+Beta release 0.1.12a (2 December, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is another bug fix release:
+
+ * Fixed a memory violation in mpileup, which causes segfault. Release
+ 0.1.9 and above are affected.
+
+ * Fixed a memory violation in the indel caller, which does not causes
+ segfault, but may potentially affect deletion calls in an unexpected
+ way. Release 0.1.10 and above are affected.
+
+ * Fixed a bug in computing r-square in bcftools. Few are using this
+ functionality and it only has minor effect.
+
+ * Fixed a memory leak in bam_fetch().
+
+ * Fixed a bug in writing meta information to the BAM index for the last
+ sequence. This bug is invisible to most users, but it is a bug anyway.
+
+ * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.
+
+(0.1.12: 2 December 2010, r862)
+
+
+
+Beta release 0.1.11 (21 November, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+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.
+
+ * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
+ failure when the first CIGAR operation is a deletion.
+
+ * 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: 21 November 2010, r851)
+
+
+
+Beta Release 0.1.10 (16 November, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release is featured as the first major improvement to the indel
+caller. The method is similar to the old one implemented in the pileup
+command, but the details are handled more carefully both in theory and
+in practice. As a result, the new indel caller usually gives more
+accurate indel calls, though at the cost of sensitivity. The caller is
+implemented in the mpileup command and is invoked by default. It works
+with multiple samples.
+
+Other notable changes:
+
+ * With the -r option, the calmd command writes the difference between
+ the original base quality and the BAQ capped base quality at the BQ
+ tag but does not modify the base quality. Please use -Ar to overwrite
+ the original base quality (the 0.1.9 behavior).
+
+ * Allow to set a maximum per-sample read depth to reduce memory. In
+ 0.1.9, most of memory is wasted for the ultra high read depth in some
+ regions (e.g. the chr1 centromere).
+
+ * Optionally write per-sample read depth and per-sample strand bias
+ P-value.
+
+ * Compute equal-tail (Bayesian) credible interval of site allele
+ frequency at the CI95 VCF annotation.
+
+ * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
+ filtering.
+
+(0.1.10: 16 November 2010, r829)
+
+
+
Beta Release 0.1.9 (27 October, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
projects / samtools.git / blobdiff