[med-svn] [subread] 02/05: Merge tag 'upstream/1.5.2+dfsg'

[Alex Mestiashvili]

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

commit 40cd25ce3bc777c81183d2dfd42669360768c99d
Merge: b750d4a 5ca905c
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Tue Mar 21 09:36:16 2017 +0100

    Merge tag 'upstream/1.5.2+dfsg'
    
    Upstream version 1.5.2+dfsg

 README.txt                                |  56 +-
 doc/SubreadUsersGuide.tex                 | 166 +++---
 src/HelperFunctions.c                     | 169 ++++++
 src/HelperFunctions.h                     |   4 +
 src/Makefile.Linux                        |   5 +-
 src/SNPCalling.c                          |  62 +-
 src/core-bigtable.c                       |   2 +-
 src/core-bigtable.h                       |   2 +-
 src/core-indel.c                          | 931 +++++++++++++++++++++++-------
 src/core-indel.h                          |  19 +-
 src/core-interface-aligner.c              | 177 ++++--
 src/core-interface-subjunc.c              | 164 ++++--
 src/core-junction.c                       | 332 +++++------
 src/core-junction.h                       |   2 +
 src/core.c                                | 824 +++++++++++++++++---------
 src/core.h                                |  20 +-
 src/coverage_calc.c                       |  67 ++-
 src/gene-algorithms.c                     |  17 +-
 src/gene-value-index.c                    |  32 +-
 src/gene-value-index.h                    |   2 +-
 src/hashtable.c                           |  45 +-
 src/hashtable.h                           |  19 +-
 src/index-builder.c                       |  57 +-
 src/input-files.c                         | 239 +++++---
 src/input-files.h                         |  12 +-
 src/makefile.version                      |   2 +-
 src/propmapped.c                          |  35 +-
 src/readSummary.c                         | 402 +++++++------
 src/sambam-file.c                         |  47 +-
 src/sambam-file.h                         |   6 +-
 src/sorted-hashtable.c                    |  57 +-
 src/subread.h                             |  10 +-
 test/featureCounts/data/test-chralias.GTF |  23 +
 test/featureCounts/del4.FC                |   9 +
 test/featureCounts/del4.FC.summary        |  12 +
 35 files changed, 2809 insertions(+), 1219 deletions(-)

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