From 727b8c146c0146f6c43b2a7ab75c4c7bc3f91eef Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 1 Mar 2011 19:48:25 +0000 Subject: [PATCH] Release samtools-0.1.13 (r926:134) --- Makefile | 1 + NEWS | 21 ++++++++++----------- bam.h | 2 +- bcftools/bcf.tex | 2 +- samtools.1 | 2 +- 5 files changed, 14 insertions(+), 14 deletions(-) diff --git a/Makefile b/Makefile index d557520..af93d9c 100644 --- a/Makefile +++ b/Makefile @@ -68,6 +68,7 @@ bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h bam2bcf_indel.o:bam2bcf.h errmod.o:errmod.h phase.o:bam.h khash.h ksort.h +bamtk.o:bam.h faidx.o:faidx.h razf.h khash.h faidx_main.o:faidx.h razf.h diff --git a/NEWS b/NEWS index 2965046..8455b48 100644 --- a/NEWS +++ b/NEWS @@ -1,5 +1,5 @@ -Beta release 0.1.13 (28 February, 2011) -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Beta release 0.1.13 (1 March, 2011) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The most important though largely invisible modification is the change of the order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF @@ -11,16 +11,14 @@ version number. Single Individual Haplotyping (SIH) is added as an experimental feature. It originally aims to produce haploid consensus from fosmid pool sequencing, but also works with short-read data. For short reads, phased blocks are usually too -short to be useful in most applications, but phasing can be powerful for ruling -out some SNPs close to INDELs and some of clustered spurious SNPs between copies -of CNVs. On one data set, phasing based SNP calling is better in terms of both -sensitivity and specificity than the standard methods. +short to be useful in many applications, but they can help to rule out part of +SNPs close to INDELs or between copies of CNVs. Other notable changes in samtools: - * Construct per-sample consensus to reduced the effect of nearby SNPs in INDEL - calling. This may reduce the power, but improves specificity. + * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL + calling. This reduces the power but improves specificity. * Improved sorting order checking in indexing. Now indexing is the preferred way to check if a BAM is sorted. @@ -31,7 +29,7 @@ Other notable changes in samtools: * Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling. - * Added `mpileup -m' to allow fine control of INDEL candidates. + * Added `mpileup -m' to allow fine control of the collection of INDEL candidates. * Added `mpileup -S' to compute per-sample strand bias P-value. @@ -40,7 +38,7 @@ Other notable changes in samtools: * Fixed segfault in indel calling related to unmapped and refskip reads. * Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL - genotypes for longer INDELs, typically over 10bp. + genotypes for longer short INDELs, typically over 10bp. * Fixed a bug in tview on big-endian machines. @@ -50,6 +48,7 @@ Other notable changes in samtools: * Fixed a compiling error when the knetfile library is not used. Fixed a library compiling error due to the lack of bam_nt16_nt4_table[] table. + Suppress a compiling warning related to the latest zlib. Other notable changes in bcftools: @@ -76,7 +75,7 @@ Other notable changes in bcftools: * Fixed a minor bug in Fisher's exact test; the results are rarely changed. -(0.1.13: 28 February 2011, r926+130) +(0.1.13: 1 March 2011, r926:134) diff --git a/bam.h b/bam.h index 0ab9c21..4ad2644 100644 --- a/bam.h +++ b/bam.h @@ -40,7 +40,7 @@ @copyright Genome Research Ltd. */ -#define BAM_VERSION "0.1.12-r925+130" +#define BAM_VERSION "0.1.13 (r926:134)" #include #include diff --git a/bcftools/bcf.tex b/bcftools/bcf.tex index 8957364..6f2171f 100644 --- a/bcftools/bcf.tex +++ b/bcftools/bcf.tex @@ -38,7 +38,7 @@ \multicolumn{1}{l}{\bf Field} & \multicolumn{1}{l}{\bf Type} & \multicolumn{1}{l}{\bf Description} \\\hline {\tt DP} & {\tt uint16\_t[n]} & Read depth \\ {\tt GL} & {\tt float[n*G]} & Log10 likelihood of data; $G=\frac{A(A+1)}{2}$, $A=\#\{alleles\}$\\ -{\tt GT} & {\tt uint8\_t[n]} & {\tt haploid\char60\char60 7 | phased\char60\char60 6 | allele1\char60\char60 3 | allele2} \\ +{\tt GT} & {\tt uint8\_t[n]} & {\tt missing\char60\char60 7 | phased\char60\char60 6 | allele1\char60\char60 3 | allele2} \\ {\tt \_GT} & {\tt uint8\_t+uint8\_t[n*P]} & {Generic GT; the first int equals the max ploidy $P$} \\ {\tt GQ} & {\tt uint8\_t[n]} & {Genotype quality}\\ {\tt HQ} & {\tt uint8\_t[n*2]} & {Haplotype quality}\\ diff --git a/samtools.1 b/samtools.1 index f4a54f5..e0c7743 100644 --- a/samtools.1 +++ b/samtools.1 @@ -1,4 +1,4 @@ -.TH samtools 1 "2 December 2010" "samtools-0.1.12" "Bioinformatics tools" +.TH samtools 1 "1 March 2011" "samtools-0.1.13" "Bioinformatics tools" .SH NAME .PP samtools - Utilities for the Sequence Alignment/Map (SAM) format -- 2.39.2