In addition to the changes listed below, I have put my "seqtk" utility in this release. Seqtk mostly works with fasta/fastq sequence. It can convert fasta to fastq while changing low-quality bases to lowercases, exact subsequences, mask regions, point mutate the reference sequence, plus a few more functionalities that may be of less interest to general users. Seqtk is small (a single C file depending only on khash.h and kseq.h) and very efficient. For example, to convert fastq to fasta, FASTX-Toolkit and EMBOSS' seqret take 10 times longer. Hope this seqtk is helpful to you sometimes.
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)
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