[med-svn] [bcftools] branch debian/jessie-backports updated (ee606b6 -> 8f98f34)

[Afif Elghraoui]

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afif pushed a change to branch debian/jessie-backports
in repository bcftools.

      from  ee606b6   bcftools (1.3-1~bpo8+1) jessie-backports; urgency=medium
      adds  a0f5384   Backport upstream patch to be able to build plugin with GSL2
      adds  0c497fa   Bump Standards-Version
      adds  9f2857a   Use encrypted protocols for VCS URLs
      adds  3e13cc4   bcftools (1.3-2) unstable; urgency=medium
      adds  692a80b   Update email address and bump copyright year
      adds  4558479   Backport upstream patch to fix build on arm64, armel, and ppc64el
      adds  45ff8ed   Update changelog
      adds  c7f7f8b   Imported Upstream version 1.3.1
      adds  d3ea0f8   Merge tag 'upstream/1.3.1'
      adds  d35e058   Remove backported patches
      adds  9d2f206   Refresh remaining patches
      adds  ab357e2   Bump htslib minimum dependency
      adds  13c1a3b   Bump Standards-Version to 3.9.8
      adds  8b2259e   Add a manpage for the color-chrs command
      adds  f9a9e80   releasing package bcftools version 1.3.1-1
       new  133abec   Merge tag 'debian/1.3.1-1' into debian/jessie-backports
       new  8f98f34   releasing package bcftools version 1.3.1-1~bpo8+1

The 2 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                        |  32 +++
 debian/control                          |  10 +-
 debian/copyright                        |   2 +-
 debian/man/color-chrs.pl.1              |  19 ++
 debian/patches/series                   |   1 -
 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 +-
 69 files changed, 1650 insertions(+), 293 deletions(-)
 create mode 100644 debian/man/color-chrs.pl.1
 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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