[med-svn] [bcftools] branch upstream updated (202ee54 -> c7f7f8b)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository bcftools.

      from  202ee54   Imported Upstream version 1.3
       new  c7f7f8b   Imported Upstream version 1.3.1

The 1 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 +-
 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 +-
 63 files changed, 1592 insertions(+), 285 deletions(-)
 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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