+------------------------------------------------------------------------
+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:
projects / samtools.git / blobdiff