Tags

Upstream version 1.8

Upstream version 1.7

Debian release 1.6-4

Upstream version 1.6

Upstream version 1.5

Release 1.4.1  (8th May 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Added options to fastq to create fastq files from BC (or other)
  tags.

* Samtools view has gained a -G <flags> option to exclude on all bits
  set.  For example to discard reads where neither end has been
  mapped use "-G 12".

* Samtools cat has a -b <fofn> option to ease concatenation of many
  files.

* Added misc/samtools_tab_completion for bash auto-completion of
  samtools sub-commands. (#560)

* Samtools tview now has J and K keys for verticale movement by 20
  lines. (#257)

* Various compilation / portability improvements.

* Fixed issue with more than 65536 CIGAR operations and SAM/CRAM files.
(#667)

Release 1.4  (13 March 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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.

samtools Debian release 1.3.1-3

samtools (1.3.1-2~bpo8+1) jessie-backports; urgency=medium

  * Team upload.
  * Rebuild for jessie-backports.

 -- Afif Elghraoui <afif@debian.org>  Fri, 05 Aug 2016 21:03:54 -0700

samtools (1.3.1-2) unstable; urgency=medium

  952da10 Build-depends on htslib 1.3.1. (Closes: #822701)

 -- Charles Plessy <plessy@debian.org>  Sun, 08 May 2016 21:11:12 +0900

samtools (1.3.1-1) unstable; urgency=medium

  0c961b2 Merge tag '1.3.1' into debian/unstable
  3666b08 Conforms with Policy version 3.9.8.

 -- Charles Plessy <plessy@debian.org>  Tue, 26 Apr 2016 21:12:05 +0900