (r510) - ------------------------------------------------------------------------- -r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.6-22 (r509) - * forget to fix a similar problem in glfgen - ------------------------------------------------------------------------- -r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.6-21 (r508) - * fixed a potential bug in the indel caller towards the end of a chromosome - ------------------------------------------------------------------------- -r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.6-19 (r494) - * allow to convert Illumina quality (64 based) to the BAM quality - ------------------------------------------------------------------------- -r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam.c - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - M /trunk/samtools/sam_header.c - - * samtools-0.1.6-18 (r493) - * fixed the bugs due to improperly incorporating Petr's header parser - * a little code clean up in sam_header.c - ------------------------------------------------------------------------- -r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line -Changed paths: - M /trunk/samtools/sam_header.c - -Added sam_header_line_free call for sam_header_parse2 ------------------------------------------------------------------------- -r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines -Changed paths: - M /trunk/samtools/sam_view.c - - * BUGGY VERSION - * fixed a minor bug - ------------------------------------------------------------------------- -r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - M /trunk/samtools/bam_import.c - M /trunk/samtools/sam.c - - * BUGGY VERSION - * improved the interface a bit - * bug unfixed - ------------------------------------------------------------------------- -r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_import.c - M /trunk/samtools/sam_header.c - M /trunk/samtools/sam_header.h - - * BUGGY VERSION. Please NOT use it. - * Fixed a minor bug, but the major bug is still there. - ------------------------------------------------------------------------- -r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_rmdup.c - M /trunk/samtools/bam_rmdupse.c - M /trunk/samtools/kaln.c - M /trunk/samtools/sam.c - M /trunk/samtools/sam_header.c - M /trunk/samtools/sam_header.h - M /trunk/samtools/sam_view.c - - * This revision is SERIOUSLY BUGGY. Please NOT use it. - * Start to incorporate header parsing from Petr Danecek - ------------------------------------------------------------------------- -r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line -Changed paths: - M /trunk/samtools/sam_header.c - M /trunk/samtools/sam_header.h - -Now possible to merge multiple HeaderDict dictionaries ------------------------------------------------------------------------- -r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line -Changed paths: - M /trunk/samtools/sam_header.c - - ------------------------------------------------------------------------- -r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line -Changed paths: - A /trunk/samtools/sam_header.c - A /trunk/samtools/sam_header.h - - ------------------------------------------------------------------------- -r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_rmdupse.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/examples/Makefile - - * samtools-0.1.6-17 (r484) - * fixed a memory leak in rmdupse - * fixed a bug in parsing @RG header lines - * test rmdup in examples/ - ------------------------------------------------------------------------- -r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam_rmdup.c - M /trunk/samtools/bam_rmdupse.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.6-16 (r483) - * unify the interface of rmdup and rmdupse - * a new bug found in rg2lib(). Have not been fixed yet. - ------------------------------------------------------------------------- -r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_rmdup.c - M /trunk/samtools/bam_rmdupse.c - M /trunk/samtools/bamtk.c - A /trunk/samtools/klist.h - - * samtools-0.1.6-15 (r482) - * rewrite rmdupse - * rmdupse is now library aware - ------------------------------------------------------------------------- -r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_rmdup.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.6-14 (r480) - * rmdup is now RG aware - ------------------------------------------------------------------------- -r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - -added a small unitity to parse SRA XML files - ------------------------------------------------------------------------- -r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_maqcns.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.6-13 (r479) - * merge: optionally use file names as RG tags - ------------------------------------------------------------------------- -r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/kaln.c - - * samtools-0.1.6-12 (r478) - * fixed a bug in the indel caller - ------------------------------------------------------------------------- -r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.6-11 (r477) - * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch) - ------------------------------------------------------------------------- -r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line -Changed paths: - A /trunk/samtools/misc/sam2vcf.pl - -Added the sam2vcf.pl script. ------------------------------------------------------------------------- -r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bamtk.c - A /trunk/samtools/kaln.c - A /trunk/samtools/kaln.h - -Unfinished modification. Please do not use this revision... - ------------------------------------------------------------------------- -r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line -Changed paths: - M /trunk/samtools/knetfile.c - -Removed the offending knet_seek message. ------------------------------------------------------------------------- -r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line -Changed paths: - M /trunk/samtools/knetfile.c - M /trunk/samtools/razf.c - -Bug fix - faidx on RAZF compressed files now working. ------------------------------------------------------------------------- -r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines -Changed paths: - M /trunk/samtools/samtools.1 - -Clarify the meaning of a region like "chr2:1,000,000". - ------------------------------------------------------------------------- -r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/novo2sam.pl - -Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus) - ------------------------------------------------------------------------- -r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile.mingw - M /trunk/samtools/bamtk.c - M /trunk/samtools/knetfile.c - M /trunk/samtools/knetfile.h - - * samtools-0.1.6-9 (r470) - * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch) - ------------------------------------------------------------------------- -r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.6-9 (r469) - * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt. - ------------------------------------------------------------------------- -r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/samtools.pl - - * samtools-0.1.6-7 (r468) - * make merge stable - ------------------------------------------------------------------------- -r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line -Changed paths: - M /trunk/samtools/bgzf.c - M /trunk/samtools/bgzip.c - M /trunk/samtools/razf.c - M /trunk/samtools/razip.c - -Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022). ------------------------------------------------------------------------- -r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.6-6 (r466) - * do not crash calmd when some sequences are absent from the reference. - ------------------------------------------------------------------------- -r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/knetfile.c - -Suppress bgzf_check_EOF() messages when reading from a pipe, as there is -no way to seek on a pipe and the messages always appear. - ------------------------------------------------------------------------- -r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line -Changed paths: - M /trunk/samtools/knetfile.c - M /trunk/samtools/razf.c - -A bug fix, "samtools view" is now working again. ------------------------------------------------------------------------- -r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/faidx.c - M /trunk/samtools/knetfile.c - M /trunk/samtools/knetfile.h - M /trunk/samtools/razf.c - M /trunk/samtools/razf.h - - * samtools-0.1.6-5 (r462) - * Added knetfile support in razf and faidx (on behalf of Petr Danecek) - ------------------------------------------------------------------------- -r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines -Changed paths: - M /trunk/samtools/samtools.1 - -fixed a formatting issue - ------------------------------------------------------------------------- -r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.6-4 (r459) - * make sort output the result to stdout when -o is in use - ------------------------------------------------------------------------- -r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/faidx.c - M /trunk/samtools/faidx.h - M /trunk/samtools/samtools.1 - - * samtools-0.1.6-2 (r458) - * added more interface to faidx (by Nils) - * updated documentation - ------------------------------------------------------------------------- -r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.6-2 (r457) - * get rid of three assert() in bam_sort.c - ------------------------------------------------------------------------- -r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines -Changed paths: - M /trunk/samtools/razf.c - -Return NULL from _razf_open() (and hence razf_open()/razf_open2()) -when opening the file fails. - ------------------------------------------------------------------------- -r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - D /trunk/samtools/source.dot - -Release samtools-0.1.6 - ------------------------------------------------------------------------- -r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_rmdup.c - M /trunk/samtools/bam_rmdupse.c - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - - * samtools-0.1.5-34 (r451) - * applied the patch by John - * improved the help message a little bit - ------------------------------------------------------------------------- -r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_color.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-33 (r450) - * fixed a bug in bam_color.c (on behalf of Nils Homer) - ------------------------------------------------------------------------- -r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/samtools.pl - - * samtools-0.1.5-32 (r449) - * fillmd: fixed a bug in modifying MD/NM tags - * in import, give a warning if the read is aligned but there is no CIGAR. - ------------------------------------------------------------------------- -r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/wgsim_eval.pl - - * samtools-0.1.5-31 (r448) - * fixed an issue when the last CIGAR is I or D - ------------------------------------------------------------------------- -r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-30 (r447) - * fixed a bug in bam_aux_get(): 'A' is not checked - ------------------------------------------------------------------------- -r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines -Changed paths: - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bamtk.c - - * - ------------------------------------------------------------------------- -r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-28 (r444) - * bug in "merge -n" - ------------------------------------------------------------------------- -r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-27 (r443) - * SEQ and QUAL can be "*" - * parse CIGAR "=" and "X" as "M" - ------------------------------------------------------------------------- -r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/md5.c - M /trunk/samtools/misc/md5.h - M /trunk/samtools/misc/md5fa.c - - * samtools-0.1.5-26 (r442) - * replace RSA Inc md5.* with ones under permissive lincense - * fixed a bug in detecting unsorted bam in pileup - ------------------------------------------------------------------------- -r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines -Changed paths: - M /trunk/samtools/bgzf.c - M /trunk/samtools/bgzf.h - M /trunk/samtools/bgzip.c - -Change copyright notices now that MIT has approved open source distribution. - ------------------------------------------------------------------------- -r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_stat.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-25 (r436) - * in flagstats, do not report singletons if both ends are unmapped - ------------------------------------------------------------------------- -r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/maq2sam.c - -fixed a SERIOUS bug in setting 0x20 flag - ------------------------------------------------------------------------- -r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - -fixed two minor bugs (suggested by Tim M Storm) - ------------------------------------------------------------------------- -r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/samtools.pl - M /trunk/samtools/sam_view.c - - * samtools-0.1.5-24 (r435) - * fixed a typo - ------------------------------------------------------------------------- -r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-23 (r434) - * in tview, press 'r' to show read names rather than sequences - ------------------------------------------------------------------------- -r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines -Changed paths: - M /trunk/samtools/knetfile.c - - * tried to fixed the buggy FTP random access in Windows. FAILED. - * anyway, MinGW seems to have problem with "%lld". - ------------------------------------------------------------------------- -r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines -Changed paths: - M /trunk/samtools/Makefile.mingw - M /trunk/samtools/bamtk.c - M /trunk/samtools/faidx.c - M /trunk/samtools/razf.c - A /trunk/samtools/win32/libcurses.a - A /trunk/samtools/win32/xcurses.h - - * samtools-0.1.5-22 (r432) - * faidx: fixed compitability issue with _WIN32 - * razf: fixed potential compitability issue with _WIN32 - * PDCurses support in Windows - ------------------------------------------------------------------------- -r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines -Changed paths: - M /trunk/samtools/win32/libz.a - -replace the GnuWin32 version of libz.a with my own build with MinGW. - ------------------------------------------------------------------------- -r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines -Changed paths: - M /trunk/samtools/knetfile.c - -add comments - ------------------------------------------------------------------------- -r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile.mingw - M /trunk/samtools/bamtk.c - M /trunk/samtools/knetfile.c - M /trunk/samtools/knetfile.h - - * samtools-0.1.5-21 (r428) - * knetfile.c is now compatible with mingw-winsock - ------------------------------------------------------------------------- -r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile.mingw - -simplify MinGW Makefile - ------------------------------------------------------------------------- -r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines -Changed paths: - A /trunk/samtools/Makefile.mingw - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - A /trunk/samtools/win32 - A /trunk/samtools/win32/libz.a - A /trunk/samtools/win32/zconf.h - A /trunk/samtools/win32/zlib.h - - * samtools-0.1.5-20 (r427) - * MinGW support. At least SAM<->BAM conversion is working. Other - functionality are not tested at the moment. - * zlib headers and Windows version of libz.a are included in win32/ - ------------------------------------------------------------------------- -r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.5-19 (r426) - * fixed a bug caused by recent modifications. Sorry. - ------------------------------------------------------------------------- -r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/bgzf.c - -compatible with Windows binary files - ------------------------------------------------------------------------- -r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_maqcns.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/samtools.pl - - * samtools-0.1.5-18 (r423) - * output additional information in pileup indel lines, for the purepose - of debugging at the moment - * in tview, optionally allow to treat reference skip as deletion - ------------------------------------------------------------------------- -r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines -Changed paths: - A /trunk/samtools/misc/psl2sam.pl - -convert BLAT psl to SAM. - ------------------------------------------------------------------------- -r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bgzf.c - M /trunk/samtools/bgzf.h - M /trunk/samtools/knetfile.c - M /trunk/samtools/sam.