[med-svn] samtools annotated tag 1.4 created (now d9811be)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to annotated tag 1.4
in repository samtools.

        at  d9811be   (tag)
   tagging  0a859b10a2343f4146fc3c0f71044d182461ad46 (commit)
  replaces  1.3.1
 tagged by  jenniferliddle
        on  Mon Mar 13 14:49:50 2017 +0000

- Log -----------------------------------------------------------------
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.

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Anton Kratz (1):
      Add plot-bamstats -l / --log-y option

David K Jackson (2):
      Amend info regarding bedcov subcommand
      Clarify bedcov subcommand usage

James Bonfield (13):
      Fixed the out by one error in --insert-size.
      Added mpileup -a and -aa options
      Improved error reporting in samtools index.
      Depth/Mpileup -a fixes.  Fixes #374.
      Added 30ish new tests for depth/mpileup -a and -aa.
      Further depth/mpileup tests. Also improved documentation.
      Added multi-threaded decoding to view, index and sort.
      Improved multi-threading support for many more samtools commands.
      Replaced bool with int to avoid confusion with true being failure.
      Merged PR#545 (Add MC support to fixmates)
      Fix to 28a611d2 to prevent samtools view crash on error handling.
      Mention multi-threaded BAM/CRAM decoding.
      Merge branch PR #649 (Use htslib_static.mk to get static link flags)

John Marshall (27):
      Merge version number bump and NEWS file from master
      HTSlib now provides errmod_cal() etc
      Use HTSlib's new sam_prob_realn() and sam_cap_mapq() functions
      Use HTSlib's new probaln_glocal() function
      Use HTSlib's new errmod_cal()/probaln_glocal()/sam_prob_realn() functions
      Explicitly set @CURSES_LIB@ for --without-curses
      Write BQ SAM line the same way as for AF
      Use bcf_hdr_format() rather than deprecated bcf_hdr_fmt_text()
      Merge sort memory requirement diagnostic (PR #581)
      Add NEWS item about mpileup zero coverage '*' fixes
      Fix Rob and Martin's whitespace [minor]
      Merge mpileup/depth -a/-aa fixes (PR #579, PR #586)
      Testclean and ignore test temporary files
      Allow finer control over program vs. script installation
      Add libst.a so test suite can use print_error()/etc
      Use print_error/_errno() in bam_sort.c and bam_split.c
      Avoid printing "error message: Success" [minor]
      Avoid strndup() and strsep() for portability reasons
      In read_file_list(), check for URL syntax or extant files
      Exterminate error(), fix memory leaks in event of write errors
      Fix language misidentification of test data [minor]
      Use print_error_errno() to report file open failures
      Improve view -s documentation
      Skip usage tests when pseudo-terminal can't be opened
      Happy New Year
      Listen to -o FILE option in samtools view -c
      Add the autoconf macros required to the repository

Kevin Murray (1):
      Fix usage description of bamshuf/collate

Martin O. Pollard (4):
      Convert quickcheck to hts_check_EOF API to check EOF on CRAM
      Add MC support to fixmates
      Add error handling to kstring functions in bam_mate
      Fixmates: add tests for two reads unmapped

Martin Pollard (1):
      bam2fq_mainloop should be using filter_it_out

Matthieu Foll (1):
      Fixed the `-a` option for zero coverage positions

Petr Danecek (1):
      Place percent mapped bases output in the correct field

Rob Davies (10):
      Add samtools view tests for extracting unmapped reads.
      Enforce a minimum memory requirement for samtools sort
      Make samtools faidx write faster and detect write errors.
      Remove redundant item from long options array
      Update some tests to run both single and multi-threaded
      Temporarily disable the large_chrom bai index test
      Use htslib_static.mk to get static link flags
      Add liblzma and libbz2 to travis.
      Stop samtools configure from always trying to configure htslib
      Update INSTALL with new library dependencies

Shane McCarthy (1):
      index: update error message for failure to index

jenniferliddle (3):
      bam_split now adds @PG header to bam files (PR #557)
      Updated with 1.4 changes
      Release 1.4: summary

steveb-cirina (1):
      Fixed a typo: changed "suffices" to "suffixes".

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