[med-svn] [bcftools] branch master updated (881d1ba -> 62310a2)

[Andreas Tille]

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

tille pushed a change to branch master
in repository bcftools.

      from  881d1ba   Release 1.5-4
       new  01bdfe5   New upstream version 1.6
       new  ebf1207   Update upstream source from tag 'upstream/1.6'
       new  7d3f4ad   Refresh patches for new upstream version, removed unused patches
       new  e3e5288   Standards-Version: 4.1.2
       new  62310a2   Upload to experimental

The 5 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                              |   4 +-
 NEWS                                  |  33 ++
 config.mk.in                          |   1 +
 consensus.c                           | 129 +++++--
 csq.c                                 | 133 ++++---
 debian/changelog                      |   8 +
 debian/control                        |   2 +-
 debian/copyright                      |   2 +-
 debian/patches/compiler-flags.patch   |  22 --
 debian/patches/external-libs.patch    |  39 --
 debian/patches/series                 |   3 -
 debian/patches/spelling.patch         |  33 --
 debian/patches/tests-pluginpath.patch |   2 +-
 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 +++-
 60 files changed, 2256 insertions(+), 604 deletions(-)
 delete mode 100644 debian/patches/compiler-flags.patch
 delete mode 100644 debian/patches/external-libs.patch
 delete mode 100644 debian/patches/spelling.patch
 create mode 100644 plugins/check-ploidy.c
 create mode 100644 test/filter.12.out
 create mode 100644 test/filter.13.out
 create mode 100644 test/filter.14.out
 create mode 100644 test/filter.15.out
 create mode 100644 test/filter.16.out
 create mode 100644 test/filter.17.out
 create mode 100644 test/filter.18.out
 create mode 100644 test/filter.19.out
 create mode 100644 test/query.34.out
 create mode 100644 test/query.35.out
 create mode 100644 test/query.36.out
 create mode 100644 test/sort.out
 create mode 100644 test/sort.vcf
 create mode 100644 test/stats.counts.chk
 create mode 100644 test/stats.counts.vcf
 create mode 100644 vcfsort.c

-- 
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