[med-svn] [bcftools] 02/08: Updated version 1.5 from 'upstream/1.5'

[Andreas Tille]

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tille pushed a commit to branch master
in repository bcftools.

commit 0def15ee2eb20815777e9121c3034b8d1bf41d74
Merge: a32fc0f 6dc018a
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jul 20 13:17:48 2017 +0200

    Updated version 1.5 from 'upstream/1.5'
    
    with Debian dir 2515594fd0ee011029f4aaacf58d037a83ec75bc

 HMM.c                          |  95 ++++----
 HMM.h                          |   9 +-
 INSTALL                        |  82 +++++--
 Makefile                       | 176 +++++++++------
 NEWS                           |  33 ++-
 bam2bcf.c                      |  35 +--
 bam2bcf_indel.c                |   8 +-
 bcftools.h                     |   6 +
 config.mk.in                   |  63 ++++++
 configure.ac                   | 218 ++++++++++++++++++
 consensus.c                    |  11 +-
 doc/bcftools.1                 |  34 +--
 doc/bcftools.html              |  37 +--
 doc/bcftools.txt               |  33 +--
 filter.c                       |  47 ++++
 install-sh                     | 501 +++++++++++++++++++++++++++++++++++++++++
 m4/ax_with_htslib.m4           | 154 +++++++++++++
 main.c                         |   6 +
 misc/plot-roh.py               | 323 +++++++++++++++++++-------
 misc/plot-vcfstats             |  20 +-
 plugins/GTisec.mk              |   2 +-
 plugins/GTsubset.mk            |   2 +-
 plugins/ad-bias.mk             |   2 +-
 plugins/af-dist.mk             |   2 +-
 plugins/color-chrs.mk          |   2 +-
 plugins/fill-from-fasta.mk     |   2 +-
 plugins/fixploidy.mk           |   4 +-
 plugins/fixref.c               |  17 +-
 plugins/isecGT.mk              |   2 +
 plugins/prune.c                | 292 ++++++++++++++++++++++++
 plugins/setGT.mk               |   2 +-
 rbuf.h                         |  66 +++++-
 test/create-bam-test           |  99 ++++++++
 test/fixref.2.out              |  11 +
 test/fixref.2a.vcf             |  10 +
 test/fixref.2b.vcf             |  10 +
 test/merge.gvcf.3.a.vcf        |   8 +
 test/merge.gvcf.3.b.vcf        |  10 +
 test/merge.gvcf.3.out          |  11 +
 test/mpileup/indel-AD.1.bam    | Bin 0 -> 15124 bytes
 test/mpileup/indel-AD.1.cram   | Bin 0 -> 9682 bytes
 test/mpileup/indel-AD.1.fa     |  13 ++
 test/mpileup/indel-AD.1.fa.fai |   1 +
 test/mpileup/indel-AD.1.out    | 323 ++++++++++++++++++++++++++
 test/mpileup/indel-AD.1.sam    | 156 +++++++++++++
 test/norm.out                  |   2 +-
 test/norm.split.and.norm.out   |   2 +-
 test/test.pl                   |  65 +++---
 vcfbuf.c                       | 442 ++++++++++++++++++++++++++++++++++++
 vcfbuf.h                       |  81 +++++++
 vcfconvert.c                   |   8 +-
 vcfmerge.c                     |  32 ++-
 vcfnorm.c                      |  27 ++-
 vcfplugin.c                    |  18 +-
 vcfroh.c                       |  18 +-
 55 files changed, 3272 insertions(+), 361 deletions(-)

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