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.5-17 (r422) - * fixed a but in knetfile.c when seek type is not SEEK_SET - * write an empty BGZF block to every BGZF file - * check BGZF EOF marker in bam_header_read() - * update ChangeLog - ------------------------------------------------------------------------- -r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/samtools.pl - M /trunk/samtools/sam.c - M /trunk/samtools/sam.h - M /trunk/samtools/sam_view.c - - * samtools-0.1.5-16 (r421) - * in view and pileup, load header from FASTA index if the input is SAM. - ------------------------------------------------------------------------- -r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/maq2sam.c - -do not set "read 1" if reads are not mapped in the PE mode of maq - ------------------------------------------------------------------------- -r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/samtools.pl - M /trunk/samtools/misc/wgsim_eval.pl - - * samtools-0.1.5-15 (r419) - * in sam_open(), return NULL when the file cannot be opened. - * make wgsim_eval.pl more robust to imperfect SAM - * add "unique" command to samtools.pl - ------------------------------------------------------------------------- -r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/wgsim_eval.pl - -skip @header lines in SAM - ------------------------------------------------------------------------- -r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.5-14 (r417) - * more help in "samtools view" due to the recent changes. - ------------------------------------------------------------------------- -r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - M /trunk/samtools/sam.h - M /trunk/samtools/sam_view.c - - * samtools-0.1.5-17 (r416) - * support import/export SAM with string tags - ------------------------------------------------------------------------- -r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - M /trunk/samtools/sam.h - M /trunk/samtools/sam_view.c - - * samtools-0.1.5-12 (r415) - * FLAG now can be in HEX - ------------------------------------------------------------------------- -r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/kstring.h - -fixed a compiling error (thank Ken for fixing it) - ------------------------------------------------------------------------- -r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/kstring.c - M /trunk/samtools/kstring.h - -Implemented Boyer-Moore search in the kstring library. - ------------------------------------------------------------------------- -r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/bam_index.c - -do not include knetfile.h when _USE_KNETFILE is not defined - ------------------------------------------------------------------------- -r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bgzf.c - - * samtools-0.1.5-11 (r408) - * force to overwirte existing MD if it is different from the one calculated - from fillmd. - * bgzf.c: improved the compatibility with Windows headers - ------------------------------------------------------------------------- -r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.h - - * samtools-0.1.5-10 (r407) - * implemented bam_aux_del() to remove a tag - * fillmd: generate the NM tag - * fillmd: cmd interface improvement - ------------------------------------------------------------------------- -r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - -Sorry. The old Makefile is for PDCurses... - ------------------------------------------------------------------------- -r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-9 (r405) - * improved the compatibility with PDCurses a little bit - ------------------------------------------------------------------------- -r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-8 (r404) - * compatible with PDCurses - ------------------------------------------------------------------------- -r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/kseq.h - - * samtools-0.1.5-7 (r403) - * fixed a bug in kseq.h for binary files (text files are fine) - ------------------------------------------------------------------------- -r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bgzf.c - - * samtools-0.1.5-6 (r402) - * fixed compiling error when "-D_USE_NETFILE" is not applied - * improve portability to MinGW - ------------------------------------------------------------------------- -r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines -Changed paths: - A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395) - A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395) - D /trunk/samtools/bam_lite.c - - * move bam_lite.c to bam-lite - * copy bam.h to bam-lite - ------------------------------------------------------------------------- -r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_lite.c - M /trunk/samtools/bam_lpileup.c - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-5 (r395) - * added bam_pileup_file() and removed bam_lpileup_file() - ------------------------------------------------------------------------- -r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/knetfile.c - M /trunk/samtools/knetfile.h - - * samtools-0.1.5-4 (r394) - * http_proxy support in knetfile library (check http_proxy ENV) - ------------------------------------------------------------------------- -r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/knetfile.c - M /trunk/samtools/knetfile.h - - * samtools-0.1.5-3 (r393) - * knetfile now supports HTTP (no proxy at the moment) - * fixed a potential issue in knetfile on opening ordinary file, although I have - not seen the sideeffect so far. - ------------------------------------------------------------------------- -r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/samtools.1 - -Remove the warning in tview - ------------------------------------------------------------------------- -r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-2 (r391) - * do not show a blank screen when no reads mapped - ------------------------------------------------------------------------- -r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam.h - A /trunk/samtools/bam_lite.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.5-1 (r390) - * removed useless _IOLIB in bam.h. This should cause no change at all. - * added bam_lite.c for light-weight BAM reading - ------------------------------------------------------------------------- -r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/knetfile.c - -Release samtools-0.1.5c (fixed a bug in piping) - ------------------------------------------------------------------------- -r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - -Release samtools-0.1.5b (BUG! so embarrassing!) - ------------------------------------------------------------------------- -r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bamtk.c - -Release samtools-0.1.5a (for compatibility with Bio::DB::Sam) - ------------------------------------------------------------------------- -r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - -Release samtools-0.1.5 - ------------------------------------------------------------------------- -r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - - * samtools-0.1.4-23 (r372) - * keep header text if "view -t" is used (by Gerton) - ------------------------------------------------------------------------- -r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/samtools.1 - -update documentation - ------------------------------------------------------------------------- -r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - -Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad. - ------------------------------------------------------------------------- -r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.4-22 (r369) - * in pileup, optionally print E2 and U2 - * remove the debugging code in bam_aux_get() (Drat!) - ------------------------------------------------------------------------- -r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bam_index.c - M /trunk/samtools/bam_lpileup.c - M /trunk/samtools/bam_md.c - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bam_rmdup.c - M /trunk/samtools/bam_stat.c - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/faidx.c - M /trunk/samtools/faidx.h - M /trunk/samtools/glf.c - - * samtools-0.1.4-21 (r368) - * propagate errors rather than exit or complain assertion failure. Assertion - should be only used for checking internal bugs, but not for external input - inconsistency. I was just a bit lazy. - * small memory leak may be present on failure, though - ------------------------------------------------------------------------- -r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/knetfile.c - -reduce the chance of blocking in FTP connection - ------------------------------------------------------------------------- -r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/knetfile.c - -minor changes to knetfile: invalid fd equals -1 rather than 0 - ------------------------------------------------------------------------- -r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/knetfile.c - M /trunk/samtools/knetfile.h - - * samtools-0.1.4-20 (r365) - * download the BAM index file if it is not found in the current working directory. - ------------------------------------------------------------------------- -r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/knetfile.c - - * samtools-0.1.4-19 (r364) - * knetfile: report error when the file is not present on FTP - ------------------------------------------------------------------------- -r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bgzf.c - M /trunk/samtools/bgzf.h - M /trunk/samtools/knetfile.c - M /trunk/samtools/knetfile.h - - * samtools-0.1.4-18 (r363) - * knetfile: do not trigger network communication in FTP seek (lazy seek) - * bgzf: cache recent blocks (disabled by default) - ------------------------------------------------------------------------- -r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/bgzf.c - -write changelog - ------------------------------------------------------------------------- -r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.4-17 (r361) - * if a file is given on FTP, search locally for the BAM index - ------------------------------------------------------------------------- -r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bgzf.c - M /trunk/samtools/bgzf.h - M /trunk/samtools/knetfile.c - M /trunk/samtools/knetfile.h - - * samtools-0.1.4-16 (r360) - * report more information in index when the input is not sorted - * change the behaviour of knet_seek() such that it returns 0 on success - * support knetfile library in BGZF - ------------------------------------------------------------------------- -r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/knetfile.c - M /trunk/samtools/knetfile.h - -fixed bugs in knetfile.* - ------------------------------------------------------------------------- -r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines -Changed paths: - A /trunk/samtools/knetfile.h - -this is the header file - ------------------------------------------------------------------------- -r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines -Changed paths: - A /trunk/samtools/knetfile.c - - * open a file at FTP - * preliminary version - ------------------------------------------------------------------------- -r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.4-15 (r354) - * fixed a memory leak in bam_view1(), although samtools is not using this routine. - ------------------------------------------------------------------------- -r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/faidx.c - - * samtools-0.1.4-13 (r351) - * make faidx more tolerant to empty lines right before or after > lines - * hope this does not introduce new bugs... - ------------------------------------------------------------------------- -r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.4-13 (r350) - * fixed a small memory leak in pileup, caused by recent modifications - ------------------------------------------------------------------------- -r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.4-12 (r347) - * added `-S' to pileup, similar to `view -S' - ------------------------------------------------------------------------- -r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam_view.c - M /trunk/samtools/samtools.1 - - * samtools-0.1.4-11 (r346) - * allow to select a read group at view command-line - ------------------------------------------------------------------------- -r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/examples/calDepth.c - -added more comments - ------------------------------------------------------------------------- -r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/examples/calDepth.c - -nothing really - ------------------------------------------------------------------------- -r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/examples/Makefile - A /trunk/samtools/examples/calDepth.c - -added an example of calculating read depth - ------------------------------------------------------------------------- -r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - A /trunk/samtools/bam_color.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - M /trunk/samtools/sam.h - - * samtools-0.1.4-10 (r341) - * only include key APIs in libbam.a - * move color-specific routines to bam_color.c - * update documentations - * remove the support of -q in pileup - ------------------------------------------------------------------------- -r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines -Changed paths: - M /trunk/samtools/INSTALL - M /trunk/samtools/Makefile - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/razf.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.4-9 (r340) - * added a warning to razf.c if zlib<1.2.2.1 - * fixed a compilation warning - * fixed a segfault caused by @RG parsing - * detect NCURSES in bam_tview.c - ------------------------------------------------------------------------- -r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/INSTALL - -update INSTALL - ------------------------------------------------------------------------- -r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/kstring.h - M /trunk/samtools/sam.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.4-8 (r338) - * parse the @RG header lines and allow to choose library at the "samtools view" - command line - ------------------------------------------------------------------------- -r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/bgzf.c - M /trunk/samtools/bgzf.h - M /trunk/samtools/sam.