[med-svn] [bcftools] branch upstream updated (0fb5584 -> 6dc018a)

[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  0fb5584   New upstream version 1.4.1
       new  6dc018a   New upstream version 1.5

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:
 HMM.c                          |  95 ++++----
 HMM.h                          |   9 +-
 INSTALL                        |  82 +++++--
 Makefile                       | 176 +++++++++------
 NEWS                           |  33 ++-
 bam2bcf.c                      |  35 +--
 bam2bcf_indel.c                |   8 +-
 bcftools.h                     |   6 +
 config.mk.in                   |  63 ++++++
 configure.ac                   | 218 ++++++++++++++++++
 consensus.c                    |  11 +-
 doc/bcftools.1                 |  34 +--
 doc/bcftools.html              |  37 +--
 doc/bcftools.txt               |  33 +--
 filter.c                       |  47 ++++
 install-sh                     | 501 +++++++++++++++++++++++++++++++++++++++++
 m4/ax_with_htslib.m4           | 154 +++++++++++++
 main.c                         |   6 +
 misc/plot-roh.py               | 323 +++++++++++++++++++-------
 misc/plot-vcfstats             |  20 +-
 plugins/GTisec.mk              |   2 +-
 plugins/GTsubset.mk            |   2 +-
 plugins/ad-bias.mk             |   2 +-
 plugins/af-dist.mk             |   2 +-
 plugins/color-chrs.mk          |   2 +-
 plugins/fill-from-fasta.mk     |   2 +-
 plugins/fixploidy.mk           |   4 +-
 plugins/fixref.c               |  17 +-
 plugins/isecGT.mk              |   2 +
 plugins/prune.c                | 292 ++++++++++++++++++++++++
 plugins/setGT.mk               |   2 +-
 rbuf.h                         |  66 +++++-
 test/create-bam-test           |  99 ++++++++
 test/fixref.2.out              |  11 +
 test/fixref.2a.vcf             |  10 +
 test/fixref.2b.vcf             |  10 +
 test/merge.gvcf.3.a.vcf        |   8 +
 test/merge.gvcf.3.b.vcf        |  10 +
 test/merge.gvcf.3.out          |  11 +
 test/mpileup/indel-AD.1.bam    | Bin 0 -> 15124 bytes
 test/mpileup/indel-AD.1.cram   | Bin 0 -> 9682 bytes
 test/mpileup/indel-AD.1.fa     |  13 ++
 test/mpileup/indel-AD.1.fa.fai |   1 +
 test/mpileup/indel-AD.1.out    | 323 ++++++++++++++++++++++++++
 test/mpileup/indel-AD.1.sam    | 156 +++++++++++++
 test/norm.out                  |   2 +-
 test/norm.split.and.norm.out   |   2 +-
 test/test.pl                   |  65 +++---
 vcfbuf.c                       | 442 ++++++++++++++++++++++++++++++++++++
 vcfbuf.h                       |  81 +++++++
 vcfconvert.c                   |   8 +-
 vcfmerge.c                     |  32 ++-
 vcfnorm.c                      |  27 ++-
 vcfplugin.c                    |  18 +-
 vcfroh.c                       |  18 +-
 55 files changed, 3272 insertions(+), 361 deletions(-)
 create mode 100644 config.mk.in
 create mode 100644 configure.ac
 create mode 100755 install-sh
 create mode 100644 m4/ax_with_htslib.m4
 create mode 100644 plugins/isecGT.mk
 create mode 100644 plugins/prune.c
 create mode 100755 test/create-bam-test
 create mode 100644 test/fixref.2.out
 create mode 100644 test/fixref.2a.vcf
 create mode 100644 test/fixref.2b.vcf
 create mode 100644 test/merge.gvcf.3.a.vcf
 create mode 100644 test/merge.gvcf.3.b.vcf
 create mode 100644 test/merge.gvcf.3.out
 create mode 100644 test/mpileup/indel-AD.1.bam
 create mode 100644 test/mpileup/indel-AD.1.cram
 create mode 100644 test/mpileup/indel-AD.1.fa
 create mode 100644 test/mpileup/indel-AD.1.fa.fai
 create mode 100644 test/mpileup/indel-AD.1.out
 create mode 100644 test/mpileup/indel-AD.1.sam
 create mode 100644 vcfbuf.c
 create mode 100644 vcfbuf.h

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