Release samtools-0.1.11

diff --git a/ChangeLog b/ChangeLog
index 973601e0cbd4498412ab7ce9e8a1817ac88cb939..dd62b49ded4f58206aa19574ffb9e473ca3283da 100644 (file)
--- 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 91434f3ff72b34358644fe3dad36c5ef9b8cf8a5..478e718c79963a052e682bbc33cfa0de695076e0 100644 (file)
--- 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 ebff30134002500216c18a1e9eeee3e8a8dba8a8..6c7403bea6b8b6ebde3c77a8a1ef55ee890fcd59 100644 (file)
--- 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 e87bef7e788f09d1c0c38219f231062868a010d4..e0595607196e577f15227c5cef8af0c9f51de2d6 100644 (file)
--- 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