[med-svn] [bcftools] branch upstream updated (6dc018a -> 01bdfe5)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository bcftools.

      from  6dc018a   New upstream version 1.5
       new  01bdfe5   New upstream version 1.6

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               |   4 +-
 NEWS                   |  33 +++
 config.mk.in           |   1 +
 consensus.c            | 129 ++++++++--
 csq.c                  | 133 +++++-----
 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 +++--
 52 files changed, 2245 insertions(+), 504 deletions(-)
 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

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