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.4-7 (r337) - * bgzf.c: support mode string "wu": uncompressed output - * "samtools view" support "-u" command-line option - ------------------------------------------------------------------------- -r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/misc/Makefile - M /trunk/samtools/razf.c - M /trunk/samtools/razf.h - M /trunk/samtools/razip.c - - * no changes to samtools itself - * remove zlib source codes - * make RAZF reading compatible with old version of zlib - * on old version of zlib, writing is not available - ------------------------------------------------------------------------- -r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines -Changed paths: - D /trunk/samtools/zlib - -remove zlib for simplification... - ------------------------------------------------------------------------- -r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.4-6 (r334) - * do not export bam_aux_get_core() for Bio::DB::Sam because it has already - been implemented in that. - * this version works with the latest Bio::DB::Sam (20090612) - ------------------------------------------------------------------------- -r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - -update ChangeLog - ------------------------------------------------------------------------- -r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/AUTHORS - M /trunk/samtools/Makefile - M /trunk/samtools/misc/Makefile - -fixed minor things in Makefile - ------------------------------------------------------------------------- -r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines -Changed paths: - M /trunk/samtools/bamtk.c - - * samtools-0.1.4-5 (r3310 - * no change to samtools itself. Version number is increased to reflect the - changes in the Makefile building system. - ------------------------------------------------------------------------- -r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/AUTHORS - D /trunk/samtools/README - -update information... - ------------------------------------------------------------------------- -r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/misc/novo2sam.pl - - * updated novoalign converter by Colin Hercus et al. - * this version works with indels - ------------------------------------------------------------------------- -r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/INSTALL - M /trunk/samtools/Makefile - M /trunk/samtools/misc/Makefile - M /trunk/samtools/zlib/Makefile - - * update Makefile - * update INSTALL instruction - ------------------------------------------------------------------------- -r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines -Changed paths: - A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325) - D /trunk/samtools/Makefile.am - D /trunk/samtools/Makefile.generic - D /trunk/samtools/Makefile.lite - D /trunk/samtools/autogen.sh - D /trunk/samtools/cleanup.sh - D /trunk/samtools/configure.ac - A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305) - D /trunk/samtools/misc/Makefile.am - D /trunk/samtools/misc/Makefile.generic - M /trunk/samtools/razf.c - A /trunk/samtools/zlib - A /trunk/samtools/zlib/Makefile - A /trunk/samtools/zlib/adler32.c - A /trunk/samtools/zlib/compress.c - A /trunk/samtools/zlib/crc32.c - A /trunk/samtools/zlib/crc32.h - A /trunk/samtools/zlib/deflate.c - A /trunk/samtools/zlib/deflate.h - A /trunk/samtools/zlib/gzio.c - A /trunk/samtools/zlib/infback.c - A /trunk/samtools/zlib/inffast.c - A /trunk/samtools/zlib/inffast.h - A /trunk/samtools/zlib/inffixed.h - A /trunk/samtools/zlib/inflate.c - A /trunk/samtools/zlib/inflate.h - A /trunk/samtools/zlib/inftrees.c - A /trunk/samtools/zlib/inftrees.h - A /trunk/samtools/zlib/trees.c - A /trunk/samtools/zlib/trees.h - A /trunk/samtools/zlib/uncompr.c - A /trunk/samtools/zlib/zconf.h - A /trunk/samtools/zlib/zlib.h - A /trunk/samtools/zlib/zutil.c - A /trunk/samtools/zlib/zutil.h - D /trunk/samtools/zutil.h - - * added zlib-1.2.3 as razip requires that - * prepare to changed back to the Makefile building system - * unfinished! (will be soon) - ------------------------------------------------------------------------- -r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - -Unfinished - ------------------------------------------------------------------------- -r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.4-4 (r325) - * further avoid wrong consensus calls in repetitive regions. - ------------------------------------------------------------------------- -r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - M /trunk/samtools/sam.h - - * samtools-0.1.4-3 (r324) - * make maqcns generate the correct call in repetitive regions. - * allow filtering on mapQ at the pileup command line - ------------------------------------------------------------------------- -r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - - * samtools.pl-0.3.2 (r322) - * indels and SNPs use different mapping quality threshold - ------------------------------------------------------------------------- -r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/export2sam.pl - -fixed a typo - ------------------------------------------------------------------------- -r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - -just typo. no real change - ------------------------------------------------------------------------- -r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - -a little bit code cleanup - ------------------------------------------------------------------------- -r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - - * samtools.pl-0.3.1 - * change default parameters - * optionally print filtered variants - ------------------------------------------------------------------------- -r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - - * samtools.pl-0.3.0 - * combine snpFilter and indelFilter - ------------------------------------------------------------------------- -r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - - * samtools.pl-0.2.3 - * change a default parameter - ------------------------------------------------------------------------- -r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_maqcns.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - - * samtools-0.1.4-2 (r316) - * pileup: cap mapping quality at 60 (by default) - * pileup: always calculate RMS mapq - * pileup: allow to output variant sites only - ------------------------------------------------------------------------- -r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - - * samtools.pl-0.2.2 - * added pileup2fq - ------------------------------------------------------------------------- -r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - - * in snpFilter, suppress non-SNP sites - ------------------------------------------------------------------------- -r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - - * samtools.pl-0.2.1 - * fixed a typo - ------------------------------------------------------------------------- -r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - - * samtools.pl-0.2.0 - * snpFilter - ------------------------------------------------------------------------- -r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bgzf.c - - * minor changes to bgzf: return NULL if fd == -1 - * suggested by {kdj,jm18}@sanger.ac.uk - ------------------------------------------------------------------------- -r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines -Changed paths: - A /trunk/samtools/misc/interpolate_sam.pl - -Script for paired-end pileup, contributed by Stephen Montgomery. - ------------------------------------------------------------------------- -r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - - * samtools-0.1.4-1 (r304) - * fixed a minor bug in printing headers - ------------------------------------------------------------------------- -r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/maq2sam.c - M /trunk/samtools/samtools.1 - -Release samtools-0.1.4 - ------------------------------------------------------------------------- -r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-24 (r296) - * another similar bug in the indel caller - ------------------------------------------------------------------------- -r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-23 (r295) - * fixed a critical bug in the indel caller - ------------------------------------------------------------------------- -r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines -Changed paths: - M /trunk/samtools/bam_stat.c - -added a missing header file - ------------------------------------------------------------------------- -r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-22 (r293) - * open tview in the dot-view mode by default - ------------------------------------------------------------------------- -r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines -Changed paths: - M /trunk/samtools/samtools.1 - -Added a note to the manual. Currently SAMtools used unaligned words in -several places. Although this does not cause bus errors to me, it may -affect portability. Please see the "Bus error" wiki page for more -information. Also thank James Bonfields for pointing this out. - - ------------------------------------------------------------------------- -r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-21 (286) - * declare bam_aux_get_core() in bam.h - ------------------------------------------------------------------------- -r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-20 (r276) - * remove bam1_t::hash again. We need to modify the Perl API anyway to - make it work with the latest SVN. - * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index - ------------------------------------------------------------------------- -r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam.h - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-19 (r275) - * a minor change to the bam1_t struct: added back "void *hash" for the - backward compatibility with Bio::DB::Sam - ------------------------------------------------------------------------- -r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_rmdupse.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-18 (r273) - * rmdupse: do not remove unmapped reads - ------------------------------------------------------------------------- -r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines -Changed paths: - M /trunk/samtools/bam_rmdupse.c - -change a parameter. It does nothing - ------------------------------------------------------------------------- -r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile.am - M /trunk/samtools/Makefile.generic - M /trunk/samtools/Makefile.lite - A /trunk/samtools/bam_rmdupse.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/configure.ac - - * samtools-0.1.3-17 (r271) - * added 'rmdupse' command - ------------------------------------------------------------------------- -r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.3-16 (r267) - * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs - ------------------------------------------------------------------------- -r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-15 (r266) - * report an error if a non-* reference is present while @SQ is absent - ------------------------------------------------------------------------- -r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.3-14 (r262) - * make samopen() recognize @SQ header lines - ------------------------------------------------------------------------- -r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bgzf.c - M /trunk/samtools/sam.c - M /trunk/samtools/sam_view.c - - * samtools-0.1.3-13 (r260) - * report error for file I/O error - ------------------------------------------------------------------------- -r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile.am - -update Makefile.am - ------------------------------------------------------------------------- -r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/sam.c - M /trunk/samtools/sam.h - - * samtools-0.1.3-12 (r259) - * use the new I/O interface in pileup - ------------------------------------------------------------------------- -r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile.generic - M /trunk/samtools/Makefile.lite - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - A /trunk/samtools/sam.c - A /trunk/samtools/sam.h - A /trunk/samtools/sam_view.c - - * samtools-0.1.3-11 (r258) - * unify the interface to BAM and SAM I/O - ------------------------------------------------------------------------- -r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile.lite - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-10 (r257) - * allow hex with "pileup -m" - ------------------------------------------------------------------------- -r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam_lpileup.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-9 (r256) - * fixed a bug in bam_lpileup.c - * I do not know if this also fixes the bug causing assertion failure in the tview - ------------------------------------------------------------------------- -r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-8 (r251) - * fixed a bug when there are reads without coordinates - ------------------------------------------------------------------------- -r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines -Changed paths: - A /trunk/samtools/AUTHORS - A /trunk/samtools/README - M /trunk/samtools/cleanup.sh - -added missing files - ------------------------------------------------------------------------- -r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile.generic - M /trunk/samtools/Makefile.lite - M /trunk/samtools/configure.ac - M /trunk/samtools/misc/Makefile.generic - -improve large file support in compilation - ------------------------------------------------------------------------- -r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines -Changed paths: - M /trunk/samtools/INSTALL - -update INSTALL - ------------------------------------------------------------------------- -r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile.am - M /trunk/samtools/autogen.sh - M /trunk/samtools/cleanup.sh - M /trunk/samtools/configure.ac - A /trunk/samtools/misc/Makefile.am - -fixed various issues about the GNU building scripts - ------------------------------------------------------------------------- -r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines -Changed paths: - M /trunk/samtools/ChangeLog - D /trunk/samtools/Makefile - A /trunk/samtools/Makefile.am - A /trunk/samtools/Makefile.generic - A /trunk/samtools/autogen.sh - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - A /trunk/samtools/cleanup.sh - A /trunk/samtools/configure.ac - D /trunk/samtools/misc/Makefile - A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245) - - * samtools-0.1.3-7 (r246) - * incorporated revisions from Nils Homer - * enhanced support of displaying color-space reads - ------------------------------------------------------------------------- -r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-6 (r244) - * fixed segfault for unmapped reads - ------------------------------------------------------------------------- -r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-5 (r243) - * fixed a long existing bug which may cause memory leak - * check MD - * consensus calling now works with "=", but indel calling not - ------------------------------------------------------------------------- -r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_md.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-4 (r242) - * fixed a memory leak - ------------------------------------------------------------------------- -r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/Makefile.lite - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - A /trunk/samtools/bam_md.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-3 (r240) - * generate MD tag - * generate "=" bases - * the plain pileup now support "=" bases, but consensus calling and glfgen may fail - ------------------------------------------------------------------------- -r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines -Changed paths: - M /trunk/samtools/bam.h - M /trunk/samtools/bam_aux.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-2 (r239) - * fixed bugs in bam_aux.c (these functions nevered used by samtools) - * removed bam_aux_init()/bam_aux_destroy() - * added tagview for testing bam_aux - ------------------------------------------------------------------------- -r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.3-1 - * fixed a bug in pileup: the first read in a chromosome may not be printed - ------------------------------------------------------------------------- -r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile.lite - -a missing file in Makefile.lite - ------------------------------------------------------------------------- -r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines -Changed paths: - M /trunk/samtools/NEWS - M /trunk/samtools/bamtk.c - -Release samtools-0.1.3 - ------------------------------------------------------------------------- -r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-28 - * make samtools more robust to weird input such as empty file - ------------------------------------------------------------------------- -r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - M /trunk/samtools/samtools.1 - -prepare for release 0.1.3 - ------------------------------------------------------------------------- -r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines -Changed paths: - A /trunk/samtools/misc/blast2sam.pl - -convert NCBI-BLASTN to SAM - ------------------------------------------------------------------------- -r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_lpileup.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-27 - * fixed a small memory leak in tview - ------------------------------------------------------------------------- -r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_rmdup.