[med-svn] [subread] 02/08: Merge tag 'upstream/1.5.0+dfsg'

[Alex Mestiashvili]

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

commit 75041475830d489aac066059b2cdf8770af84e1d
Merge: 7b55f96 32f5127
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Nov 6 15:00:22 2015 +0100

    Merge tag 'upstream/1.5.0+dfsg'
    
    Upstream version 1.5.0+dfsg

 doc/MDSplot.png                                    |  Bin 22947 -> 0 bytes
 doc/SubreadUsersGuide.bib                          |   73 -
 doc/SubreadUsersGuide.tex                          |  220 +-
 doc/indel.png                                      |  Bin 108132 -> 0 bytes
 doc/junction.png                                   |  Bin 172344 -> 0 bytes
 doc/seed-and-vote.png                              |  Bin 112767 -> 0 bytes
 doc/voom_mean_variance.png                         |  Bin 99213 -> 0 bytes
 src/BACK-sambam-file.h                             |   56 -
 src/HelperFunctions.c                              |  305 +-
 src/HelperFunctions.h                              |   20 +-
 src/Makefile.FreeBSD                               |    3 +-
 src/Makefile.Linux                                 |   14 +-
 src/Makefile.MacOS                                 |   17 +-
 src/SNPCalling.c                                   |   11 +-
 src/SUBindel.c                                     |   11 +-
 src/SeekGZ.h                                       |   10 +
 src/core-bigtable.c                                |  488 +++
 src/core-bigtable.h                                |   49 +
 src/core-indel.c                                   |  561 ++-
 src/core-indel.h                                   |   71 +-
 src/core-interface-aligner.c                       |  275 +-
 src/core-interface-subjunc.c                       |  326 +-
 src/core-junction-V2.c                             | 2922 --------------
 src/core-junction.c                                | 4140 +++++++++++++++-----
 src/core-junction.h                                |   53 +-
 src/core.c                                         | 3216 ++++++++-------
 src/core.h                                         |  358 +-
 src/coverage_calc.c                                |   25 +-
 src/del4-mmap-test.c                               |   44 +
 src/filterJunctionTable.c                          |    7 +-
 src/fullscan.c                                     |   35 +-
 src/gene-algorithms.c                              |   36 +-
 src/gene-algorithms.h                              |    6 +-
 src/global-reassembly.c                            |   30 +-
 src/hashtable.c                                    |   15 +-
 src/hashtable.h                                    |    4 +-
 src/index-builder.c                                |   83 +-
 src/input-files.c                                  | 3017 ++++++++++++--
 src/input-files.h                                  |  121 +-
 src/makefile.version                               |    2 +-
 src/propmapped.c                                   |   18 +-
 src/qualityScores.c                                |   33 +-
 src/read-repair.c                                  |  130 +
 src/readSummary.c                                  | 2770 +++++++------
 src/removeDupReads.c                               |   23 +-
 src/samMappedBases.c                               |  124 +
 src/sambam-file.c                                  |   55 +-
 src/sambam-file.h                                  |    3 +
 src/seek-zlib.c                                    |  338 ++
 src/seek-zlib.h                                    |   23 +
 src/sorted-hashtable.c                             |   20 +-
 src/subfilter.c                                    |   48 +
 src/subread.h                                      |   87 +-
 src/subtools.c                                     |    9 +-
 src/t.c                                            |    4 +
 src/test-seek-zlib.c                               |  101 +
 src/test_qs.c                                      |  106 +
 src/zlib_test.c                                    |   88 +
 src/zpipe.c                                        |  192 -
 test/featureCounts/data/DEL4-1385690721.FC         |    9 -
 test/featureCounts/data/DEL4-1385690721.FC.summary |    9 -
 test/featureCounts/data/corner-BINS.SAF            |    7 +
 test/featureCounts/data/corner-BINS.sam            |    9 +
 test/featureCounts/data/corner-JUNC.sam            |    8 +-
 test/featureCounts/data/test-chrname.sam           |  604 +--
 test/featureCounts/data/test-minimum-dup.ora       |    9 +
 ...ce.ora.summary => test-minimum-dup.ora.summary} |    9 +-
 test/featureCounts/featureCounts-test.sh           |    2 +-
 test/featureCounts/result/test-minimum.FC          |    9 -
 test/featureCounts/result/test-minimum.FC.summary  |   12 -
 test/featureCounts/test_all.sh                     |    6 -
 test/featureCounts/test_corner_cases.sh            |    2 +
 test/subjunc/subjunc-test.sh                       |    4 +-
 test/subread-align/subread-align-test.sh           |   14 +-
 test/subread-align/test-tmp.log                    |   36 +-
 75 files changed, 12848 insertions(+), 8697 deletions(-)

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