[med-svn] [subread] branch upstream updated (5c4e244 -> e3249b5)

[Alex Mestiashvili]

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malex-guest pushed a change to branch upstream
in repository subread.

      from  5c4e244   Imported Upstream version 1.5.0-p3+dfsg
       new  e3249b5   Imported Upstream version 1.5.1+dfsg

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:
 .../{mm10_RefSeq_exon.txt => hg38_RefSeq_exon.txt} | 484748 ++++++++++--------
 doc/SubreadUsersGuide.tex                          |    143 +-
 src/Makefile                                       |      2 +-
 src/Makefile.FreeBSD                               |      2 +-
 src/Makefile.Linux                                 |      2 +-
 src/Makefile.MacOS                                 |      2 +-
 src/SNPCalling.c                                   |      8 +-
 src/core-indel.c                                   |     38 +-
 src/core-interface-aligner.c                       |      5 +
 src/core-interface-subjunc.c                       |      6 +
 src/core-junction.c                                |      2 +-
 src/core.c                                         |     86 +-
 src/core.h                                         |      5 +-
 src/gene-value-index.c                             |      5 +-
 src/input-files.c                                  |     54 +-
 src/input-files.h                                  |      2 +
 src/interval_merge.c                               |     24 +-
 src/makefile.version                               |      2 +-
 src/readSummary.c                                  |   1166 +-
 test/featureCounts/data/corner-MinOverlap.ora      |      8 +-
 test/featureCounts/data/corner-fractions.SAF       |      5 +
 test/featureCounts/data/corner-fractions.ora       |      3 +
 test/featureCounts/data/corner-fractions.sam       |      7 +
 test/featureCounts/data/test-fracOverlap.ora       |      4 +
 test/featureCounts/data/test-fracOverlap.sam       |      4 +
 test/featureCounts/test_corner_cases.sh            |      8 +-
 26 files changed, 262872 insertions(+), 223469 deletions(-)
 copy annotation/{mm10_RefSeq_exon.txt => hg38_RefSeq_exon.txt} (58%)
 create mode 100644 test/featureCounts/data/corner-fractions.SAF
 create mode 100644 test/featureCounts/data/corner-fractions.ora
 create mode 100644 test/featureCounts/data/corner-fractions.sam
 create mode 100644 test/featureCounts/data/test-fracOverlap.ora
 create mode 100644 test/featureCounts/data/test-fracOverlap.sam

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/subread.git