From 604b0bc8d9afd4002efff7f4963c84cc36b18435 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 22 Nov 2010 03:16:52 +0000 Subject: [PATCH] Release samtools-0.1.11 --- ChangeLog | 60 +++++++++++++++++++++++++++++++++++++++++++++ NEWS | 15 +++++++++--- bcftools/bcftools.1 | 5 ++++ samtools.1 | 2 +- 4 files changed, 78 insertions(+), 4 deletions(-) diff --git a/ChangeLog b/ChangeLog index 973601e..dd62b49 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,63 @@ +------------------------------------------------------------------------ +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: diff --git a/NEWS b/NEWS index 91434f3..478e718 100644 --- a/NEWS +++ b/NEWS @@ -1,7 +1,7 @@ -Beta release 0.1.11 (19 November, 2010) +Beta release 0.1.11 (21 November, 2010) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -This is a bug fix release: +This is mainly a bug fix release: * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads are retrieved from a small region containing no reads. @@ -11,12 +11,21 @@ This is a bug fix release: * Improved fault tolerence in remote access. +One minor feature has been implemented in bcftools: + + * Added a reference-free variant calling mode. In this mode, a site is + regarded as a variat iff the sample(s) contains two or more alleles; + the meaning of the QUAL field in the VCF output is changed + accordingly. Effectively, the reference allele is irrelevant to the + result in the new mode, although the reference sequence has to be + used in realignment when SAMtools computes genotype likelihoods. + In addition, since 0.1.10, the `pileup' command has been deprecated by `mpileup' which is more powerful and more accurate. The `pileup' command will not be removed in the next few releases, but new features will not be added. -(0.1.11: 19 November 2010, r842) +(0.1.11: 21 November 2010, r851) diff --git a/bcftools/bcftools.1 b/bcftools/bcftools.1 index ebff301..6c7403b 100644 --- a/bcftools/bcftools.1 +++ b/bcftools/bcftools.1 @@ -74,6 +74,11 @@ Skip sites where the REF field is not A/C/G/T .B -Q Output the QCALL likelihood format .TP +.B -f +Reference-free variant calling mode. In this mode, the prior will be +folded; a variant is called iff the sample(s) contains at least two +alleles; the QUAL field in the VCF/BCF output is changed accordingly. +.TP .BI "-1 " INT Number of group-1 samples. This option is used for dividing input into two groups for comparing. A zero value disables this functionality. [0] diff --git a/samtools.1 b/samtools.1 index e87bef7..e059560 100644 --- a/samtools.1 +++ b/samtools.1 @@ -1,4 +1,4 @@ -.TH samtools 1 "15 November 2010" "samtools-0.1.10" "Bioinformatics tools" +.TH samtools 1 "21 November 2010" "samtools-0.1.11" "Bioinformatics tools" .SH NAME .PP samtools - Utilities for the Sequence Alignment/Map (SAM) format -- 2.39.2