Release 1.4 of HTSlib, Samtools, and BCFtools are now available on github and sourceforge.— Samtools Team (@htslib) March 13, 2017
Share and Enjoy
The Samtools Team
Noteworthy changes in samtools:
* Fixed Issue #345 - out-by-one error in insert-size in samtools stats * bam_split now add a @PG header to the bam file * Added mate cigar tag support to fixmate * Multi-threading is now supported for decoding BAM and CRAM (as well as the previously supported encoding). Most commands that read BAM or CRAM have gained an -@ or --threads arguments, providing a significant speed bonus. For commands that both read and write files the threads are shared between decoding and encoding tasks. * Added -a option to samtools mpileup to show all locations, including sites with zero depth; repeating the option as -aa or -a -a additionally shows reference sequences without any reads mapped to them (#496). * The mpileup text output no longer contains empty columns at zero coverage positions. Previously it would output "...0\t\t..." in some circumstances (zero coverage due to being below a minumum base quality); this has been fixed to output as "...0\t*\t*..." with placeholder '*' characters as in other zero coverage circumstances (see PR #537). * To stop it from creating too many temporary files, samtools sort will now not run unless its per-thread memory limit (-m) is set to at least 1 megabyte (#547). * The misc/plot-bamstats script now has a -l / --log-y option to change various graphs to display their Y axis log-scaled. Currently this affects the Insert Size graph (PR #589; thanks to Anton Kratz). * Fixmate will now also add and update MC (mate CIGAR) tags.