From: Heng Li Date: Wed, 17 Nov 2010 04:14:15 +0000 (+0000) Subject: Release samtools-0.1.10 (r829) X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=624c76e0c2b7f98b0fdf734345a61e3019e68fd3 Release samtools-0.1.10 (r829) --- diff --git a/ChangeLog b/ChangeLog index a1beffd..f8456a3 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,137 @@ +------------------------------------------------------------------------ +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: diff --git a/NEWS b/NEWS index 82646ba..6c2195e 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,38 @@ +Beta Release 0.1.10 (16 November, 2010) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +This release is featured as the first major improvement to the indel +caller. The method is similar to the old one implemented in the pileup +command, but the details are handled more carefully both in theory and +in practice. As a result, the new indel caller usually gives more +accurate indel calls, though at the cost of sensitivity. The caller is +implemented in the mpileup command and is invoked by default. It works +with multiple samples. + +Other notable changes: + + * With the -r option, the calmd command writes the difference between + the original base quality and the BAQ capped base quality at the BQ + tag but does not modify the base quality. Please use -Ar to overwrite + the original base quality (the 0.1.9 behavior). + + * Allow to set a maximum per-sample read depth to reduce memory. In + 0.1.9, most of memory is wasted for the ultra high read depth in some + regions (e.g. the chr1 centromere). + + * Optionally write per-sample read depth and per-sample strand bias + P-value. + + * Compute equal-tail (Bayesian) credible interval of site allele + frequency at the CI95 VCF annotation. + + * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel + filtering. + +(0.1.10: 16 November 2010, r829) + + + Beta Release 0.1.9 (27 October, 2010) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/bamtk.c b/bamtk.c index 11502f2..88328d4 100644 --- a/bamtk.c +++ b/bamtk.c @@ -9,7 +9,7 @@ #endif #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.9-20 (r828)" +#define PACKAGE_VERSION "0.1.10 (r829)" #endif int bam_taf2baf(int argc, char *argv[]);