[med-svn] [tvc] 04/05: Merge tag 'upstream/5.0.3+dfsg1'

[Andreas Tille]

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tille pushed a commit to branch master
in repository tvc.

commit 6c8dc1825b6f4530789c1c846ccb561d63e4db7a
Merge: 1961741 c7f1a0f
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jan 13 13:31:43 2017 +0100

    Merge tag 'upstream/5.0.3+dfsg1'
    
    Upstream version 5.0.3+dfsg1

 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 -
 55 files changed, 12233 deletions(-)

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