[med-svn] [bcftools] branch master updated (a32fc0f -> e7d0b97)

[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  a32fc0f   Fix FTBFS on architectures where char is unsigned by default
       new  6dc018a   New upstream version 1.5
       new  0def15e   Updated version 1.5 from 'upstream/1.5'
       new  96556f7   New upstream version
       new  3a7371b   Attempt to adapt patches - may be failed since several entries moved from Makefile to config.mk.in.  Check seriously if something might fail.
       new  4c32893   Bump version in Build-Depends libhts-dev from 1.3.1 to 1.5
       new  36778a3   Standards-Version: 4.0.0 (no changes needed)
       new  dc6a12c   Work around issues in clean target
       new  e7d0b97   deactivate patches that might mess up configure

The 8 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 +-
 debian/changelog                      |   9 +
 debian/control                        |   4 +-
 debian/patches/compiler-flags.patch   |  24 +-
 debian/patches/destdir.patch          |  22 +-
 debian/patches/external-libs.patch    |  94 +++----
 debian/patches/series                 |   6 +-
 debian/patches/tests-pluginpath.patch |   2 +-
 debian/rules                          |   6 +
 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 +-
 63 files changed, 3351 insertions(+), 449 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

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