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
 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
 
 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
 
 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
 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:
 
 
 
 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.
 
  * 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 -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.
 
 
  * 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
  * 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.
 
 
  * 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.
 
  * 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:
 
 
 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.
 
 
  * 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.
  */
 
   @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>
 
 #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; $G=\frac{A(A+1)}{2}$, $A=\#\{alleles\}$\\
 \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}\\
 {\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
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format