Release samtools-0.1.13 (r926:134)

diff --git a/Makefile b/Makefile
index d557520dd5b0c60b7ab4763e34939d3031b2acb1..af93d9ca5fb9010943877317bdb64b88d65e4ea1 100644 (file)
--- 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 296504621b3efe763cf413403e8917317b98c80a..8455b484a0ce46bac6ca004e8ef2e2fb6e8239cf 100644 (file)
--- 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 0ab9c217dee28c3708c07fa694ca9be523524fa4..4ad264447a94e11b63aab2ba9fba7501bdb2203c 100644 (file)
--- 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 <stdint.h>
 #include <stdlib.h>

diff --git a/bcftools/bcf.tex b/bcftools/bcf.tex
index 89573642621a4adf99e224d40f23b680eb43fd1c..6f2171fa56ee39c6d1baa23da8e18794764ddcb5 100644 (file)
--- 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 f4a54f57cf3796581ab6f881f1957f5fc016d732..e0c77439751765b90aeb3c4ef50b8f4cb7d4a096 100644 (file)
--- 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