[med-svn] [bcftools] 02/05: Update upstream source from tag 'upstream/1.6'

[Andreas Tille]

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tille pushed a commit to branch master
in repository bcftools.

commit ebf12076b5f133e657054a669cfc1d4cf6e21fb6
Merge: 881d1ba 01bdfe5
Author: Andreas Tille <tille at debian.org>
Date:   Mon Dec 11 13:22:12 2017 +0100

    Update upstream source from tag 'upstream/1.6'
    
    Update to upstream version '1.6'
    with Debian dir e7ed99011d387db90edd205de9f8b3b4cbfee785

 Makefile               |   4 +-
 NEWS                   |  33 +++
 config.mk.in           |   1 +
 consensus.c            | 129 ++++++++--
 csq.c                  | 133 +++++-----
 doc/bcftools.1         | 179 ++++++++++++--
 doc/bcftools.html      | 116 +++++++--
 doc/bcftools.txt       |  98 +++++++-
 filter.c               | 652 +++++++++++++++++++++++++++++++++++--------------
 kheap.h                |   5 +-
 main.c                 |   5 +
 misc/plot-roh.py       |  38 +--
 misc/plot-vcfstats     |  21 +-
 misc/run-roh.pl        |   2 +-
 mpileup.c              |   9 +-
 plugins/check-ploidy.c | 165 +++++++++++++
 plugins/mendelian.c    | 110 +++++++--
 plugins/setGT.c        | 264 +++++++++++++++-----
 test/check.chk         |  22 +-
 test/convert.gvcf.out  |   2 +-
 test/convert.gvcf.vcf  |   2 +-
 test/filter.12.out     |   1 +
 test/filter.13.out     |   2 +
 test/filter.14.out     |   8 +
 test/filter.15.out     |   2 +
 test/filter.16.out     |   3 +
 test/filter.17.out     |   3 +
 test/filter.18.out     |  11 +
 test/filter.19.out     |   1 +
 test/mendelian.1.out   |  40 ++-
 test/mendelian.2.out   |  29 ++-
 test/mendelian.3.out   |  23 +-
 test/mendelian.vcf     |  40 ++-
 test/query.34.out      |   1 +
 test/query.35.out      |   1 +
 test/query.36.out      |   1 +
 test/sort.out          |  15 ++
 test/sort.vcf          |  21 ++
 test/stats.B.chk       |   6 +-
 test/stats.chk         |  18 +-
 test/stats.counts.chk  |  37 +++
 test/stats.counts.vcf  |  18 ++
 test/test.pl           |  28 ++-
 vcfcnv.c               |   6 +
 vcfconvert.c           |   5 +-
 vcfindex.c             |   7 +
 vcfisec.c              |  14 +-
 vcfmerge.c             |  14 +-
 vcfnorm.c              |  18 ++
 vcfquery.c             |  17 ++
 vcfsort.c              | 306 +++++++++++++++++++++++
 vcfstats.c             |  63 +++--
 52 files changed, 2245 insertions(+), 504 deletions(-)

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