[med-svn] [subread] 04/10: Update upstream source from tag 'upstream/1.6.0+dfsg'

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository subread.

commit 08ecce9cfdc96bdb1ce1211bb446e990e291bff4
Merge: 139eabe e99d951
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Nov 17 13:31:58 2017 +0100

    Update upstream source from tag 'upstream/1.6.0+dfsg'
    
    Update to upstream version '1.6.0+dfsg'
    with Debian dir 59767e5208ed36e03f2c39df9ee4fa3bd19f7a1c

 doc/SubreadUsersGuide.tex                   |   53 +-
 src/Makefile.FreeBSD                        |   13 +-
 src/Makefile.Linux                          |   11 +-
 src/Makefile.MacOS                          |   10 +-
 src/core-interface-aligner.c                |    5 +-
 src/core-interface-subjunc.c                |    3 +-
 src/core-junction.c                         |   66 +-
 src/core.c                                  |   57 +-
 src/gene-algorithms.c                       |   29 +-
 src/gene-value-index.c                      |   48 +-
 src/input-files.c                           |  131 +-
 src/longread-mapping/LRMbase-index.c        |  285 ++++
 src/longread-mapping/LRMbase-index.h        |   38 +
 src/longread-mapping/LRMchro-event.c        | 1241 +++++++++++++++++
 src/longread-mapping/LRMchro-event.h        |   40 +
 src/longread-mapping/LRMconfig.h            |  389 ++++++
 src/longread-mapping/LRMfile-io.c           |  673 +++++++++
 src/longread-mapping/LRMfile-io.h           |   55 +
 src/longread-mapping/LRMhelper.c            |   77 +
 src/longread-mapping/LRMhelper.h            |   28 +
 src/longread-mapping/LRMsorted-hashtable.c  |  534 +++++++
 src/longread-mapping/LRMsorted-hashtable.h  |   44 +
 src/longread-mapping/Makefile               |   23 +
 src/longread-mapping/hashtable.c            |  797 +++++++++++
 src/longread-mapping/hashtable.h            |  471 +++++++
 src/longread-mapping/longread-mapping-one.c | 1231 ++++++++++++++++
 src/longread-mapping/longread-mapping.c     | 2012 +++++++++++++++++++++++++++
 src/longread-mapping/seek-zlib.c            |  363 +++++
 src/longread-mapping/seek-zlib.h            |   86 ++
 src/makefile.version                        |    2 +-
 src/propmapped.c                            |   13 +-
 src/readSummary.c                           |  257 +++-
 src/subread.h                               |   23 +-
 33 files changed, 8933 insertions(+), 175 deletions(-)

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