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-26 - * fixed a bug in rmdup when there are unmapped reads - ------------------------------------------------------------------------- -r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - -proposed NEWS for the new release (have not yet) - ------------------------------------------------------------------------- -r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines -Changed paths: - M /trunk/samtools/misc/samtools.pl - - * samtools.pl-0.1.1 - * improve indelFilter to avoid filtering true indels. The new filter relies - on the new pileup indel line implemented in samtools-0.1.2-25 - ------------------------------------------------------------------------- -r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - - * samtools-0.1.2-25 - * change the pileup indel line to shows the number of alignments actually - containing indels - ------------------------------------------------------------------------- -r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - -update ChangeLog from "svn log" - ------------------------------------------------------------------------- -r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/kseq.h - - * samtools-0.1.2-24 - * in merge, gives a warning rather than error if the target sequence length is different - * allow empty header - ------------------------------------------------------------------------- -r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam.c - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-23 - * recognize '*' at the QUAL field - ------------------------------------------------------------------------- -r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_import.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/kseq.h - - * samtools-0.1.2-22 - * the field separater is TAB only, now - ------------------------------------------------------------------------- -r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines -Changed paths: - M /trunk/samtools/examples/ex1.sam.gz - - * fixed the problem in the example alignment due to the bug in fixmate - ------------------------------------------------------------------------- -r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_mate.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/soap2sam.pl - - * samtools-0.1.2-21 - * fixed a nasty bug in `fixmate' - ------------------------------------------------------------------------- -r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/bowtie2sam.pl - M /trunk/samtools/misc/soap2sam.pl - M /trunk/samtools/misc/wgsim_eval.pl - -make the script robust to the bugs in SOAP-2.1.7 - ------------------------------------------------------------------------- -r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_stat.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-20 - * check if file is truncated in flagstat - ------------------------------------------------------------------------- -r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-19 - * print the header if requested - ------------------------------------------------------------------------- -r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-18 - * fixed a minor bug reported by Nils Homer - ------------------------------------------------------------------------- -r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines -Changed paths: - A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184) - D /trunk/samtools/Makefile.std - A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184) - D /trunk/samtools/misc/Makefile.std - -rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time... - ------------------------------------------------------------------------- -r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines -Changed paths: - D /trunk/samtools/Makefile - A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183) - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bam_tview.c - M /trunk/samtools/bamtk.c - D /trunk/samtools/misc/Makefile - A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182) - M /trunk/samtools/samtools.1 - - * samtools-0.1.2-17 - * incorporating Nils' changes - * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils) - ------------------------------------------------------------------------- -r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_maqcns.h - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/kseq.h - A /trunk/samtools/kstring.c - A /trunk/samtools/kstring.h - - * samtools-0.1.2-16 - * made pileup take a list of proposed indels. An insertion is N at the moment. - * added my kstring library for a bit complex parsing of the position list. - ------------------------------------------------------------------------- -r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines -Changed paths: - M /trunk/samtools/misc/soap2sam.pl - - * soap2sam.pl-0.1.2 - * more robust to truncated soap output - ------------------------------------------------------------------------- -r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile.lite - -added bam_stat.o to Makefile.lite - ------------------------------------------------------------------------- -r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-15 - * generate RMS of mapQ instead of max mapQ - ------------------------------------------------------------------------- -r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/glf.c - M /trunk/samtools/glf.h - M /trunk/samtools/misc/Makefile - - * samtools-0.1.2-14 - * implemented GLFv3 - ------------------------------------------------------------------------- -r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-13 - * fixed a minor bug in displaying pileup - ------------------------------------------------------------------------- -r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-12 - * optionally print SAM header - ------------------------------------------------------------------------- -r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines -Changed paths: - M /trunk/samtools/bamtk.c - M /trunk/samtools/glf.c - - * samtools-0.1.2-11 - * use "GLF\3" as the magic for GLFv3 files - ------------------------------------------------------------------------- -r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines -Changed paths: - M /trunk/samtools/Makefile - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_index.c - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/glf.c - M /trunk/samtools/glf.h - - * samtools-0.1.2-10 - * fixed a bug in import: core.bin is undefined for unmapped reads - * this bug can be alleviated (not completely solved) in bam_index.c - * update to GLFv3: pos is changed to offset for better compression - ------------------------------------------------------------------------- -r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines -Changed paths: - M /trunk/samtools/misc/wgsim.c - - * wgsim-0.2.3 - * fixed a bug in simulating indels - ------------------------------------------------------------------------- -r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines -Changed paths: - M /trunk/samtools/misc/wgsim.c - - * wgsim-0.2.2 - * allow to print mismatch information as fastq comment. MAQ does - not like long read names. - ------------------------------------------------------------------------- -r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/misc/wgsim.c - M /trunk/samtools/misc/wgsim_eval.pl - - * wgsim-0.2.1 - * fixed a bug about color read coordinates - * fixed a bug in read names - * wgsim_eval.pl-0.1.3 - * make the script work with color reads - ------------------------------------------------------------------------- -r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/Makefile - M /trunk/samtools/misc/wgsim.c - - * wgsim: added a note - ------------------------------------------------------------------------- -r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines -Changed paths: - M /trunk/samtools/misc/wgsim.c - M /trunk/samtools/misc/wgsim_eval.pl - - * wgsim-0.2.0 - * considerable code clean up - * print number of substitutions/indels/errors on each read - * potentially support SOLiD simulation, though not tested at the moment - * wgsim_eval.pl-0.1.2 - * change in accordant with wgsim - ------------------------------------------------------------------------- -r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-9 - * fixed a bug in bam_fetch, caused by completely contained adjacent chunks - ------------------------------------------------------------------------- -r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines -Changed paths: - M /trunk/samtools/bamtk.c - -Fix annoying segv when invalid region specified. - ------------------------------------------------------------------------- -r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines -Changed paths: - D /trunk/samtools/misc/indel_filter.pl - A /trunk/samtools/misc/samtools.pl - - * move indel_filter.pl to samtools.pl - ------------------------------------------------------------------------- -r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_mate.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-7 - * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP - ------------------------------------------------------------------------- -r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_stat.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-7 - * fixed a minor bug in flagstat - ------------------------------------------------------------------------- -r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/misc/indel_filter.pl - - * samtools-0.1.2-6 - * improve indel caller by setting maximum window size - ------------------------------------------------------------------------- -r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines -Changed paths: - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bamtk.c - - * output max mapping quality in indel line - ------------------------------------------------------------------------- -r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines -Changed paths: - M /trunk/samtools/misc/maq2sam.c - -fixed a bug in generating tag AM - ------------------------------------------------------------------------- -r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines -Changed paths: - M /trunk/samtools/bam_index.c - M /trunk/samtools/bamtk.c - -fixed a potential memory problem in indexing - ------------------------------------------------------------------------- -r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines -Changed paths: - M /trunk/samtools/Makefile - -Pass LIBS to recursive targets to facilitate building at Broad. - ------------------------------------------------------------------------- -r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/bam_plcmd.c - M /trunk/samtools/bam_stat.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-3 - * fixed a bug in generating GLFv2 for indels - * improve flagstat report a little bit - ------------------------------------------------------------------------- -r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines -Changed paths: - M /trunk/samtools/Makefile - A /trunk/samtools/bam_stat.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.2-1 - * added flagstat command - ------------------------------------------------------------------------- -r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/NEWS - M /trunk/samtools/bamtk.c - M /trunk/samtools/samtools.1 - -Release SAMtools-0.1.2 - ------------------------------------------------------------------------- -r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines -Changed paths: - A /trunk/samtools/misc/indel_filter.pl - -Script for filtering indel results - ------------------------------------------------------------------------- -r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines -Changed paths: - A /trunk/samtools/misc/zoom2sam.pl - -convert ZOOM to SAM - ------------------------------------------------------------------------- -r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines -Changed paths: - A /trunk/samtools/misc/novo2sam.pl - -add a script to convert novo alignment to SAM - ------------------------------------------------------------------------- -r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines -Changed paths: - M /trunk/samtools/ChangeLog - M /trunk/samtools/ChangeLog.old - M /trunk/samtools/samtools.1 - -update documentation and ChangeLog - ------------------------------------------------------------------------- -r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines -Changed paths: - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - - * samtools-0.1.1-19 - * fixed a bug in "merge" command line - ------------------------------------------------------------------------- -r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines -Changed paths: - M /trunk/samtools/misc/Makefile - A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108) - M /trunk/samtools/misc/export2sam.pl - A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108) - A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108) - A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108) - - * merge from branches/dev/ - * all future development will happen here - ------------------------------------------------------------------------- -r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines -Changed paths: - M /trunk/samtools/COPYING - M /trunk/samtools/ChangeLog - A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108) - M /trunk/samtools/Makefile - A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108) - M /trunk/samtools/bam.c - M /trunk/samtools/bam.h - M /trunk/samtools/bam_import.c - M /trunk/samtools/bam_index.c - M /trunk/samtools/bam_lpileup.c - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_maqcns.h - A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108) - M /trunk/samtools/bam_pileup.c - M /trunk/samtools/bam_plcmd.c - A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108) - M /trunk/samtools/bam_sort.c - M /trunk/samtools/bamtk.c - M /trunk/samtools/bgzf.h - M /trunk/samtools/examples/00README.txt - A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108) - D /trunk/samtools/examples/ex1.fa.fai - M /trunk/samtools/examples/ex1.sam.gz - M /trunk/samtools/faidx.c - A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108) - M /trunk/samtools/glf.h - M /trunk/samtools/misc/Makefile - M /trunk/samtools/misc/maq2sam.c - M /trunk/samtools/razf.c - M /trunk/samtools/source.dot - - * Merge from branches/dev/ - * all future development will happen here at trunk/ - ------------------------------------------------------------------------- -r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines -Changed paths: - M /trunk/samtools/bam_maqcns.c - M /trunk/samtools/bam_tview.c - -Fix problem with compiling without curses. - ------------------------------------------------------------------------- -r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines -Changed paths: - A /trunk/samtools (from /branches/dev/samtools:62) - -Create trunk copy - ------------------------------------------------------------------------- -r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines -Changed paths: - A /branches/dev/samtools/NEWS - M /branches/dev/samtools/bamtk.c - M /branches/dev/samtools/samtools.1 - -Release samtools-0.1.1 - ------------------------------------------------------------------------- -r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines -Changed paths: - M /branches/dev/samtools/bam_aux.c - M /branches/dev/samtools/bam_index.c - M /branches/dev/samtools/bam_plcmd.c - M /branches/dev/samtools/bam_tview.c - M /branches/dev/samtools/bamtk.c - M /branches/dev/samtools/razf.c - M /branches/dev/samtools/samtools.1 - - * samtools-0.1.0-66 - * fixed a bug in razf.c: reset z_eof when razf_seek() is called - * fixed a memory leak in parsing a region - * changed pileup a little bit when -s is in use: output ^ and $ - * when a bam is not indexed, output more meaningful error message - * fixed a bug in indexing for small alignment - * fixed a bug in the viewer when we come to the end of a reference file - * updated documentation - * prepare to release 0.1.1 - ------------------------------------------------------------------------- -r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines -Changed paths: - A /branches/dev/samtools/examples - A /branches/dev/samtools/examples/00README.txt - A /branches/dev/samtools/examples/ex1.fa - A /branches/dev/samtools/examples/ex1.fa.fai - A /branches/dev/samtools/examples/ex1.sam.gz - -example - ------------------------------------------------------------------------- -r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/ChangeLog - -update ChangeLog - ------------------------------------------------------------------------- -r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/misc/export2sam.pl - - * added comments - * fixed several bugs - ------------------------------------------------------------------------- -r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines -Changed paths: - A /branches/dev/samtools/misc/export2sam.pl - -convert Export format to SAM; not thoroughly tested - ------------------------------------------------------------------------- -r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines -Changed paths: - M /branches/dev/samtools/bam_import.c - M /branches/dev/samtools/bam_plcmd.c - M /branches/dev/samtools/bam_tview.c - M /branches/dev/samtools/bamtk.c - A /branches/dev/samtools/source.dot - - * samtools-0.1.0-65 - * pileup: generate maq-like simple output - * pileup: allow to output pileup at required sites - * source.dot: source file relationship graph - * tview: fixed a minor bug - ------------------------------------------------------------------------- -r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines -Changed paths: - D /branches/dev/samtools/misc/all2sam.pl - -remove all2sam.pl - ------------------------------------------------------------------------- -r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines -Changed paths: - A /branches/dev/samtools/COPYING - M /branches/dev/samtools/bam.h - M /branches/dev/samtools/faidx.h - M /branches/dev/samtools/khash.h - M /branches/dev/samtools/kseq.h - M /branches/dev/samtools/ksort.h - M /branches/dev/samtools/samtools.1 - -Added copyright information and a bit more documentation. No code change. - ------------------------------------------------------------------------- -r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/bam.c - M /branches/dev/samtools/bam.h - M /branches/dev/samtools/bam_index.c - M /branches/dev/samtools/bam_maqcns.