Mention ‘SAMtools’ in libbam-dev's description, to make it easier to find with apt...

[samtools.git] / NEWS

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+Beta Release 0.1.18 (2 September, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes in samtools:
+
+ * Support the new =/X CIGAR operators (by Peter Cock).
+
+ * Allow to subsample BAM while keeping the pairing intact (view -s).
+
+ * Implemented variant distance bias as a new filter (by Petr Danecek).
+
+ * Bugfix: huge memory usage during indexing
+
+ * Bugfix: use of uninitialized variable in mpileup (rare)
+
+ * Bugfix: wrong BAQ probability (rare)
+
+Notable changes in bcftools:
+
+ * Support indel in the contrast caller.
+
+ * Bugfix: LRT2=nan in rare cases
+
+(0.1.18: 2 September 2011, r982:295)
+
+
+
+Beta Release 0.1.17 (6 July, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+With the maturity of `mpileup' and the lack of update in the `pileup' command,
+the `pileup' command is now formally dropped. Most of the pileup functionality,
+such as outputting mapping quality and read positions, have been added
+`mpileup'.
+
+Since this release, `bcftools view' is able to perform contrast SNP calling
+(option -T) for discovering de novo and/or somatic mutations between a pair of
+samples or in a family trio. Potential mutations are scored by a log likelihood
+ratio, which is very simple in math, but should be comparable to more
+sophisticated methods. Note that getting the score is only the very first step.
+A lot more need to be done to reduce systematical errors due to mapping and
+reference errors and structural variations.
+
+Other notable changes in samtools:
+
+ * Improved sorting order checking during indexing.
+
+ * Improved region parsing. Colons in reference sequence names are parsed
+   properly.
+
+ * Fixed an issue where mpileup does not apply BAQ for the first few reads when
+   a region is specified.
+
+ * Fixed an issue where `faidx' does not work with FASTA files with long lines.
+
+ * Bugfix: wrong SP genotype information in the BCF output.
+
+Other notable changes in bcftools:
+
+ * Output the ML esitmate of the allele count.
+
+ * Added the HWE plus F<0 filter to varFilter. For multiple samples, it
+   effectively filters false heterozygous calls around centromeres.
+
+ * For association mapping, perform both 1-degree and 2-degree test. The
+   2-degree test is conservative but more robust to HWE violation.
+
+(0.1.17: 6 July 2011, r973:277)
+
+
+
+Beta Release 0.1.16 (21 April, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes in samtools:
+
+ * Support the new SAM/BAM type `B' in the latest SAM spec v1.4.
+
+ * When the output file of `samtools merge' exists, do not overwrite it unless
+   a new command-line option `-f' is applied.
+
+ * Bugfix: BED support is not working when the input BED is not sorted.
+
+ * Bugfix: some reads without coordinates but given on the reverse strand are
+   lost in merging.
+
+Notable changes in bcftools:
+
+ * Code cleanup: separated max-likelihood inference and Bayesian inference.
+
+ * Test Hardy-Weinberg equilibrium with a likelihood-ratio test.
+
+ * Provided another association test P-value by likelihood-ratio test.
+
+ * Use Brent's method to estimate the site allele frequency when EM converges
+   slowly. The resulting ML estimate of allele frequnecy is more accurate.
+
+ * Added the `ldpair' command, which computes r^2 between SNP pairs given in
+   an input file.
+
+Also, the `pileup' command, which has been deprecated by `mpileup' since
+version 0.1.10, will be dropped in the next release. The old `pileup' command
+is substandard and causing a lot of confusion.
+
+(0.1.16: 21 April 2011, r963:234)
+
+
+
 Beta Release 0.1.15 (10 April, 2011)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~