[med-svn] [subread] 03/06: Updated version 1.5.3+dfsg from 'upstream/1.5.3+dfsg'

[Alex Mestiashvili]

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

commit 490dbe4faf8c565440e36fa25947a12b3561d397
Merge: 1e72188 9d897ea
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Jul 28 11:04:55 2017 +0200

    Updated version 1.5.3+dfsg from 'upstream/1.5.3+dfsg'
    
    with Debian dir 5f74f3cdc26e670259ad719cc7b841ba5ac6cbed

 doc/SubreadUsersGuide.tex                |  159 +--
 src/HelperFunctions.c                    |   42 +-
 src/HelperFunctions.h                    |    4 +-
 src/Makefile.FreeBSD                     |   11 +-
 src/Makefile.Linux                       |   29 +-
 src/Makefile.MacOS                       |    6 +-
 src/core-indel.c                         |   37 +-
 src/core-interface-aligner.c             |   37 +-
 src/core-interface-subjunc.c             |   39 +-
 src/core-junction.c                      |   29 +-
 src/core-junction.h                      |    3 +
 src/core.c                               |  373 ++++---
 src/core.h                               |   23 +-
 src/hashtable.c                          |   70 +-
 src/hashtable.h                          |    5 +-
 src/input-files.c                        |  574 ++++++++---
 src/input-files.h                        |   15 +-
 src/makefile.version                     |    2 +-
 src/read-repair.c                        |    2 +-
 src/readSummary.c                        | 1620 +++++++++++++++++++++---------
 src/sambam-file.c                        |  184 +++-
 src/sambam-file.h                        |    4 +-
 src/subread.h                            |    6 +-
 src/tx-unique.c                          |  443 ++++++++
 src/tx-unique.h                          |   37 +
 test/subread-align/subread-align-test.sh |    4 +-
 26 files changed, 2757 insertions(+), 1001 deletions(-)

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