[med-svn] [bcftools] branch master updated (45ff8ed -> f9a9e80)

[Afif Elghraoui]

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afif pushed a change to branch master
in repository bcftools.

      from  45ff8ed   Update changelog
       new  c7f7f8b   Imported Upstream version 1.3.1
       new  d3ea0f8   Merge tag 'upstream/1.3.1'
       new  d35e058   Remove backported patches
       new  9d2f206   Refresh remaining patches
       new  ab357e2   Bump htslib minimum dependency
       new  13c1a3b   Bump Standards-Version to 3.9.8
       new  8b2259e   Add a manpage for the color-chrs command
       new  f9a9e80   releasing package bcftools version 1.3.1-1

The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 Makefile                                 |   8 +-
 bcftools.h                               |   3 +-
 consensus.c                              |   2 +-
 debian/changelog                         |  11 +
 debian/control                           |   4 +-
 debian/man/color-chrs.pl.1               |  19 ++
 debian/patches/getopt-return-types.patch |  98 -------
 debian/patches/peakfit-gsl2.patch        |  36 ---
 debian/patches/series                    |   3 -
 debian/patches/tests-pluginpath.patch    |   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/{annots2.vcf => annotate10.out}     |   3 +-
 test/{annots2.vcf => annotate10.vcf}     |  12 +-
 test/annots10.tab                        |   4 +
 test/concat.1.a.vcf                      |   2 -
 test/concat.1.b.vcf                      |   2 -
 test/{view.vcf => fill-tags.2.out}       |  33 ++-
 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/{reheader.2.out => reheader.3.out}  |   2 +-
 test/{reheader.2.out => reheader.4.out}  |   2 +-
 test/{empty.vcf => reheader.empty.hdr}   |   1 +
 test/{empty.vcf => reheader.empty.out}   |   2 +
 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 +-
 70 files changed, 1625 insertions(+), 425 deletions(-)
 create mode 100644 debian/man/color-chrs.pl.1
 delete mode 100644 debian/patches/getopt-return-types.patch
 delete mode 100644 debian/patches/peakfit-gsl2.patch
 create mode 100644 plugins/GTisec.c
 create mode 100644 plugins/GTisec.mk
 create mode 100644 test/annotate10.hdr
 copy test/{annots2.vcf => annotate10.out} (91%)
 copy test/{annots2.vcf => annotate10.vcf} (67%)
 create mode 100644 test/annots10.tab
 copy test/{view.vcf => fill-tags.2.out} (69%)
 create mode 100644 test/norm.telomere.out
 create mode 100644 test/norm.telomere.vcf
 copy test/{reheader.2.out => reheader.3.out} (98%)
 copy test/{reheader.2.out => reheader.4.out} (98%)
 copy test/{empty.vcf => reheader.empty.hdr} (87%)
 copy test/{empty.vcf => reheader.empty.out} (72%)
 create mode 100644 test/reheader.samples3
 create mode 100644 test/reheader.samples4
 create mode 100644 test/view.GTisec.H.out
 create mode 100644 test/view.GTisec.Hm.out
 create mode 100644 test/view.GTisec.Hmv.out
 create mode 100644 test/view.GTisec.Hv.out
 create mode 100644 test/view.GTisec.m.out
 create mode 100644 test/view.GTisec.mv.out
 create mode 100644 test/view.GTisec.out
 create mode 100644 test/view.GTisec.v.out

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