[med-svn] [tvc] branch master updated (9d67d4e -> 381c43e)

[Andreas Tille]

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

tille pushed a change to branch master
in repository tvc.

      from  9d67d4e   cme fix dpkg-control
       new  672baa5   debhelper 10
       new  1961741   Use debian packaged vcflib and drop own code copy
       new  c7f1a0f   New upstream version 5.0.3+dfsg1
       new  6c8dc18   Merge tag 'upstream/5.0.3+dfsg1'
       new  381c43e   Add libraries that are missing from cmake file but needed when using Debian packaged cvflib

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:
 debian/changelog                                   |    4 +-
 debian/compat                                      |    2 +-
 debian/control                                     |    5 +-
 debian/copyright                                   |   29 +-
 debian/patches/series                              |    1 +
 debian/patches/use_debian_packaged_vcflib.patch    |   58 +
 debian/rules                                       |    2 +-
 external/vcflib/BedReader.h                        |  123 --
 external/vcflib/LICENSE                            |   19 -
 external/vcflib/README                             |   29 -
 external/vcflib/Variant.cpp                        | 2004 --------------------
 external/vcflib/Variant.h                          |  480 -----
 external/vcflib/convert.h                          |   22 -
 external/vcflib/join.h                             |   36 -
 external/vcflib/multichoose/Makefile               |   17 -
 external/vcflib/multichoose/README                 |   40 -
 external/vcflib/multichoose/multichoose.c          |   53 -
 external/vcflib/multichoose/multichoose.cpp        |   66 -
 external/vcflib/multichoose/multichoose.h          |   79 -
 external/vcflib/multichoose/multichoose.py         |   55 -
 external/vcflib/multichoose/multipermute.cpp       |   66 -
 external/vcflib/multichoose/multipermute.h         |  132 --
 external/vcflib/multichoose/multipermute.py        |   98 -
 .../vcflib/smithwaterman/BandedSmithWaterman.cpp   |  670 -------
 .../vcflib/smithwaterman/BandedSmithWaterman.h     |  111 --
 external/vcflib/smithwaterman/IndelAllele.cpp      |   62 -
 external/vcflib/smithwaterman/IndelAllele.h        |   37 -
 external/vcflib/smithwaterman/LeftAlign.cpp        |  853 ---------
 external/vcflib/smithwaterman/LeftAlign.h          |   32 -
 external/vcflib/smithwaterman/Makefile             |   34 -
 external/vcflib/smithwaterman/Mosaik.h             |   73 -
 external/vcflib/smithwaterman/Repeats.cpp          |   69 -
 external/vcflib/smithwaterman/Repeats.h            |    8 -
 external/vcflib/smithwaterman/SWMain.cpp           |  126 --
 .../vcflib/smithwaterman/SmithWatermanGotoh.cpp    |  741 --------
 external/vcflib/smithwaterman/SmithWatermanGotoh.h |  100 -
 external/vcflib/smithwaterman/convert.h            |   22 -
 external/vcflib/smithwaterman/smithwaterman.cpp    |  246 ---
 external/vcflib/split.cpp                          |   23 -
 external/vcflib/split.h                            |   53 -
 external/vcflib/tabixpp/ChangeLog                  |  593 ------
 external/vcflib/tabixpp/NEWS                       |  126 --
 external/vcflib/tabixpp/README                     |    6 -
 external/vcflib/tabixpp/bam_endian.h               |   42 -
 external/vcflib/tabixpp/bedidx.c                   |  156 --
 external/vcflib/tabixpp/bgzf.c                     |  711 -------
 external/vcflib/tabixpp/bgzf.h                     |  157 --
 external/vcflib/tabixpp/bgzip.c                    |  206 --
 external/vcflib/tabixpp/index.c                    |  998 ----------
 external/vcflib/tabixpp/khash.h                    |  486 -----
 external/vcflib/tabixpp/knetfile.c                 |  632 ------
 external/vcflib/tabixpp/knetfile.h                 |   75 -