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-64 - * improved efficiency of the indel caller for spliced alignments - ------------------------------------------------------------------------- -r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/bam.c - M /branches/dev/samtools/bam.h - M /branches/dev/samtools/bam_aux.c - M /branches/dev/samtools/bam_index.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-63 - * a bit code cleanup: reduce the dependency between source files - ------------------------------------------------------------------------- -r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/bam_maqcns.c - M /branches/dev/samtools/bam_plcmd.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-62 - * fixed a memory leak - ------------------------------------------------------------------------- -r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/ChangeLog - M /branches/dev/samtools/bam.h - M /branches/dev/samtools/samtools.1 - -update documentation, ChangeLog and a comment - ------------------------------------------------------------------------- -r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines -Changed paths: - M /branches/dev/samtools/Makefile - M /branches/dev/samtools/bam.h - M /branches/dev/samtools/bam_maqcns.c - M /branches/dev/samtools/bam_maqcns.h - M /branches/dev/samtools/bam_pileup.c - A /branches/dev/samtools/bam_plcmd.c - M /branches/dev/samtools/bamtk.c - M /branches/dev/samtools/samtools.1 - - * samtools-0.1.0-61 - * moved pileup command to a separate source file - * added indel caller - * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!) - * updated documentation - ------------------------------------------------------------------------- -r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/bam_maqcns.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-60 - * fixed another bug in maqcns when there is a nearby deletion - ------------------------------------------------------------------------- -r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines -Changed paths: - M /branches/dev/samtools/bam_maqcns.c - M /branches/dev/samtools/bam_pileup.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-59 - * pileup: outputing consensus is now optional - * fixed a bug in glfgen. This bug also exists in maq's glfgen. However, - I am not quite sure why the previous version may have problem. - ------------------------------------------------------------------------- -r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines -Changed paths: - M /branches/dev/samtools/bam_pileup.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-58 - * add maq consensus to pileup. However, I will move this part to a new - command as strictly speaking, consensus callin is not part of pileup, - and imposing it would make it harder to generate for other language - bindings. - ------------------------------------------------------------------------- -r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/bgzf.c - -Fix bug in tell() after reads that consume to the exact end of a block. - ------------------------------------------------------------------------- -r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/samtools.1 - -update manual - ------------------------------------------------------------------------- -r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines -Changed paths: - M /branches/dev/samtools/bam_import.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-57 - * fixed a bug in parser when there is auxiliary fields - * made the parser a bit more robust - ------------------------------------------------------------------------- -r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines -Changed paths: - M /branches/dev/samtools/bam_index.c - M /branches/dev/samtools/bamtk.c - M /branches/dev/samtools/bgzf.c - - * samtools-0.1.0-56 - * fixed a bug in bgzf (only reading is affected) - * fixed a typo in bam_index.c - * in bam_index.c, check potential bugs in the underlying I/O library - ------------------------------------------------------------------------- -r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/samtools.1 - -update manual - ------------------------------------------------------------------------- -r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines -Changed paths: - M /branches/dev/samtools/bam.h - M /branches/dev/samtools/bam_pileup.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-55 - * tried to make pileup work with clipping (previously not), though NOT tested - * removed -v from pileup - * made pileup take the reference sequence - ------------------------------------------------------------------------- -r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines -Changed paths: - M /branches/dev/samtools/bam_import.c - M /branches/dev/samtools/bamtk.c - M /branches/dev/samtools/samtools.1 - - * samtools-0.1.0-54 - * in parser, recognize "=", rather than ",", as a match - * in parser, correctl parse "=" at the MRNM field. - ------------------------------------------------------------------------- -r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/misc/maq2sam.c - -fixed a bug in handling maq flag 64 and 192 - ------------------------------------------------------------------------- -r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/misc/md5fa.c - -also calculate unordered md5sum check - ------------------------------------------------------------------------- -r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/misc/md5fa.c - -fixed a minor bug when there are space in the sequence - ------------------------------------------------------------------------- -r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/misc/md5fa.c - -fixed a potential memory leak - ------------------------------------------------------------------------- -r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/bam_import.c - M /branches/dev/samtools/bam_index.c - M /branches/dev/samtools/bamtk.c - - * fixed a bug in import: bin is wrongly calculated - ------------------------------------------------------------------------- -r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/misc/all2sam.pl - -nothing, really - ------------------------------------------------------------------------- -r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/Makefile - M /branches/dev/samtools/kseq.h - M /branches/dev/samtools/misc/Makefile - A /branches/dev/samtools/misc/md5.c - A /branches/dev/samtools/misc/md5.h - A /branches/dev/samtools/misc/md5fa.c - - * fixed two warnings in kseq.h - * added md5sum utilities - ------------------------------------------------------------------------- -r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines -Changed paths: - M /branches/dev/samtools/Makefile - M /branches/dev/samtools/bam_import.c - M /branches/dev/samtools/bamtk.c - A /branches/dev/samtools/kseq.h - D /branches/dev/samtools/kstream.h - - * samtools-0.1.0-52 - * replace kstream with kseq. kseq is a superset of kstream. I need the - extra functions in kseq.h. - * also compile stand-alone faidx - ------------------------------------------------------------------------- -r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/bam.h - M /branches/dev/samtools/bam_sort.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-51 - * sorting by read names is available - ------------------------------------------------------------------------- -r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/bam.c - M /branches/dev/samtools/bam.h - M /branches/dev/samtools/bam_import.c - M /branches/dev/samtools/bam_maqcns.c - M /branches/dev/samtools/bam_pileup.c - M /branches/dev/samtools/bam_sort.c - M /branches/dev/samtools/bam_tview.c - M /branches/dev/samtools/bamtk.c - M /branches/dev/samtools/misc/maq2sam.c - - * samtools-0.1.0-50 - * format change to meet the latest specification - ------------------------------------------------------------------------- -r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/bam_maqcns.c - M /branches/dev/samtools/misc/maq2sam.c - - * minor change in maqcns: special care when n==0 - * change maq2sam to meet the latest specification - ------------------------------------------------------------------------- -r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/razf.c - M /branches/dev/samtools/razf.h - -considerable code clean up in razf - ------------------------------------------------------------------------- -r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/ChangeLog - M /branches/dev/samtools/Makefile - M /branches/dev/samtools/faidx.c - -make RAZF optional in faidx.c - ------------------------------------------------------------------------- -r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/Makefile - M /branches/dev/samtools/bam.h - M /branches/dev/samtools/bam_aux.c - M /branches/dev/samtools/bamtk.c - M /branches/dev/samtools/samtools.1 - - * samtools-0.1.0-49 - * added routines for retrieving aux data, NOT TESTED YET! - ------------------------------------------------------------------------- -r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines -Changed paths: - M /branches/dev/samtools/bam.c - M /branches/dev/samtools/bam_import.c - M /branches/dev/samtools/bam_maqcns.c - M /branches/dev/samtools/bamtk.c - M /branches/dev/samtools/bgzf.c - M /branches/dev/samtools/samtools.1 - - * samtools-0.1.0-48 - * bgzf: fixed a potential integer overflow on 32-it machines - * maqcns: set the minimum combined quality as 0 - * supporting hex strings - ------------------------------------------------------------------------- -r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/bam_maqcns.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-47 - * fixed the bug in maqcns - ------------------------------------------------------------------------- -r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/Makefile - M /branches/dev/samtools/bam.h - A /branches/dev/samtools/bam_maqcns.c - A /branches/dev/samtools/bam_maqcns.h - M /branches/dev/samtools/bam_tview.c - M /branches/dev/samtools/bamtk.c - A /branches/dev/samtools/glf.h - - * samtools-0.1.0-46 - * add MAQ consensus caller, currently BUGGY! - ------------------------------------------------------------------------- -r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines -Changed paths: - M /branches/dev/samtools/bam_pileup.c - M /branches/dev/samtools/bam_tview.c - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-45 - * tview: display padded alignment (but not P operation) - * better coordinates and reference sequence - ------------------------------------------------------------------------- -r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines -Changed paths: - A /branches/dev/samtools/ChangeLog - -new ChangeLog - ------------------------------------------------------------------------- -r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines -Changed paths: - D /branches/dev/samtools/ChangeLog - A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6) - -Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from -the log of my personal SVN repository. - ------------------------------------------------------------------------- -r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines -Changed paths: - M /branches/dev/samtools/Makefile - M /branches/dev/samtools/bamtk.c - M /branches/dev/samtools/bgzf.c - - * samtools-0.1.0-44 - * declare fseeko and ftello as some Linux may not do this by default and - missing these declarations will make bgzf buggy - * get rid of some harmless warings - * use BGZF by default, now - ------------------------------------------------------------------------- -r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines -Changed paths: - M /branches/dev/samtools/bam_index.c - M /branches/dev/samtools/bamtk.c - M /branches/dev/samtools/razf.c - - * samtools-0.1.0-43 - * fixed a bug in razf_read() - * give more warnings when the file is truncated (or due to bugs in I/O library) - ------------------------------------------------------------------------- -r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/bgzf.c - -fixed a bug in bgzf.c at the end of the file - ------------------------------------------------------------------------- -r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines -Changed paths: - M /branches/dev/samtools/bamtk.c - - * samtools-0.1.0-42 - * a lot happened to RAZF, although samtools itself is untouched. Better - also update the version number anyway to avoid confusion - ------------------------------------------------------------------------- -r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/razf.c - -a change from Jue, but I think it should not matter - ------------------------------------------------------------------------- -r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines -Changed paths: - M /branches/dev/samtools/razf.c - -fixed a potential bug in razf. However, it seems still buggy, just -rarely happens, very rarely. - ------------------------------------------------------------------------- -r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/razf.c - -fixed a bug in razf, with the help of Jue - ------------------------------------------------------------------------- -r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/bam_index.c - -remove a comment - ------------------------------------------------------------------------- -r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines -Changed paths: - M /branches/dev/samtools/Makefile - M /branches/dev/samtools/bam.h - M /branches/dev/samtools/razf.c - M /branches/dev/samtools/razf.h - - * Jue has updated razf to realize Bob's scheme - ------------------------------------------------------------------------- -r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines -Changed paths: - A /branches/dev/samtools/samtools.1 - -the manual page - ------------------------------------------------------------------------- -r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines -Changed paths: - A /branches/dev/samtools/ChangeLog - A /branches/dev/samtools/Makefile - A /branches/dev/samtools/bam.c - A /branches/dev/samtools/bam.h - A /branches/dev/samtools/bam_aux.c - A /branches/dev/samtools/bam_endian.h - A /branches/dev/samtools/bam_import.c - A /branches/dev/samtools/bam_index.c - A /branches/dev/samtools/bam_lpileup.c - A /branches/dev/samtools/bam_pileup.c - A /branches/dev/samtools/bam_sort.c - A /branches/dev/samtools/bam_tview.c - A /branches/dev/samtools/bamtk.c - A /branches/dev/samtools/bgzf.c - A /branches/dev/samtools/bgzf.h - A /branches/dev/samtools/bgzip.c - A /branches/dev/samtools/faidx.c - A /branches/dev/samtools/faidx.h - A /branches/dev/samtools/khash.h - A /branches/dev/samtools/ksort.h - A /branches/dev/samtools/kstream.h - A /branches/dev/samtools/misc - A /branches/dev/samtools/misc/Makefile - A /branches/dev/samtools/misc/all2sam.pl - A /branches/dev/samtools/misc/maq2sam.c - A /branches/dev/samtools/razf.c - A /branches/dev/samtools/razf.h - A /branches/dev/samtools/razip.c - A /branches/dev/samtools/zutil.h - -The initial version of samtools, replicated from my local SVN repository. -The current version is: 0.1.0-42. All future development will happen here. - ------------------------------------------------------------------------- -r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines -Changed paths: - A /branches/dev/samtools - -samtools (C version) - ------------------------------------------------------------------------- diff --git a/ChangeLog.old b/ChangeLog.old index def5438..19aefae 100644 --- a/ChangeLog.old +++ b/ChangeLog.old @@ -1,3 +1,2141 @@ +commit db2ad3e19068cbafde72ecde75d0638bbb3598ba +Author: Heng Li +Date: Thu Feb 16 14:45:17 2012 -0500 + + removed downsample.c + +commit 6c55c576903992c6fef148fe3b606fbc8bd10655 +Author: Heng Li +Date: Thu Feb 16 14:45:06 2012 -0500 + + print to output + +commit db1044a34e6049c87eaa63c39ed6e56f03e7d4c1 +Author: Heng Li +Date: Thu Feb 16 14:39:34 2012 -0500 + + removed sample + + Downsampling already exists in "view". View also keeps pairing while "sample" does not. + +commit ffdeed3e5d4a530bfdf6f9ba97fff0ba7add6cba +Merge: 2daad7b accf026 +Author: Heng Li +Date: Thu Feb 16 14:22:15 2012 -0500 + + Merge branch 'master' of github.com:lh3/samtools + +commit accf0260fd1117e10047344345d40b31a9ec31bb +Merge: 9134e0d c554160 +Author: Heng Li +Date: Thu Feb 16 11:21:14 2012 -0800 + + Merge pull request #8 from nh13/master + + Patches + +commit c554160df16ec7748cfdda4c7b54c641be7b809f +Author: Nils Homer +Date: Thu Feb 16 14:06:52 2012 -0500 + + * more README.md work + +commit 2a81ffe349208d917666808fbc9f3041e0cb57de +Author: Nils Homer +Date: Thu Feb 16 14:06:10 2012 -0500 + + * more README work + +commit fb3125f732715f62cded8685a23a002a96ce009b +Author: Nils Homer +Date: Thu Feb 16 14:05:19 2012 -0500 + + * more README work + +commit 444d41002c37e1c3d0f9208b4a88126c47276386 +Author: Nils Homer +Date: Thu Feb 16 14:02:13 2012 -0500 + + * updating README + +commit dec53cb1043fe7efadfde75fa2fd39b76de22e54 +Author: Nils Homer +Date: Thu Feb 16 13:55:01 2012 -0500 + + updating the README for markdown syntax + +commit 798da18c346dca8ec6005582a0ddb1d5420b04ca +Author: Nils Homer +Date: Thu Feb 16 13:48:35 2012 -0500 + + adding a README with the current differences between this repository and + the official one + +commit 4d22d86c0f28636662f2144a88cd168e104c4275 +Author: Nils Homer +Date: Thu Feb 16 13:35:03 2012 -0500 + + adding "samtools sample" to the main + +commit 893c25a37c21005dc42f45d45e9ad78ddc5f29bb +Author: Nils Homer +Date: Thu Feb 16 13:33:51 2012 -0500 + + * removing some compile flags to work with OS X + +commit 7ac22f72fdc32edd5c24af6baebfa7db5faf8e7b +Author: Jonathan Manning +Date: Thu Feb 16 10:47:14 2012 -0500 + + Check write filehandle after opening for write. tamw/tamr is a union type, so change is only semantic. + + Signed-off-by: Nils Homer + +commit fef53330416631690f60fdff42b6e43d764170dc +Author: Jonathan Manning +Date: Thu Feb 16 10:44:59 2012 -0500 + + Catch and report invalid BAM header, instead of segfaulting later on. + + Signed-off-by: Nils Homer + +commit 5cc013fe4930bf9b6e7963aab1cd4a3c94f695bc +Author: Jonathan Manning +Date: Thu Feb 16 10:44:16 2012 -0500 + + Add downsample to examples. + + Signed-off-by: Nils Homer + +commit b3fa9e7071532905a81dc7aa48eadc24b8c8846b +Author: Jonathan Manning +Date: Thu Feb 16 10:43:48 2012 -0500 + + Adjust for leading hard clip on colorspace reads. + + Signed-off-by: Nils Homer + +commit 1a9296c1389469d1c1db5b8069f0e11ffcc8abb2 +Author: Jonathan Manning +Date: Thu Feb 16 10:42:52 2012 -0500 + + Add samtools sample command, contributed by Davide Cittaro . + + Signed-off-by: Nils Homer + +commit 2a804f3379748aeba944f1dec306dd726ff3235e +Author: Jonathan Manning +Date: Thu Feb 16 10:42:07 2012 -0500 + + Add samtools qa command, contributed by Roman Valls Guimera . + + Signed-off-by: Nils Homer + +commit 0f3207fe8fd93e44d40fcf57204079c8c06d24a6 +Author: Jonathan Manning +Date: Thu Feb 16 10:39:08 2012 -0500 + + Makefile cleanup - allow CC, CFLAGS, LDFLAGS to be passed on make command line. Use LDFLAGS in samtools compile. + + Signed-off-by: Nils Homer + +commit 6e7df604025f6a86881bf7f4a16f30e15d31538a +Author: Jonathan Manning +Date: Thu Feb 16 10:31:15 2012 -0500 + + Allow max_mem for sort to be specified with units. + + Signed-off-by: Nils Homer + +commit f12ebcaf6e60d34180a27d70e09b743cef140b98 +Author: Jonathan Manning +Date: Thu Feb 16 10:29:11 2012 -0500 + + Allow user defined [lowercase] tags in header elements. + + Signed-off-by: Nils Homer + +commit 50b931fa3312dc109537a4260698ddecd0f06a05 +Author: Jonathan Manning +Date: Thu Feb 16 10:27:11 2012 -0500 + + Check lowerbound in text entry box to avoid segfault in tview. Remove redundant call to bam_aux_get. + + Signed-off-by: Nils Homer + +commit 5e729da5190949a813d20d329eab7ddb661816bd +Author: Nils Homer +Date: Thu Feb 16 10:31:48 2012 -0500 + + * fixing overflow/underflow in integer parsing + +commit fa50a4330b9abedaf07c26e13d31f05e57f1d319 +Author: Nils Homer +Date: Thu Feb 16 10:30:40 2012 -0500 + + * updating help message for samtools depth + +commit 79e52c9624b6dd3bdfdf439f4b4bc6f774c230a4 +Author: Nils Homer +Date: Thu Feb 16 10:29:32 2012 -0500 + + * adding support for outputting a circos histogram file in "samtools depth". Use + the "-c/-B" options. + +commit 2daad7b52daa86561c0fb65fe366691fad9f5ed3 +Author: Heng Li +Date: Thu Feb 16 09:31:57 2012 -0500 + + bugfix: wrong SP; missing DV in the VCF hdr + +commit 9134e0d5047c281ef3bd53da91771d4814a5131c +Author: Heng Li +Date: Wed Feb 8 11:19:12 2012 -0500 + + missing support of DV + +commit 34ebf12078c1d1015a0b8b9a9221243a60b22893 +Author: Heng Li +Date: Wed Feb 8 11:08:56 2012 -0500 + + new BCF DV format: number of variant reads + +commit 9589d3312fa2d076f48bdd68e2a5edd419c8070c +Author: Heng Li +Date: Tue Jan 10 10:30:27 2012 -0500 + + scale depth to quality (hidden option) + +commit 704473e14668333ecaca5fb7b238af405c43e3b1 +Author: Heng Li +Date: Tue Jan 10 10:18:17 2012 -0500 + + really nothing + +commit 01b307fd287962372bbf07461c88b54f41636817 +Author: Heng Li +Date: Wed Dec 7 13:07:42 2011 -0500 + + added an example containing 'B' + +commit c678791f0451ceb9205c1ab5c52c84641863c99a +Author: Heng Li +Date: Sat Dec 3 12:10:30 2011 -0500 + + 'B' now moves backward w.r.t. the query + +commit 152119bc06a073933ca830e8e1407538e44626cc +Author: Heng Li +Date: Fri Dec 2 10:50:12 2011 -0500 + + better consensus; a little more robust + +commit 454da4754ac503edda5b1329b67757d797e46e07 +Author: Heng Li +Date: Fri Dec 2 00:20:22 2011 -0500 + + in pileup call remove_B() + +commit ff2bcac1cc078ba1879f18c89cfae314439d7086 +Author: Heng Li +Date: Fri Dec 2 00:17:32 2011 -0500 + + working on a few toy examples + +commit 745ca7260158d6df7897b52598033ffb055a9e4f +Author: Heng Li +Date: Thu Dec 1 22:55:39 2011 -0500 + + bam_remove_B(); not tested + +commit 07e4cdc7300abfcc82e03105b4689f95cab551cd +Author: Heng Li +Date: Thu Nov 10 12:58:55 2011 -0500 + + baseQ threshold on plain pipleup; removed -E + +commit 322ebf2082dfa91df44b3a996d26c85357e5d5a2 +Author: Heng Li +Date: Wed Oct 19 09:28:04 2011 -0400 + + fixed two gcc warnings + +commit a632457b4c4adc50d833b56b5a5231feafaf8193 +Author: Heng Li +Date: Tue Oct 4 10:13:23 2011 -0400 + + change size_t to uint32_t in bam_header_t + + This may cause issues on 64-bit big-endian machines. Reported and fixed by Paolo Emilio Mazzon. + +commit af31bf5a78aea03baf6eb90fe50076549d499f6e +Author: Heng Li +Date: Mon Sep 26 20:17:57 2011 -0400 + + rename pad2unpad to depad + +commit 77b198b73dfad1048e5d1c5a64aa75ee7b90f596 +Author: Heng Li +Date: Fri Sep 23 01:22:40 2011 -0400 + + convert padded BAM to unpadded BAM + +commit adb9e2342b7b7501d9527d3c23afab10469ae2c6 +Author: Heng Li +Date: Wed Sep 7 11:40:50 2011 -0400 + + generate template cigar with "fixmate" + +commit 46e5ab445a0fe880216cbc0daf1225725b569d7a +Author: Heng Li +Date: Fri Sep 2 12:50:18 2011 -0400 + + update kseq.h to the latest version + +commit 68e9e4a73eb91405bb3e56bf0cdaf12d1b487abb +Author: Heng Li +Date: Fri Sep 2 12:44:45 2011 -0400 + + Release samtools-0.1.18 + +commit aa06bdadb2d109a79f927f478102f96a1f5fd258 +Author: Heng Li +Date: Fri Sep 2 12:14:17 2011 -0400 + + updated the revision number + +commit 267e1e1b6e54c0ab24f94cd9aee9cbd2d1923f9f +Merge: 19ff1d3 aebab30 +Author: Heng Li +Date: Fri Sep 2 12:13:08 2011 -0400 + + Merge https://github.com/lh3/samtools into reduce + + Conflicts: + bam_md.c + + Fixed a few typos in the merge + +commit aebab302399c24eaa6c5ab79d13d6bd5e2e9ea9a +Merge: c2c63d0 da62663 +Author: Heng Li +Date: Fri Sep 2 09:03:49 2011 -0700 + + Merge pull request #4 from peterjc/x_equals2 + + Implement basic support for =/X CIGAR operations + +commit 19ff1d3d7f47d7e61b121292aefe5a74bb8a18d2 +Author: Heng Li +Date: Thu Aug 25 16:38:12 2011 -0400 + + reduce BAM size (experimental) + +commit da626630fd98fd4e07ceb4d58c5c9a42d312a85d +Author: peterjc +Date: Mon Aug 22 06:58:08 2011 +0100 + + Support =/X CIGAR operations (treated like M) + +commit 461d8003529db77a4d5ecbd108312e868b051a3d +Author: peterjc +Date: Mon Aug 22 05:52:56 2011 +0100 + + Define CIGAR equals and X operationss (7 and 8) + +commit c2c63d067113baab41f3bc35fb28f4f00578accb +Merge: 7ab3ef3 9a0ed9a +Author: Heng Li +Date: Thu Aug 18 17:21:54 2011 -0700 + + Merge pull request #3 from peterjc/x_equals + + Accept SAM files using = in CIGAR (treats X and = as M) + +commit 9a0ed9a6b85c7981465f459300208dbd93e3c6f5 +Author: peterjc +Date: Thu Aug 18 19:28:52 2011 +0100 + + Accept SAM files using = in CIGAR (treats X and = as M) + +commit 7ab3ef388c1eb34d7912fd70cc5656c955240263 +Author: Heng Li +Date: Mon Aug 8 10:22:22 2011 -0400 + + bugfix: indexing takes huge memory + + This happens when an unmapped mate has coordinate 1. Thank Joel Martin for the fix. + +commit a3f6738593e944354a8f75306687d8b3acf08bf1 +Merge: a8bdca9 bc67ea2 +Author: Heng Li +Date: Mon Aug 8 09:52:26 2011 -0400 + + Merge branch 'master' of github.com:lh3/samtools + +commit bc67ea225da653f36a70b38382d6111dd494f659 +Author: Petr Danecek +Date: Thu Jul 28 20:03:16 2011 +0100 + + Variant Distance Bias + +commit deb578f0c49d0b7d8c3bc6be220b4d67e2e7dfdf +Author: Petr Danecek +Date: Tue Jul 26 09:57:37 2011 +0100 + + If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but use the tag instead. + +commit a8bdca9cf482a637b89ee4f98469a93e0ab5e69b +Author: Heng Li +Date: Mon Jul 25 10:10:55 2011 -0400 + + bugfix: LRT2=nan + +commit 0afe33137d046a3e849eeb4a54590f27cbad4228 +Author: Heng Li +Date: Fri Jul 22 21:55:38 2011 -0400 + + fixed a bug/typo + +commit 62d5849658c10222d40308c6b53ab4f99a448494 +Author: Heng Li +Date: Fri Jul 15 16:04:19 2011 -0400 + + allow to set see in subsampling + +commit 5f46243824cc9435b167973e1d51e13128794ea1 +Author: Heng Li +Date: Fri Jul 15 15:54:47 2011 -0400 + + support subsampling + +commit 5e55b6f34fc86cba7cf98d52ccaed405c3ffabbc +Author: Heng Li +Date: Fri Jul 15 15:53:38 2011 -0400 + + support indels + +commit f31c162926d6f43e8b60171789a258d02e1f9be5 +Author: Heng Li +Date: Thu Jul 7 17:02:33 2011 -0400 + + do not count indel with "view -Y" + +commit e412dae587883b4c17e5fbf4b7c33f38bfa8458a +Author: Heng Li +Date: Thu Jul 7 00:35:25 2011 -0400 + + for WIN32 compatibility + +commit 70a52501bcfa63824749893a5ab8ed3c38e34958 +Author: Heng Li +Date: Thu Jul 7 00:32:46 2011 -0400 + + for WIN32 compatibility + +commit 00438f14ed5984f08e8f7645a9b95644a812f969 +Author: Heng Li +Date: Wed Jul 6 23:41:45 2011 -0400 + + fixed an uninitialized variable + +commit 7609c4a01059c326544b3d0142dfe9c4229d68c6 +Author: Heng Li +Date: Wed Jul 6 23:39:31 2011 -0400 + + fixed an uninitialized variable + +commit cec7189a412f80ccb068a73bd28528915c16b0bf +Author: Heng Li +Date: Wed Jul 6 22:53:19 2011 -0400 + + Release samtools-0.1.17 + +commit 93c06a249de3bb666029bf07b66de5e8e5e314fa +Author: Heng Li +Date: Wed Jul 6 09:46:09 2011 -0400 + + bugfix: incorrect idxstats for the last seq + + Again, this bug is caused by 3rd-party code for the sorting order checking. + +commit 84f6ca62db6e27b8c4c711e7b5f3ca704bf27b4f +Author: Heng Li +Date: Tue Jul 5 23:30:23 2011 -0400 + + output mapping quality in the old pileup format + +commit 362e05fd670886acaede69b864903d730b9db3ca +Author: Heng Li +Date: Tue Jul 5 21:59:22 2011 -0400 + + added a brief description of the VCF format + +commit e690a696468205e0cc4560016361c997660dd496 +Author: Heng Li +Date: Tue Jul 5 16:23:10 2011 -0400 + + improved samtools manual page + +commit 362b4a1408ef3c32311d638aa8d85ce39c1c7b2d +Author: Heng Li +Date: Tue Jul 5 15:58:29 2011 -0400 + + merge bcftools.1 to samtools.1 + +commit 643e0e61ba7266efbc9e5bfcb8e41f369ba2ce0a +Author: Heng Li +Date: Tue Jul 5 13:39:02 2011 -0400 + + mpileup: when region set, set reference properly + +commit 613e4d67624a94f62563935fbd5cc294df69605a +Author: Heng Li +Date: Mon Jul 4 23:29:02 2011 -0400 + + compute the min PL diff + +commit 5b7d5d3f52b97ca42c8500eede808dab88a46a53 +Author: Heng Li +Date: Mon Jul 4 22:57:48 2011 -0400 + + rename trio.c to mut.c + +commit 84fe96ad64b0365ead93a4115d1684b9bebb98fc +Author: Heng Li +Date: Sun Jul 3 15:38:51 2011 -0400 + + added pair caller interface; not tested + +commit 2f2867b87b84c35319cc416d6173819d5c8a4e8c +Author: Heng Li +Date: Sun Jul 3 15:24:23 2011 -0400 + + inital implementation of a pair caller + +commit e97653cf2ad653c95886933c42a2b5492ccab5ff +Author: Heng Li +Date: Sun Jul 3 00:06:28 2011 -0400 + + convert bam to single-end fastq + +commit e8013e11f7a8db0a8d18c60d130169cca39bf2bd +Author: Heng Li +Date: Sat Jul 2 14:39:18 2011 -0400 + + improve BED parsing + +commit 1025714325fdc636aeee47a76db8dafbbbfde64b +Author: Heng Li +Date: Fri Jul 1 14:19:54 2011 -0400 + + update the manual page + +commit 8022d0039dff47b1c11b2421357d510c1f28ae15 +Author: Heng Li +Date: Fri Jul 1 14:17:03 2011 -0400 + + output the best constrained genotypes in trio + +commit 18c87295e12f5bebafdcae00d52000fb94c8a566 +Author: Heng Li +Date: Fri Jul 1 11:18:14 2011 -0400 + + added documentations for view -T + +commit daf7a8d96bd495296bf7c7d99cddb808a3ced7d5 +Author: Heng Li +Date: Thu Jun 30 22:45:20 2011 -0400 + + fixed a bug in writing SP + +commit e5c32bf9b28c6e3e861db88de56b5dbe11058b61 +Author: Heng Li +Date: Thu Jun 30 22:35:25 2011 -0400 + + optionally output read positions in mpileup + +commit 1008051155ec994c1901e18f3eb03ea32a62e5d7 +Author: Heng Li +Date: Thu Jun 30 22:17:25 2011 -0400 + + make faidx works with <2GB lines + +commit 2daebb63762425dd3074ddf71582ad189001e394 +Author: Heng Li +Date: Thu Jun 30 17:28:58 2011 -0400 + + fixed an issue in the trio caller and the indel caller + +commit 9fdd52cf0716fb342a94946433d564b28b230835 +Author: Heng Li +Date: Thu Jun 30 13:34:01 2011 -0400 + + Added trio caller; NOT tested yet + +commit ea22a8ed83625e9c82382b56acc42a2d9cfd17e5 +Author: Heng Li +Date: Thu Jun 30 11:42:29 2011 -0400 + + convert PL to 10-likelihood GL + +commit 10d7065267b0d12c2bfcb6c70204fb6944cd395d +Author: Heng Li +Date: Thu Jun 30 10:49:05 2011 -0400 + + fix a compatibility issue with the new bcftools + +commit d340f01f609c61b719d38a6a55629a3fc899e1cd +Author: Heng Li +Date: Sun Jun 26 23:41:20 2011 -0400 + + allow to ignore RG + +commit d6321faf98ebfe899b9409fb23c90a4aa8c6b542 +Author: Heng Li +Date: Sun Jun 5 23:05:21 2011 -0400 + + fixed a bug in SO checking due to a recent change + +commit bc995abf666d0c9ab4258f6c1b3518a45a89209f +Author: Heng Li +Date: Fri Jun 3 14:45:36 2011 -0400 + + update the version number + +commit 9e7cd83a08383858d008e0ccb2238a2b93831d6c +Author: Heng Li +Date: Fri Jun 3 14:43:12 2011 -0400 + + smarter way to parse a region string + +commit e58a90a0fde54053dac65352b34c13c3fea815fc +Author: Heng Li +Date: Wed Jun 1 14:36:22 2011 -0400 + + output LRT2 instead of LRT1 + +commit 08f78c9af3e5661f04f80bef424232de721dba03 +Author: Heng Li +Date: Wed Jun 1 14:02:28 2011 -0400 + + genotype test, but assuming 1-degree + +commit 587b852340d7e60f6f7cf474a92ef77aeab46018 +Author: Heng Li +Date: Wed Jun 1 12:55:19 2011 -0400 + + perform 2-degree test by default + +commit 3d38e403c5c830478b7eb157a484776997440501 +Author: Heng Li +Date: Wed Jun 1 12:44:34 2011 -0400 + + fixed a typo; but the result is still not good + +commit 06291624f7dcc57445676f3be25d0bc355dd7110 +Author: Heng Li +Date: Wed Jun 1 12:24:18 2011 -0400 + + fixed a typo + +commit 63b98aa33636b0d82a435bf49153c8c1502e7d42 +Author: Heng Li +Date: Wed Jun 1 12:23:37 2011 -0400 + + added HWE+F<0 filter + +commit 37d926e8999999b593d0637ab7dc379dbd3d6006 +Author: Heng Li +Date: Wed May 4 10:11:59 2011 -0400 + + improved sorting order checking in index + + Patches from Jonathan Manning + +commit 1c2dc6762c5f7cd946046b53346513f2f9761dbf +Author: Heng Li +Date: Tue May 3 23:09:05 2011 -0400 + + added r^2 estimate; added Brent's method + +commit c2d3bcd8f98e31668b5f1321222fbc6fd6336e75 +Author: Heng Li +Date: Sun May 1 23:45:23 2011 -0400 + + combine several utilites into vcfutils.lua + +commit be2e7362d7593ea4d03fb33cdb6af2aa096ca6c4 +Author: Heng Li +Date: Wed Apr 27 21:09:22 2011 -0400 + + minor warning + +commit 683ef0443860813d743cf84fa86dda9bfaf5445a +Author: Heng Li +Date: Wed Apr 27 10:10:38 2011 -0400 + + added versioning + +commit ed72f25ec85671f7646dbc92fa7b5b1dda427f7d +Author: Heng Li +Date: Wed Apr 27 10:04:02 2011 -0400 + + Output ML allele count + +commit 2a9e36d2d6c405b2411ca47458f028ada8fe1000 +Author: Heng Li +Date: Tue Apr 26 16:14:20 2011 -0400 + + use ar -s + +commit 7a4f54e6dbcd7c94acbb3f1050a93f94b8a07949 +Author: Heng Li +Date: Sat Apr 23 01:22:31 2011 -0400 + + added another type of LRT + +commit b9c5e84762a4aacce3a3771b51ea80967c79a2e5 +Author: Heng Li +Date: Fri Apr 22 16:00:31 2011 -0400 + + added version + +commit 8fad6677c5952efd67391581d64e67e02e7f6e68 +Author: Heng Li +Date: Fri Apr 22 00:30:19 2011 -0400 + + remove the pileup command + +commit 3a962fb6ebf779de70f9e6effb2d8701a9aa3dd9 +Author: Heng Li +Date: Thu Apr 21 23:10:45 2011 -0400 + + Release 0.1.16 (r963:234) + +commit b4d683cffbd98c43f05aff8610b37d63dd7e54aa +Author: Heng Li +Date: Thu Apr 21 12:44:44 2011 -0400 + + fixed a bug when coordinate-less reads are on the reverse strand + +commit c5ec45a128f409debc6a56a798024f53004037dc +Author: Heng Li +Date: Wed Apr 20 11:36:52 2011 -0400 + + added option '-f' to merge to avoid overwritting + +commit 68d431531370d24907c01a27f166f2341d7c4d35 +Author: Heng Li +Date: Wed Apr 20 10:26:58 2011 -0400 + + do not print a warning + +commit 32922607e51ad2260c337eb022b9e4aedacb049f +Author: Heng Li +Date: Wed Apr 20 10:21:06 2011 -0400 + + Added ldpair to compute LD between requested pairs + +commit b8d6fa71b91678fa02338257e0707d1e5ca098dd +Author: Heng Li +Date: Sun Apr 17 21:51:43 2011 -0400 + + On a toy sample, type "B" seems to be accepted + +commit 0e7ee9a6bb4029184202aa6e6738105ba0c0510b +Author: Heng Li +Date: Sun Apr 17 21:21:20 2011 -0400 + + added type "B"; not tested yet + +commit a513dfad0ac0062b03871eb6ecf26cb8d18dc895 +Author: Heng Li +Date: Sun Apr 17 19:25:54 2011 -0400 + + fixed a bug in bedidx.c: input BED not sorted + +commit de1e192bb0a8a762a54a6eee81d882fab01c3d32 +Author: Heng Li +Date: Sun Apr 17 18:51:08 2011 -0400 + + by default, always perform posterior chi^2 + +commit df6e0d1099895fc6cd7a19dc89fba95ed6654d35 +Author: Heng Li +Date: Sat Apr 16 12:33:28 2011 -0400 + + added debugging + +commit 8ce52e024dc2ef361dbd5399c232163055057e70 +Author: Heng Li +Date: Sat Apr 16 00:59:05 2011 -0400 + + avoid a segfault given wrong input + +commit e66b6684fc9a397f91ec29fdeecae9f8eb986a55 +Author: Heng Li +Date: Fri Apr 15 19:55:39 2011 -0400 + + do not segfault when there is no PL + +commit 9ce3c584ec0cebfa45576f2ef538df4dad2b7e55 +Author: Heng Li +Date: Fri Apr 15 11:59:55 2011 -0400 + + remove another unused part + +commit f53a051d68bf312ac8d5865210fae7a9808c0fb9 +Author: Heng Li +Date: Fri Apr 15 10:41:25 2011 -0400 + + print G3 if HWE is small + +commit 4b2c08bb86ca4ed4959e4cb77a28f7d6fc19f5c9 +Author: Heng Li +Date: Fri Apr 15 10:04:34 2011 -0400 + + fixed a bug + + actually not fix, but hide it + +commit 088e13c32453fb533b7bb1c65a573f9b90a23625 +Author: Heng Li +Date: Fri Apr 15 09:48:47 2011 -0400 + + added LRT based permutation; not used though + +commit 1e3c2001afcb80b5eaa4c3f88df9da7b01b62524 +Author: Heng Li +Date: Fri Apr 15 09:28:55 2011 -0400 + + Perform posterior contrast for small LRT + + Posterior contrast is much slower than LRT. Nonetheless, posterior P-value is + more robust to sequencing artifacts. Thus we may combine the two to achieve a + balance between speed and low FPR. + +commit 6f1b066270902198a7175ff6c1b05ebc8d1919be +Author: Heng Li +Date: Fri Apr 15 01:36:06 2011 -0400 + + Added Brent's method + +commit 3d061e5db25b67b25f6ff87afe4162e121354232 +Author: Heng Li +Date: Thu Apr 14 23:30:10 2011 -0400 + + fixed a typo in printing + +commit 7fd14ceb5990bb350b8e97346ef3537d80058def +Author: Heng Li +Date: Thu Apr 14 23:14:23 2011 -0400 + + fixed a stupid bug + +commit f5b2c3459ec098b3cafd9619b9077132516baf58 +Author: Heng Li +Date: Thu Apr 14 22:42:35 2011 -0400 + + separate EM and posterior + + Now, constrast is not performed unless -C is in use. EM can be invoked + independently with -e without computing the posterior. + +commit 9eefcac963697fae554789b11ae3cb2c23f224d0 +Author: Heng Li +Date: Thu Apr 14 22:00:19 2011 -0400 + + further code cleanup; prepare to add EM interface + +commit c2cce52355262743711e4742b0c8542bfcab1cdd +Author: Heng Li +Date: Thu Apr 14 21:44:03 2011 -0400 + + drop EM from prob1 + +commit 24016f04bd3bdffb7eeb50cb25854f5007feb70f +Author: Heng Li +Date: Thu Apr 14 21:08:33 2011 -0400 + + drop posterior LRT; prepare for clean up + +commit 3670d8bd88c3eb22873f0a80e2a5913f64ca8c9a +Author: Heng Li +Date: Thu Apr 14 20:57:43 2011 -0400 + + better initial values for LD + +commit d48a8873c060b18b57799cfe3a0e5496ba069457 +Author: Heng Li +Date: Thu Apr 14 20:36:25 2011 -0400 + + finished EM + +commit b101f2db476188a950c23f5c1b6185fdb7f8f40b +Author: Heng Li +Date: Wed Apr 13 01:19:04 2011 -0400 + + genotype frequency estimate + +commit d79bdcbf6242ecfb8accba9ac9a22fbcbd543cf2 +Author: Heng Li +Date: Wed Apr 13 00:37:22 2011 -0400 + + prepare for code clean up + +commit e0ce416abfc094f0c090957080b1404fd0edf752 +Author: Heng Li +Date: Wed Apr 13 00:34:15 2011 -0400 + + rename ld.c to em.c + +commit 45ede3ad181f35c1be24bed5d75841e472357ab7 +Author: Heng Li +Date: Wed Apr 13 00:22:10 2011 -0400 + + implemeted EM likelihood ratio test + + The idea is learned from a brief chat with Rasmus Nielsen. + +commit 0454a346b60e42b75a2f742272089810279c7131 +Author: Heng Li +Date: Tue Apr 12 15:45:52 2011 -0400 + + added likelihood-ratio test (idea from Nick) + +commit f6287c8646c690440a1554c8958e7268f4134dc2 +Author: Heng Li +Date: Sun Apr 10 18:24:37 2011 -0400 + + Release samtools-0.1.15 (r949:203) + +commit de6023f38f4d652438557cf7a0ac6eec324e7416 +Author: Heng Li +Date: Sun Apr 10 15:54:58 2011 -0400 + + improved help information + +commit d3b337f2b7eda1e6f8f5575a19d1b5ed55cae279 +Author: Heng Li +Date: Sat Apr 9 16:28:01 2011 -0400 + + fixed a minor issue + +commit 82f6e4f49247e75fbd8ec08c285b8d3047b3d235 +Author: Heng Li +Date: Sat Apr 9 15:49:04 2011 -0400 + + separate QC-pass and QC-fail reads + +commit 8362b4a255081ee7ca0a4ca2eabc8c76758b6863 +Author: Heng Li +Date: Fri Apr 8 17:45:19 2011 -0400 + + added verbose level + +commit f7bf419c290462be7d289249a4a6d28f825b4c93 +Author: Heng Li +Date: Fri Apr 8 16:08:14 2011 -0400 + + fixed a bug + +commit 890cbb1ac93b3004fb6cf42ff47195077dcfc8ad +Author: Heng Li +Date: Fri Apr 8 16:00:37 2011 -0400 + + drop unrelated @RG when "-R" is in use + +commit a62dc929c950fb51311b705f5b5bfba8e3f704d7 +Author: Heng Li +Date: Fri Apr 8 16:00:14 2011 -0400 + + skip header validation + +commit 39da810e2c56c8f0eff1ab726600b41f26d3d8e9 +Author: Heng Li +Date: Tue Apr 5 23:52:22 2011 -0400 + + change error message + +commit c0c50a34df250ef8a7a29b172058cd229be582b5 +Author: Heng Li +Date: Tue Apr 5 23:50:46 2011 -0400 + + fixed a bug caused by recent modifications + +commit 25226e8c468404cb5e1b5272efcea57e4193c762 +Author: Heng Li +Date: Tue Apr 5 13:31:19 2011 -0400 + + reduce the indel filtering window + +commit 5e18d7014437734f9dac9ab45a95e43ec2526101 +Author: Heng Li +Date: Mon Apr 4 13:56:20 2011 -0400 + + only output hwe if it is small enough + +commit 614941fb7dd276de662e7820eb8c7bae871a18cc +Author: Heng Li +Date: Mon Apr 4 13:34:02 2011 -0400 + + added HWE back + +commit 7abe8825aa0bacccdeb38125934ae94d18f0ad4d +Author: Heng Li +Date: Mon Apr 4 12:46:24 2011 -0400 + + EM estimate of genotype frequency + +commit 2bfeff9c645d177416664f1cb811e85cac3ff9e3 +Author: Heng Li +Date: Mon Apr 4 11:29:12 2011 -0400 + + minor + +commit 401e40647e7e3abbac6e4ec3d8bb68eb6f2d401b +Author: Heng Li +Date: Mon Apr 4 11:24:04 2011 -0400 + + Added genotype freq estimate and association test + +commit 6cc226df6e3b480f1bd6e763ce8ef47f785bbb74 +Author: Heng Li +Date: Sun Apr 3 20:57:23 2011 -0400 + + minor changes + +commit 7e47a39630e812f09b80369f14606245976f687e +Author: Heng Li +Date: Fri Apr 1 15:21:59 2011 -0400 + + print the grayscale + +commit 2f675d9c0dde3c166c99e335fa17c7873a5ae8d5 +Author: Heng Li +Date: Fri Apr 1 08:55:16 2011 -0400 + + change to comment + +commit 0592bb514994544ed84f51e509b233cf8821e0cf +Author: Heng Li +Date: Fri Apr 1 08:54:35 2011 -0400 + + added base quality filtering + +commit fc1b47e04a7b94f6362c45856cbeb89d9d0b5ca5 +Author: Heng Li +Date: Thu Mar 31 23:31:14 2011 -0400 + + fixed a few typos in comments + +commit 60be79bc8f0d24656e5e8a329af7e9b5b91d4c8b +Author: Heng Li +Date: Thu Mar 31 23:13:23 2011 -0400 + + comments + +commit 2432864acc25ebe5cee4217dbb0120439077a7f8 +Author: Heng Li +Date: Thu Mar 31 22:42:46 2011 -0400 + + added bam2depth.c, a demo program + +commit 39625f7c6bea9ccbfd9af0feb22348d52079f012 +Author: Heng Li +Date: Thu Mar 31 16:37:22 2011 -0400 + + added bgzf_check_bgzf() (used by tabix) + +commit 6de6bd3fb67fd22753a5f07d4cc25bf94e1b5a8c +Author: Heng Li +Date: Thu Mar 31 16:37:08 2011 -0400 + + fixed a bug in bedidx.c + +commit 3b9e257d25b2e81eed1625bc5d2882ed486ef20e +Author: Heng Li +Date: Wed Mar 30 13:27:15 2011 -0400 + + added bed support to bcftools + +commit 47bcce3d14ec4d205283b61e5e653803996c42e0 +Author: Heng Li +Date: Wed Mar 30 12:56:40 2011 -0400 + + Added BED support to "samtools view" + +commit a812386017faedfc86c0e6562adbb2138329cfeb +Author: Heng Li +Date: Wed Mar 30 12:47:04 2011 -0400 + + support BED file + +commit 3052dddc929f1825e6e7f7f6f6724d9465d6cf9a +Author: Heng Li +Date: Mon Mar 28 15:51:55 2011 -0400 + + relax RG matching; proper mismatching message + +commit f86d60c8fe25785523f01fae1486d2a6df4ee6ef +Author: Heng Li +Date: Sat Mar 26 10:38:23 2011 -0400 + + Avoid reporting association when something unexpected, which I do not understand, happens. + +commit dd41e6b26fd9fe30218748b9a0a1f49bdb1862b9 +Author: Heng Li +Date: Sat Mar 26 10:38:01 2011 -0400 + + Added -1 to merge + +commit 4a0364b0d7f87f1c88d71ec5857a1f1d40710681 +Author: Heng Li +Date: Wed Mar 23 16:56:55 2011 -0400 + + plot pairwise r^2 + +commit 452629a711582e612bec22b3b082e234bd37039b +Author: Heng Li +Date: Wed Mar 23 14:31:01 2011 -0400 + + pairwise LD; case-control AF2 + +commit 52862951adcaecde26ba8f0d9c1897944640a674 +Author: Heng Li +Date: Mon Mar 21 23:03:14 2011 -0400 + + Release samtools-0.1.14 (r933:170) + +commit 59a5a8ba8e2940f0e38238f9339f02c91a8a0ce4 +Author: Heng Li +Date: Mon Mar 21 13:52:55 2011 -0400 + + optionally skip loci with too low sample coverage + +commit 6434264b5c69514d4fafe62cbd30b3bbaddc1d41 +Author: Heng Li +Date: Sat Mar 19 14:38:25 2011 -0400 + + mpileup support Illumina1.3+ quality; skip non-variant sites when "view -v" is in use + +commit 5f59e01987e1d5eca7d6359cae64a9734b18beea +Author: Heng Li +Date: Fri Mar 18 17:19:18 2011 -0400 + + update version to r933:167 + +commit 4d2c3c950910aa3d2c87760c3532e458fe01c0fa +Author: Heng Li +Date: Fri Mar 18 16:25:01 2011 -0400 + + added "-1" to the command-line help + +commit 55313a015a7bd6369cf5a66fed7fab2333201dc9 +Author: Heng Li +Date: Fri Mar 18 16:22:12 2011 -0400 + + added the "cat" command (by Chris Saunders) + +commit b670272cadf3efa4dc456ac4c76104f73477d60d +Author: Heng Li +Date: Fri Mar 18 15:59:46 2011 -0400 + + support varying the compression level + +commit c5dd3c9ca5f75f880e52c8cd2beae983bcb8d3b1 +Author: Heng Li +Date: Wed Mar 16 14:33:45 2011 -0400 + + update the manual pages + +commit 12fb4b596dc51bccd154fc4bd0593442f7937a46 +Author: Heng Li +Date: Wed Mar 16 12:49:26 2011 -0400 + + update changelog + +commit e7fe4fd66e02d60a1ca7952ad1938809e77729a9 +Author: Heng Li +Date: Wed Mar 16 12:10:05 2011 -0400 + + do not call indels when the depth is very high + +commit 7455eeaa32b949bb3856f75810890aabf7cacb18 +Author: Heng Li +Date: Wed Mar 16 11:56:56 2011 -0400 + + code clean up + +commit 5f16679e54ced8e67a75d949f9175c50480b914e +Author: Heng Li +Date: Tue Mar 15 14:45:24 2011 -0400 + + when -s is specified, change the sample order + +commit 7ba95adee09d3b06a7eaf797d25efef837e592f5 +Author: Heng Li +Date: Tue Mar 15 14:11:42 2011 -0400 + + compute the rank in permutation + +commit d219783cea7643fc7e10e1bd3a98e9b3165b4506 +Author: Heng Li +Date: Sun Mar 13 21:35:13 2011 -0400 + + I have found a SERIOUS BUG!!! + +commit 8e20d04ecdac1a7788eef71c4bb91b8479cf7150 +Author: Heng Li +Date: Sun Mar 13 17:04:04 2011 -0400 + + optionally shuffle samples in a BCF (debugging) + +commit fc7b261f181f2a411427bc9ee5d586c883ca9cdc +Author: Heng Li +Date: Fri Mar 11 09:34:20 2011 -0500 + + fixed a bug + +commit b3bbcc3d40994ae85705ab6fef9866ec8c142201 +Author: Heng Li +Date: Thu Mar 10 20:25:59 2011 -0500 + + use mode instead of mean + +commit f1161262d137098a19143b5cb0de810e5db3243e +Author: Heng Li +Date: Thu Mar 10 20:09:16 2011 -0500 + + start from the mean instead of the mode + +commit 2ba56f5e99e90674855c4ffc8bf583340b932e1e +Author: Heng Li +Date: Thu Mar 10 17:13:34 2011 -0500 + + fixed an error in Chi^2 test + +commit b4ce7ae400290bc43dd287240479667f99b3b11e +Author: Heng Li +Date: Thu Mar 10 00:23:39 2011 -0500 + + minor + +commit 8487fa5d3a73a43443964e731ea2a4c873c9d4e5 +Author: Heng Li +Date: Wed Mar 9 21:33:19 2011 -0500 + + added -F to accept BCFs generated by old samtools + +commit fd51d2093f7fd775a7eaaeea57fa34716ab59ac2 +Author: Heng Li +Date: Wed Mar 9 17:39:09 2011 -0500 + + update version + +commit b6da54335df943015a998a934075331b467abb5b +Author: Heng Li +Date: Wed Mar 9 17:37:14 2011 -0500 + + compute pseudo-chi2 probability + +commit 9f73cefdb8935421d872b989dd98fbc8e1295029 +Author: Heng Li +Date: Wed Mar 9 15:54:04 2011 -0500 + + remove a comment which is wrong + +commit b10b1e47ece522e97ab8ef23417bcb6454f8b9db +Author: Heng Li +Date: Wed Mar 9 15:51:12 2011 -0500 + + clean up + +commit 353bfae2c6ff59205bd9223db04084cf7f507f01 +Author: Heng Li +Date: Wed Mar 9 15:45:29 2011 -0500 + + for backup + +commit 53915d1c6410c2537d18bfa8eb8c657a2233c35e +Author: Heng Li +Date: Wed Mar 9 15:27:56 2011 -0500 + + having debugging code + +commit 0d0dbf66995b1511390d593981eae7b5d36fe17b +Author: Heng Li +Date: Wed Mar 9 14:58:23 2011 -0500 + + temporary backup + +commit 5b74a174a8b637dee43b7f30250df6fb96580e12 +Author: Heng Li +Date: Tue Mar 8 15:46:11 2011 -0500 + + the output makes sense, but there may be a typo... + +commit d81ec654b6c0c1eef6b0625d96f14b3155cee7c6 +Author: Heng Li +Date: Tue Mar 8 15:19:09 2011 -0500 + + added contrast2(); fixed a bug in haploid mode + +commit 0cfd896fad5f7737cca49efa94a11892dafcd812 +Author: Heng Li +Date: Mon Mar 7 21:40:17 2011 -0500 + + fixed a bug in haploid genotyping + +commit ccd52155ef61273f2b42ad9c7b31ff1915f81b24 +Author: Heng Li +Date: Sat Mar 5 18:10:35 2011 -0500 + + fixed a few bugs; still not fully working + +commit edc3af753f96f831968ae32f2e0f915b74f31e6e +Author: Heng Li +Date: Fri Mar 4 17:31:33 2011 -0500 + + drop HWE calculation + +commit 92dac194debb66ca0718c21c871822dda2dd5bc1 +Author: Heng Li +Date: Fri Mar 4 17:28:35 2011 -0500 + + implemented hap/dipoind mode; probably BUGGY! + +commit 7f26804bc27937e36fdc967e5c76514653ea40f5 +Author: Heng Li +Date: Fri Mar 4 16:01:27 2011 -0500 + + read ploidy + +commit e7b7213475b5e61a69aab77ffb02b4983c8e7678 +Author: Heng Li +Date: Fri Mar 4 14:12:14 2011 -0500 + + added math notes + +commit 46023e2f21321da83fc8e83e9229757a4e821acb +Author: Heng Li +Date: Fri Mar 4 13:34:10 2011 -0500 + + update BCF spec + +commit 13190c49eeb006ad7013b7f1e9fc1b3beca3ae78 +Author: Heng Li +Date: Tue Mar 1 14:45:19 2011 -0500 + + Release samtools-0.1.13 (r926:134) + +commit be8fabbb6001d9fd5263a70a3e21ed6dfe5a9837 +Author: Heng Li +Date: Tue Mar 1 14:07:15 2011 -0500 + + prepare to finalize 0.1.13 + +commit 1e8c753660978bed7e9289fe50becd596d9314bb +Author: Heng Li +Date: Tue Mar 1 09:40:17 2011 -0500 + + allow to change whether to drop ambiguous reads + +commit 412210bfdb46606023f2e4b9086f2787f0cf1c62 +Author: Heng Li +Date: Mon Feb 28 22:01:29 2011 -0500 + + revert to the old behavior of phase + +commit 46035589518cf84738de8666b866e2619457c1fb +Author: Heng Li +Date: Mon Feb 28 16:46:23 2011 -0500 + + change version number + +commit 7f40c33e37fc16fcb0a375ce46ae1d09cafb6d50 +Author: Heng Li +Date: Mon Feb 28 16:37:42 2011 -0500 + + bugfix in indel calling: interger overflow + +commit 75849470efbe30042e5ddd516f9bcbe3b9bf6062 +Author: Heng Li +Date: Mon Feb 28 15:35:47 2011 -0500 + + fixed a typo + +commit 9e6fb569885f906fabaab7fc2f02eae82f4bd602 +Author: Heng Li +Date: Mon Feb 28 15:34:09 2011 -0500 + + minor changes to heuristic rules + +commit 30a799a91f5e2c10b761aa5437f902c6649fceb3 +Author: Heng Li +Date: Mon Feb 28 15:20:26 2011 -0500 + + fixed a bug in the latest change + +commit e21ba9df950ea37f5c1b35c2af9ba9a4e0bba02a +Author: Heng Li +Date: Mon Feb 28 12:47:06 2011 -0500 + + put version in bam.h + +commit 918b14780c1dceb39c7010638ecd61c626e17166 +Author: Heng Li +Date: Mon Feb 28 12:00:38 2011 -0500 + + frag_t::phased==0 reads are dumped to chimera.bam + +commit 657293c7bdba3ac69f53cd1ffa2874ed8756475e +Author: Heng Li +Date: Mon Feb 28 11:05:29 2011 -0500 + + change default -q to 37 (previously 40) + +commit 33d8d3bea76e466798ea322d68d34deb8d2dff06 +Author: Heng Li +Date: Mon Feb 28 10:39:57 2011 -0500 + + fixed a minor bug in BAM reading + +commit daa25d426d42465d76c7317c95772bbb36bb3f47 +Author: Heng Li +Date: Sat Feb 26 21:07:24 2011 -0500 + + suppress gzopen64() warning + +commit 9cec4256eb9e7848d4711adb67b540659c141e32 +Author: Heng Li +Date: Fri Feb 25 22:14:52 2011 -0500 + + fixed a long existing bug in vcf2fq + +commit 304487c83067a733add71cbc3886fa8c49f7ef2a +Author: Heng Li +Date: Fri Feb 25 16:37:40 2011 -0500 + + change version number + +commit 10ba6bf4f16692760f696f7b17f3719065786f77 +Author: Heng Li +Date: Fri Feb 25 16:34:08 2011 -0500 + + Change the order of PL; change SP to int32_t + +commit c5cc2a8036a9c3579fbfde651efec4f6763b0228 +Author: