[med-svn] [subread] branch debian/jessie-backports updated (791782a -> 38cbeb4)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch debian/jessie-backports
in repository subread.

      from  791782a   Rebuild for jessie-backports
      adds  6019350   make build reproducible
      adds  3961be8   upload to unstable
      adds  38d1d19   fix tarball member permissions
      adds  e3249b5   Imported Upstream version 1.5.1+dfsg
      adds  5fe196a   Merge tag 'upstream/1.5.1+dfsg'
      adds  c8668e1   Fix copyright Format: s/http/https/
      adds  8fb55bb   Refresh and remove applied patches
      adds  1f34cc4   Update changelog, upload to unstable
      adds  e940950   make build reproducible
      adds  c158b0f   Pass triplet-prefixed CC to make
      adds  885f23c   Fix watch file
      adds  b9999d5   debhelper 10
      adds  b750d4a   Upload to unstable
       new  6196733   Merge tag 'debian/1.5.1+dfsg-4' into debian/jessie-backports
       new  38cbeb4   Rebuild for jessie-backports

The 2 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/README.source                               |      6 -
 debian/changelog                                   |     51 +
 debian/compat                                      |      2 +-
 debian/control                                     |      2 +-
 debian/copyright                                   |      2 +-
 debian/patches/arch_specific_flags.patch           |      6 +-
 debian/patches/fix_ftbfs_kfreebsd.patch            |      4 +-
 debian/patches/series                              |      1 -
 debian/patches/syntax_err.patch                    |     13 -
 debian/rules                                       |     15 +-
 debian/watch                                       |      4 +-
 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 +-
 37 files changed, 262945 insertions(+), 223502 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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