[med-svn] [tvc] branch upstream updated (7484ae9 -> c7f1a0f)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository tvc.

      from  7484ae9   Import Upstream version 5.0.3+dfsg
       new  c7f1a0f   New upstream version 5.0.3+dfsg1

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:
 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(-)
 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

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