Heng Li +Date: Fri Feb 25 14:52:03 2011 -0500 + + claim X defined in the header + +commit 4ee8cb29f6092fd14a89f0cc5d3575112a204f39 +Author: Heng Li +Date: Fri Feb 25 14:40:24 2011 -0500 + + minor changes + +commit 00065e9336a2831dc53bee7da2f4719845be1a2a +Author: Heng Li +Date: Fri Feb 25 11:39:06 2011 -0500 + + fixed an error in the BCF spec + +commit 1e2a73afcb72a02aa448718cb017c0438de89f90 +Author: Heng Li +Date: Fri Feb 25 11:36:40 2011 -0500 + + update BCF spec + +commit dbf8eedaa38a405cb2fba5b3952b85776f51d035 +Author: Heng Li +Date: Fri Feb 25 11:28:43 2011 -0500 + + update BCF spec + +commit eed1d91af9fad3c9d965333a55e623757f9c4e9d +Author: Heng Li +Date: Fri Feb 25 09:51:39 2011 -0500 + + fixed a flaw in targetcut + +commit 59bc980bb832b92a8b0cc244cf106e6150e4db6f +Author: Heng Li +Date: Fri Feb 25 00:54:35 2011 -0500 + + update manual page + +commit fcc4738c4abdca79e3de159e21208df1b98ac76c +Author: Heng Li +Date: Fri Feb 25 00:45:39 2011 -0500 + + update version format + +commit 5748639ae542b7f6b853562edc2bb3faf43030e4 +Author: Heng Li +Date: Fri Feb 25 00:45:12 2011 -0500 + + update version number + +commit 06b44cc366cf27ce8976ee6a05810a0b3c48b56d +Author: Heng Li +Date: Fri Feb 25 00:44:21 2011 -0500 + + update version number + +commit ab7f4529d12739ff66fd4c09af9d992ab59c53ef +Author: Heng Li +Date: Fri Feb 25 00:42:55 2011 -0500 + + various help message + +commit a092e1f6f963272f8bb23616986ddaf604fd0f82 +Author: Heng Li +Date: Thu Feb 24 23:43:13 2011 -0500 + + disable unfinished functionality + +commit f00a78db72b14ee4c6689fc13f20ed31aeaecd40 +Author: Heng Li +Date: Thu Feb 24 10:04:56 2011 -0500 + + added "const" to bcf_p1_cal() + +commit 91049c4a8db3bf50dcc9d07506f22fa4ca5b5a96 +Author: Heng Li +Date: Wed Feb 23 11:53:47 2011 -0500 + + randomly allocate unphased reads + +commit f4405354a8d4cb3441141fa734573031059d7f57 +Author: Heng Li +Date: Tue Feb 22 15:36:07 2011 -0500 + + fixed a typo + +commit 3075e4dc5c7c9d954426aabda6a73fa788357100 +Author: Heng Li +Date: Tue Feb 22 15:33:40 2011 -0500 + + make output more informative + +commit 628cf3235e2815a40acf089fb1d3357be6437787 +Author: Heng Li +Date: Tue Feb 22 14:50:06 2011 -0500 + + change the scoring rule; change default k to 13 + +commit f22fd99831e4b5c74f898719216f359dbe987bbf +Author: Heng Li +Date: Tue Feb 22 14:45:15 2011 -0500 + + update scoring in masking + +commit 2f23547b81984555032aa0eefd064b8e07986fdc +Author: Heng Li +Date: Tue Feb 22 14:37:17 2011 -0500 + + remove dropreg() + +commit 4d8b6b1f1f331ca9041983c66e34a857c3b8f1bb +Author: Heng Li +Date: Tue Feb 22 13:10:16 2011 -0500 + + accept files from stdin + +commit 9b50c5038e6fc0185e29ca5b50fe0806a9a939b9 +Author: Heng Li +Date: Tue Feb 22 11:16:57 2011 -0500 + + fixed a bug in consensus generation + +commit 1332ab32fb788fdc81b2ba8653b905d106238fad +Author: Heng Li +Date: Mon Feb 21 22:53:23 2011 -0500 + + print dropped fragments + +commit a288761b4ca1584e51076a71cbc4d72fe923dda1 +Author: Heng Li +Date: Mon Feb 21 22:37:04 2011 -0500 + + bugfix: singletons are not phased + +commit 683365f534c0223dea7d72532015ac16a45ba22b +Author: Heng Li +Date: Mon Feb 21 17:27:10 2011 -0500 + + output singleton blocks + +commit 841a4609084d81f1bc81e0b00dd806002461e7d9 +Author: Heng Li +Date: Mon Feb 21 15:58:55 2011 -0500 + + fixed a bug; not working with -l right now + +commit fdd57ea31732b5516dc212d72174b60206952636 +Author: Heng Li +Date: Mon Feb 21 15:17:00 2011 -0500 + + skip mapQ==0 reads + +commit 4eb6ba75c23c1c9be5f76814fa1b93a2e304b2af +Author: Heng Li +Date: Mon Feb 21 14:03:03 2011 -0500 + + print the "targetcut" command + +commit 0123d9559ba58b026c0dfd15bc26019a193cd21a +Author: Heng Li +Date: Mon Feb 21 11:22:13 2011 -0500 + + allow to set the maximum depth + +commit 0f92eb248a4d06645b2c3d736a0faea8a7a9f731 +Author: Heng Li +Date: Mon Feb 21 09:56:41 2011 -0500 + + use a proper error model to call hets + +commit 587a01504af5aea6288740d121dccf48fb8a75f4 +Author: Heng Li +Date: Mon Feb 21 09:16:38 2011 -0500 + + phase is UNFINISHED; strip RG when merging + +commit 723bf3cd79e4f4a558373d4c707fa6b3db0fb357 +Author: Heng Li +Date: Sat Feb 19 23:38:11 2011 -0500 + + use a proper model to compute consensus + +commit 891a6b02d4a9af2ed98fbaac4915bf1f0da4f6c8 +Author: Heng Li +Date: Sat Feb 19 22:14:19 2011 -0500 + + added comment + +commit 8b55e0a581ecc9e4ba754d1f3c8784f3038b6e48 +Author: Heng Li +Date: Fri Feb 18 17:23:39 2011 -0500 + + change the output format + +commit 75c36e8c563eddd0a362ba3b38cf0aea21aafb1f +Author: Heng Li +Date: Tue Feb 15 20:31:00 2011 -0500 + + fixed a bug in writing BAM + +commit bb0ce52f066cfebaa35a125d57b353bb717a5165 +Author: Heng Li +Date: Mon Feb 14 23:39:09 2011 -0500 + + skip uncovered; unknown alleles taken as X + +commit ba67f4d119c7d06907db3015d337d9a01a3fc9fe +Author: Heng Li +Date: Mon Feb 14 23:21:19 2011 -0500 + + fixed a bug + +commit e4448d49e6129a5e1ee9c7f04f43612f12d6aad6 +Author: Heng Li +Date: Mon Feb 14 22:43:09 2011 -0500 + + prepare to read hets from a list; unfinished + +commit 129ea29c1f12177c0a7c3e21676f6210370fc59b +Author: Heng Li +Date: Mon Feb 14 16:32:22 2011 -0500 + + updated khash.h to 0.2.5 + +commit 15b44ed93bd949dffcf79ac8dbea6d9b7dfcb58c +Author: Heng Li +Date: Mon Feb 14 16:15:04 2011 -0500 + + use the latest version of khash + +commit 486c05f06f44d981dfb2069bcb43e4b35fd8389c +Author: Heng Li +Date: Mon Feb 14 15:04:40 2011 -0500 + + change the default -k to 11 + +commit 07cf9d1e443d73cf053de38dd01671e3781f6e29 +Author: Heng Li +Date: Mon Feb 14 14:50:51 2011 -0500 + + sort fragments by vpos instead of by beg + +commit d0d3e7faabf5cbb7e5ff7b294f7e220da807c4c0 +Author: Heng Li +Date: Mon Feb 14 14:45:41 2011 -0500 + + shuffling the two haplotypes for better randomness + +commit 3be28eaf5f6033229aedf12ddb11a0084ba01cd8 +Author: Heng Li +Date: Mon Feb 14 14:09:17 2011 -0500 + + write chimeras to a separate BAM + +commit 80ccbc26f43918fe42be123cc1da9d3d7ce30816 +Author: Heng Li +Date: Mon Feb 14 13:54:13 2011 -0500 + + no mem leak/violation on small files; correctness is not checked + +commit 5c923867432fa14c26a19e3782e7f48d4080f6ac +Author: Heng Li +Date: Mon Feb 14 13:50:25 2011 -0500 + + bam separation; at least not immediate segfault + +commit cea2643ec30a59735bf89b2f562b563bf7263e79 +Author: Heng Li +Date: Sun Feb 13 23:24:11 2011 -0500 + + on the way to implement BAM separation; unfinished + +commit 964269cd15036a470ca89e43d0952201a0825671 +Author: Heng Li +Date: Sun Feb 13 18:07:56 2011 -0500 + + keep singletons in the hash table + +commit 2d4aa649bd670d5e038a1acaefd33c5fe24ae0e8 +Author: Heng Li +Date: Sun Feb 13 17:42:24 2011 -0500 + + Revert "prepare to add bam separation" + + This reverts commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f. + +commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f +Author: Heng Li +Date: Sun Feb 13 00:24:28 2011 -0500 + + prepare to add bam separation + +commit d211e652d93791d2e112d334added243ffe5fc3e +Author: Heng Li +Date: Sat Feb 12 18:50:20 2011 -0500 + + accelerate kstrtok + +commit 2d6af49d331ff5afe7b9e9b102e79d7d4512fdbe +Author: Heng Li +Date: Fri Feb 11 21:08:21 2011 -0500 + + split unlinked blocks + +commit 68e4cd1b560b0a6fd4c77e5e51eadde9fda26ea4 +Author: Heng Li +Date: Fri Feb 11 10:47:58 2011 -0500 + + remove heading and tailing ambiguous positions + +commit d2b685141426a902ae76660c1fbe8020da150cf8 +Author: Heng Li +Date: Fri Feb 11 10:02:21 2011 -0500 + + code clean up for further features + +commit c6980e062d55928b59f287c03e599dd5a37ed509 +Author: Heng Li +Date: Fri Feb 11 08:00:08 2011 -0500 + + change /64 to >>6; the latter is faster + +commit 91635b9c2687f24d72ee6a8aad2050a79bb8400f +Merge: 41d4df2 9a7e155 +Author: Heng Li +Date: Fri Feb 11 01:22:55 2011 -0500 + + Merge branch 'master' into devel + +commit 9a7e155cc591c1b6c9f7f9cb939364a6becb65b2 +Author: Heng Li +Date: Fri Feb 11 01:21:07 2011 -0500 + + output an unrecognized field as '.'; autofix GL/PL + +commit 41d4df2e9545e9abe97151cfe5d6c763f3d00db1 +Merge: c00c41c aacce0c +Author: Heng Li +Date: Thu Feb 10 23:00:14 2011 -0500 + + Merge branch 'master' into devel + +commit aacce0ce7276f451e4fddf81832f9e5f7f65198b +Author: Heng Li +Date: Thu Feb 10 22:57:53 2011 -0500 + + finished VCF->BCF conversion + +commit 0e875df643e41d848b709e2fa877de8ae53cdd4c +Author: Heng Li +Date: Thu Feb 10 21:57:28 2011 -0500 + + fixed a bug in reading VCF files + +commit c00c41c2a5da69cccea64adb542a0b365e56b4fc +Author: Heng Li +Date: Thu Feb 10 16:28:37 2011 -0500 + + suppres one-allele blocks + +commit 2e2354b673722e2f00d72970a043f80a66270da1 +Author: Heng Li +Date: Thu Feb 10 16:06:56 2011 -0500 + + fixed the bug in filtering + +commit d971e1fe24de4ecaf94055efffc5f641e2bdb563 +Author: Heng Li +Date: Thu Feb 10 12:24:23 2011 -0500 + + prepare to add filtering; buggy right now + +commit a0a5a3fbf504c3b02f7b9212e72315c1047cc249 +Author: Heng Li +Date: Thu Feb 10 11:55:02 2011 -0500 + + make masking optional + +commit 28db71ccd95054a5f8a47c2332794f8968f6a822 +Author: Heng Li +Date: Thu Feb 10 11:40:47 2011 -0500 + + routine to mask poorly called regions + +commit a3f6c439262bc10a4067860440f4d4dde9e0c515 +Author: Heng Li +Date: Wed Feb 9 17:18:33 2011 -0500 + + code clean up: remove globals + +commit 0b711978492f6ad39d459d78723c299468906818 +Author: Heng Li +Date: Wed Feb 9 16:52:54 2011 -0500 + + output more information + +commit f69d217ae5b691bf42ad07a97f29a7cc6456046f +Author: Heng Li +Date: Wed Feb 9 16:11:54 2011 -0500 + + fixed another bug in flipping + +commit d47882d549337fbcc251597508a2c7faf1bb92e2 +Author: Heng Li +Date: Wed Feb 9 16:01:35 2011 -0500 + + fixed a stupid bug in flipping + +commit e33f89de499496537f5fbde396a66557f0353f1b +Author: Heng Li +Date: Wed Feb 9 15:54:42 2011 -0500 + + fix chimeras; a little weird... + +commit 03d3c1d0b945245108ce0942d4772536a32212c7 +Author: Heng Li +Date: Wed Feb 9 13:27:35 2011 -0500 + + no effective change; prepare to fix chimera + +commit 6bc0a4676dd2252085a6e67bb06daa5ae05a554f +Author: Heng Li +Date: Wed Feb 9 11:52:58 2011 -0500 + + better count output + +commit dcac515439d25f71125d6de8111da417776ab9ce +Author: Heng Li +Date: Wed Feb 9 10:31:07 2011 -0500 + + prepare for another way of filtering + +commit ca7e4f1899b86d2e077994c789e8f69d699b3cd9 +Author: Heng Li +Date: Tue Feb 8 16:10:08 2011 -0500 + + fixed the bug; I can do better. + +commit 0733f77b98af121bdcb198cea6151d159831bb9c +Author: Heng Li +Date: Tue Feb 8 15:55:38 2011 -0500 + + fixed two bugs; still not working... + +commit 80f18cba9ba73c9592380fc1ecd53c351d294782 +Author: Heng Li +Date: Tue Feb 8 15:42:58 2011 -0500 + + filter false SNPs; NOT working right now + +commit 69a66e2f96d5b102cd712ff1527a3802fa84c590 +Author: Heng Li +Date: Tue Feb 8 14:39:09 2011 -0500 + + write sequence in the SAM format for debugging + +commit b6f1c9d160822af2b713be206f37bd6dde00546a +Author: Heng Li +Date: Mon Feb 7 11:51:21 2011 -0500 + + fixed two bugs + +commit 400aa5c06100af9c47cd5e4ce8b95b7deb84f54b +Author: Heng Li +Date: Mon Feb 7 11:22:38 2011 -0500 + + Optionally apply BAQ + +commit 4c82e0e19682e424f5cdb8381364114c307b329e +Author: Heng Li +Date: Mon Feb 7 01:23:31 2011 -0500 + + improved output; the result makes sense at a glance + +commit dc7853a581ab24bcc496e96b123ccf637e32ed1d +Author: Heng Li +Date: Sun Feb 6 14:12:43 2011 -0500 + + process per linked block instead of per chr + +commit e867d9c6c2e61d9e748e78163e5481dca5697a36 +Author: Heng Li +Date: Sun Feb 6 00:45:46 2011 -0500 + + DP seems to work on toy examples + +commit 445ad72fc43d4354d56f5f759790e8ae0be73d02 +Author: Heng Li +Date: Sat Feb 5 01:24:42 2011 -0500 + + implemented backtrack; not tested + +commit ba38e180b9cd545956583b22e97e09b4bb12073e +Author: Heng Li +Date: Fri Feb 4 23:55:23 2011 -0500 + + More "correct" DP; backtrack not implemented + +commit d69761fd9351273ccd37ea431b10509add91e7cf +Author: Heng Li +Date: Fri Feb 4 17:22:31 2011 -0500 + + scratch of dynamic programming; unfinished... + +commit 769ffcb44e26e59300791658801d321559b33858 +Author: Heng Li +Date: Fri Feb 4 16:29:55 2011 -0500 + + UNFINISHED commit. + +commit 9adab9591317c3467f3d8cdf2d19ec1f65d1b5b7 +Author: Heng Li +Date: Thu Feb 3 16:20:59 2011 -0500 + + another way of counting; can be even faster + +commit bbafbdc01ed1ceaab44927def1ad47c4c78aeb9c +Author: Heng Li +Date: Thu Feb 3 14:48:20 2011 -0500 + + for backup + +commit eba7446389cad62a19133bced1386a4334dcab79 +Merge: a44a98e f01a593 +Author: Heng Li +Date: Wed Feb 2 14:06:07 2011 -0500 + + Merge branch 'master' into devel + +commit f01a5930445b5fda7e6b5b813ed63c652160ada2 +Author: Heng Li +Date: Wed Feb 2 11:31:54 2011 -0500 + + Better truncation warning when EOF is absent + +commit dd3ee5ed26c8bbef4a62fa5b2bfb0a75833f2c31 +Author: Heng Li +Date: Wed Feb 2 10:38:28 2011 -0500 + + fixed a typo in BCF/VCF headers + +commit b9d1137c55f401387113d1ad8a387489afe741db +Author: Heng Li +Date: Wed Feb 2 09:13:44 2011 -0500 + + fixed an out-of-boundary bug (fixed by Roel Kluin) + +commit a44a98e16559b9672e8a3492c8f8c640074b7ee2 +Merge: ef68a14 d0443d5 +Author: Heng Li +Date: Tue Feb 1 21:54:48 2011 -0500 + + Merge branch 'master' into devel + +commit d0443d5c2f648e0f69bd4c56eaac7868e501c18b +Author: Heng Li +Date: Tue Feb 1 17:31:52 2011 -0500 + + improved sorting order checking + +commit ef68a14fab91399b2ecd38345936c3d6e7391cf3 +Merge: 1e597b3 1a39a2e +Author: Heng Li +Date: Tue Feb 1 15:12:37 2011 -0500 + + Merge branch 'master' into devel + +commit 1a39a2eb08a270e20a34a0983e8bed6ffb3e2008 +Author: Heng Li +Date: Tue Feb 1 15:12:14 2011 -0500 + + more precise error message + +commit e028e7a47c02232e06a9dd3009262c00dede1060 +Author: Heng Li +Date: Tue Feb 1 14:48:01 2011 -0500 + + improved sorting order validation in index + +commit 1e597b3356744e2b791b12c9187f91c8054511d5 +Author: Heng Li +Date: Tue Feb 1 14:44:27 2011 -0500 + + testing only; not working + +commit 5753ace1e54228822d8ee95f69943f586e42f6e8 +Author: Heng Li +Date: Mon Jan 31 17:37:08 2011 -0500 + + reduce the effect of seq errors at the cost of SN + +commit 6f239ce5e0abd47babee33174476d48b723260d8 +Author: Heng Li +Date: Mon Jan 31 17:29:34 2011 -0500 + + added testing code + +commit 3db42fe22d27d61ab5735cd2308f73d93def8ebe +Author: Heng Li +Date: Mon Jan 31 14:33:21 2011 -0500 + + routine for phasing fosmid resequencing (incomplete) + +commit ed88f2797323229ae8f38fbcd107b231007956a8 +Author: Heng Li +Date: Mon Jan 31 10:12:53 2011 -0500 + + SAM output + +commit abc6acae28dc4794f6422255f077cf370d34e414 +Merge: f1985a9 b133dbf +Author: Heng Li +Date: Sat Jan 29 22:56:10 2011 -0500 + + Merge branch 'master' into devel + +commit b133dbf82de4e8cea5eb56e5bbf0c4b3e9368fd5 +Author: Heng Li +Date: Sat Jan 29 22:37:11 2011 -0500 + + fixed a bug in tview on big-endian by Nathan Weeks + +commit 9d3fdaef29f91e21dbfcb9ff0165b9573e7c1042 +Author: Heng Li +Date: Sat Jan 29 22:24:00 2011 -0500 + + update INSTALL + +commit 9d074a38bde53961f96157b6fb3683b6dded38d7 +Author: Heng Li +Date: Sat Jan 29 21:56:25 2011 -0500 + + avoid a segfault when network connect fails + +commit f1985a93f7455b3ea1b0ef9b959d50b896ccd620 +Author: Heng Li +Date: Sat Jan 29 21:53:18 2011 -0500 + + fixed a bug about bit ordering + +commit d09797db6fef648a6823cbe718d67664660c6ebe +Author: Heng Li +Date: Thu Jan 27 16:53:19 2011 -0500 + + point out there are 4 or fewer free parameters + +commit 5fd1717650ed68ab6c55d094d1648c16a054891a +Author: Heng Li +Date: Thu Jan 27 16:09:18 2011 -0500 + + updated .gitignore + +commit fccb19fbe8f9de91f59d85bb49a248683dc6266c +Author: Heng Li +Date: Thu Jan 27 16:08:14 2011 -0500 + + fixed a bug; better scoring + +commit b4dcb844bde3d09eedcd9f6832186ece60ae5afd +Merge: ffc3e89 6f502de +Author: Heng Li +Date: Thu Jan 27 14:50:30 2011 -0500 + + Merge branch 'master' into devel + +commit 6f502dec46b18dae4bb5b2319715d028b5e193d0 +Author: Heng Li +Date: Thu Jan 27 14:47:31 2011 -0500 + + skip unmapped and ref-skip reads in indel calling + +commit 3639f37dd8257b24560c35effcc3b6c16c3c1bcb +Author: Heng Li +Date: Thu Jan 27 14:19:15 2011 -0500 + + fixed an out-of-boundary bug in rare cases + +commit ffc3e89678ab9052b84f403da1e43044b045e73f +Author: Heng Li +Date: Thu Jan 27 14:00:17 2011 -0500 + + targetcut can be compiled, though probably buggy + +commit f452b3ac51306865ddde31a8d715b155d4d3e6e6 +Author: Heng Li +Date: Wed Jan 26 18:58:43 2011 -0500 + + this is for a very special application... + +commit ca1451c6406c7ee757cb31349ea0b8de70db0656 +Author: Heng Li +Date: Wed Jan 26 18:48:09 2011 -0500 + + fixed compiling errors + +commit 085b87a7642865f17239fb6a436e626e25417838 +Author: Heng Li +Date: Wed Jan 26 18:45:09 2011 -0500 + + This script was put in a wrong place... + +commit 090d360828622520de60385af4928ce1aebe0e48 +Author: Heng Li +Date: Wed Jan 26 18:33:58 2011 -0500 + + Imported from samtools-r902 ------------------------------------------------------------------------ r108 | lh3lh3 | 2009-01-20 11:56:45 +0000 (Tue, 20 Jan 2009) | 2 lines Changed paths: