[med-svn] samtools annotated tag 1.4.1 created (now 61f9c63)

[Andreas Tille]

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tille pushed a change to annotated tag 1.4.1
in repository samtools.

        at  61f9c63   (tag)
   tagging  8f8600a1e8fbabd7a5a49f307061c3029897a7bc (commit)
  replaces  1.4
 tagged by  jenniferliddle
        on  Mon May 8 11:11:07 2017 +0100

- Log -----------------------------------------------------------------
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)

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Blaise Li (1):
      Option -G to exclude based on a set of bits.

George Hall (6):
      Implemented tab completion
      Dynamically generate options
      Cleaned up subcommand name retrieval
      Changed '==' to '-eq'
      Captialised variables for consistency
      Fixed slight bug in default behaviour

James Bonfield (10):
      Document the "-b bam-list" option to samtools cat.
      Remove two tiny memory leaks in samtools merge.
      Cram lossy names (#543)
      Improved wording of usage and updated man page.
      Another change to view/bam2fq filtering wording.
      Improvements for C99/XOPEN compliance.
      Switch to -lpthread instead of -pthread for linking.
      Output CRAM as temporary sort format iff there are more than 64k cigar ops.
      Bam2fq comment improvements (no code changed).
      NEWS update.

Jennifer Liddle (1):
      Merge pull request #560 from george-hall-wtsi/tab_completion

Rob Davies (1):
      Merge pull request to enable large vertical movement in tview (#257)

awenger (1):
      Add "-b <bam.fofn>" flag to samtools cat.

jenniferliddle (3):
      Merge version number bump and NEWS file from master
      Added option to produce fastq files from BC or other tags
      Release 1.4.1: summary

uzbit (1):
      Update bam_tview_curses.c

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No new revisions were added by this update.

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