 external/vcflib/tabixpp/kseq.h                     |  227 ---
 external/vcflib/tabixpp/ksort.h                    |  271 ---
 external/vcflib/tabixpp/kstring.c                  |  165 --
 external/vcflib/tabixpp/kstring.h                  |   68 -
 external/vcflib/tabixpp/main.c                     |  290 ---
 external/vcflib/tabixpp/main.cpp                   |   47 -
 external/vcflib/tabixpp/tabix.1                    |  132 --
 external/vcflib/tabixpp/tabix.cpp                  |   90 -
 external/vcflib/tabixpp/tabix.h                    |  145 --
 external/vcflib/tabixpp/tabix.hpp                  |   31 -
 62 files changed, 69 insertions(+), 12265 deletions(-)
 create mode 100644 debian/patches/use_debian_packaged_vcflib.patch
 delete mode 100644 external/vcflib/BedReader.h
 delete mode 100644 external/vcflib/LICENSE
 delete mode 100644 external/vcflib/README
 delete mode 100644 external/vcflib/Variant.cpp
 delete mode 100644 external/vcflib/Variant.h
 delete mode 100644 external/vcflib/convert.h
 delete mode 100644 external/vcflib/join.h
 delete mode 100644 external/vcflib/multichoose/Makefile
 delete mode 100644 external/vcflib/multichoose/README
 delete mode 100644 external/vcflib/multichoose/multichoose.c
 delete mode 100644 external/vcflib/multichoose/multichoose.cpp
 delete mode 100644 external/vcflib/multichoose/multichoose.h
 delete mode 100644 external/vcflib/multichoose/multichoose.py
 delete mode 100644 external/vcflib/multichoose/multipermute.cpp
 delete mode 100644 external/vcflib/multichoose/multipermute.h
 delete mode 100644 external/vcflib/multichoose/multipermute.py
 delete mode 100644 external/vcflib/smithwaterman/BandedSmithWaterman.cpp
 delete mode 100644 external/vcflib/smithwaterman/BandedSmithWaterman.h
 delete mode 100644 external/vcflib/smithwaterman/IndelAllele.cpp
 delete mode 100644 external/vcflib/smithwaterman/IndelAllele.h
 delete mode 100644 external/vcflib/smithwaterman/LeftAlign.cpp
 delete mode 100644 external/vcflib/smithwaterman/LeftAlign.h
 delete mode 100644 external/vcflib/smithwaterman/Makefile
 delete mode 100644 external/vcflib/smithwaterman/Mosaik.h
 delete mode 100644 external/vcflib/smithwaterman/Repeats.cpp
 delete mode 100644 external/vcflib/smithwaterman/Repeats.h
 delete mode 100644 external/vcflib/smithwaterman/SWMain.cpp
 delete mode 100644 external/vcflib/smithwaterman/SmithWatermanGotoh.cpp
 delete mode 100644 external/vcflib/smithwaterman/SmithWatermanGotoh.h
 delete mode 100644 external/vcflib/smithwaterman/convert.h
 delete mode 100644 external/vcflib/smithwaterman/smithwaterman.cpp
 delete mode 100644 external/vcflib/split.cpp
 delete mode 100644 external/vcflib/split.h
 delete mode 100644 external/vcflib/tabixpp/ChangeLog
 delete mode 100644 external/vcflib/tabixpp/NEWS
 delete mode 100644 external/vcflib/tabixpp/README
 delete mode 100644 external/vcflib/tabixpp/bam_endian.h
 delete mode 100644 external/vcflib/tabixpp/bedidx.c
 delete mode 100644 external/vcflib/tabixpp/bgzf.c
 delete mode 100644 external/vcflib/tabixpp/bgzf.h
 delete mode 100644 external/vcflib/tabixpp/bgzip.c
 delete mode 100644 external/vcflib/tabixpp/index.c
 delete mode 100644 external/vcflib/tabixpp/khash.h
 delete mode 100644 external/vcflib/tabixpp/knetfile.c
 delete mode 100644 external/vcflib/tabixpp/knetfile.h
 delete mode 100644 external/vcflib/tabixpp/kseq.h
 delete mode 100644 external/vcflib/tabixpp/ksort.h
 delete mode 100644 external/vcflib/tabixpp/kstring.c
 delete mode 100644 external/vcflib/tabixpp/kstring.h
 delete mode 100644 external/vcflib/tabixpp/main.c
 delete mode 100644 external/vcflib/tabixpp/main.cpp
 delete mode 100644 external/vcflib/tabixpp/tabix.1
 delete mode 100644 external/vcflib/tabixpp/tabix.cpp
 delete mode 100644 external/vcflib/tabixpp/tabix.h
 delete mode 100644 external/vcflib/tabixpp/tabix.hpp

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