[med-svn] [bcftools] 02/08: Merge tag 'upstream/1.3.1'

[Afif Elghraoui]

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

afif pushed a commit to branch master
in repository bcftools.

commit d3ea0f8c80464cc7b098b9a7fb2a5d6e3de892e8
Merge: 45ff8ed c7f7f8b
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Apr 25 21:57:20 2016 -0700

    Merge tag 'upstream/1.3.1'
    
    Upstream version 1.3.1

 Makefile                                       |   8 +-
 bcftools.h                                     |   3 +-
 consensus.c                                    |   2 +-
 doc/bcftools.1                                 |  96 ++++-
 doc/bcftools.html                              | 101 +++++-
 doc/bcftools.txt                               |  87 ++++-
 khash_str2str.h                                |  19 +-
 main.c                                         |   4 +-
 peakfit.c                                      |   6 +
 ploidy.c                                       |  30 +-
 plot-vcfstats                                  |   6 +-
 plugins/GTisec.c                               | 470 +++++++++++++++++++++++++
 plugins/GTisec.mk                              |   2 +
 plugins/color-chrs.c                           |   2 +-
 plugins/fill-tags.c                            |  46 ++-
 plugins/impute-info.c                          |  10 +-
 plugins/mendelian.c                            |   2 +-
 plugins/tag2tag.c                              |   4 +-
 plugins/vcf2sex.c                              |  11 +-
 polysomy.c                                     |   3 +-
 reheader.c                                     |  62 ++--
 test/annotate10.hdr                            |   3 +
 test/annotate10.out                            |  18 +
 test/annotate10.vcf                            |  17 +
 test/annots10.tab                              |   4 +
 test/concat.1.a.vcf                            |   2 -
 test/concat.1.b.vcf                            |   2 -
 test/fill-tags.2.out                           |  49 +++
 test/norm.fa                                   |   2 +
 test/norm.fa.fai                               |   1 +
 test/norm.merge.out                            |   2 +-
 test/norm.merge.strict.out                     |   2 +-
 test/norm.merge.vcf                            |   4 +-
 test/norm.telomere.out                         |   5 +
 test/norm.telomere.vcf                         |   4 +
 test/{norm.merge.strict.out => reheader.3.out} |  43 +--
 test/{norm.merge.strict.out => reheader.4.out} |  43 +--
 test/reheader.empty.hdr                        |   7 +
 test/reheader.empty.out                        |   8 +
 test/reheader.samples3                         |   2 +
 test/reheader.samples4                         |   1 +
 test/test.pl                                   |  96 ++---
 test/view.GTisec.H.out                         |  20 ++
 test/view.GTisec.Hm.out                        |  25 ++
 test/view.GTisec.Hmv.out                       |  25 ++
 test/view.GTisec.Hv.out                        |  20 ++
 test/view.GTisec.m.out                         |  20 ++
 test/view.GTisec.mv.out                        |  20 ++
 test/view.GTisec.out                           |  15 +
 test/view.GTisec.v.out                         |  15 +
 test/view.filter.annovar.vcf                   |   1 +
 vcfannotate.c                                  | 212 +++++++++--
 vcfcall.c                                      |  43 ++-
 vcfconcat.c                                    | 139 +++++++-
 vcfconvert.c                                   |  18 +-
 vcffilter.c                                    |   8 +-
 vcfindex.c                                     |   3 +-
 vcfisec.c                                      |  12 +-
 vcfmerge.c                                     |  10 +-
 vcfnorm.c                                      |  20 +-
 vcfplugin.c                                    |  41 +--
 vcfroh.c                                       |  43 ++-
 vcfview.c                                      |   8 +-
 63 files changed, 1706 insertions(+), 301 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bcftools.git