[med-svn] [subread] branch master updated (38d1d19 -> 1f34cc4)

[Alex Mestiashvili]

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

      from  38d1d19   fix tarball member permissions
       new  e3249b5   Imported Upstream version 1.5.1+dfsg
       new  5fe196a   Merge tag 'upstream/1.5.1+dfsg'
       new  c8668e1   Fix copyright Format: s/http/https/
       new  8fb55bb   Refresh and remove applied patches
       new  1f34cc4   Update changelog, upload to unstable

The 5 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 ++++++++++--------
 debian/changelog                                   |      8 +
 debian/copyright                                   |      2 +-
 debian/patches/fix_ftbfs_kfreebsd.patch            |      4 +-
 debian/patches/series                              |      1 -
 debian/patches/syntax_err.patch                    |     13 -
 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 +-
 31 files changed, 262883 insertions(+), 223486 deletions(-)
 copy annotation/{mm10_RefSeq_exon.txt => hg38_RefSeq_exon.txt} (58%)
 delete mode 100644 debian/patches/syntax_err.patch
 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

-- 
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