[med-svn] [subread] branch master updated (f629caa -> a3a9304)

[Alex Mestiashvili]

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

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

      from  f629caa   d/changelog: upload to unstable
       new  8f89778   Remove trailing white spaces
       new  5e128f5   d/tests/subread-tests: Cleanup TMPDIR
       new  8b7078e   Imported Upstream version 1.5.0-p2+dfsg
       new  0d7e546   Merge tag 'upstream/1.5.0-p2+dfsg'
       new  e55fbce   Refresh quilt patches
       new  f25da35   Update d/changelog
       new  e418da6   Add --parallel to dh $@
       new  ea05377   Update arch_specific_flags.patch
       new  7b3908d   Cme fix dpkg, update VCS fields, bump Standards-Version
       new  0aadd3a   Enable more tests
       new  0f57550   Add python and bc to Build-Depends, needed for tests
       new  c66fb68   Run all tests
       new  7bb8e36   Add workardound for autopkgtest
       new  a3a9304   Update chnagelog, upload to unstable

The 14 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:
 debian/README.source                               |    2 +-
 debian/README.test                                 |    2 +-
 debian/changelog                                   |   13 +
 debian/control                                     |    6 +-
 debian/filter.pl                                   |    2 +-
 debian/patches/arch_specific_flags.patch           |   18 +-
 debian/patches/series                              |    2 +-
 debian/patches/syntax_err.patch                    |    2 +-
 debian/rules                                       |    6 +-
 debian/tests/subread-tests                         |   47 +-
 doc/SubreadUsersGuide.tex                          |   20 +-
 src/HelperFunctions.c                              |  148 +++
 src/HelperFunctions.h                              |    1 +
 src/Makefile                                       |    2 +-
 src/Makefile.Linux                                 |    8 +-
 src/SNPCalling.c                                   |   20 +-
 src/core-bigtable.c                                |   40 +-
 src/core-indel.c                                   |   19 +-
 src/core-interface-aligner.c                       |    2 +
 src/core-interface-subjunc.c                       |   20 +-
 src/core-junction.c                                | 1166 ++++++++++++++++----
 src/core.c                                         |  222 ++--
 src/core.h                                         |    3 +-
 src/coverage_calc.c                                |    4 +-
 src/gene-algorithms.c                              |   20 +-
 src/gene-algorithms.h                              |    2 +-
 src/gene-value-index.c                             |   16 +-
 src/global-reassembly.c                            |    5 +-
 src/index-builder.c                                |    2 +
 src/input-files.c                                  |   62 +-
 src/input-files.h                                  |    5 +-
 src/makefile.version                               |    6 +-
 src/propmapped.c                                   |    8 +-
 src/read-repair.c                                  |    6 +-
 src/readSummary.c                                  |  282 +++--
 src/removeDupReads.c                               |    6 +-
 src/sambam-file.c                                  |    6 +
 src/sambam-file.h                                  |    1 +
 src/subread.h                                      |    2 +-
 src/subtools.c                                     |    5 +-
 test/featureCounts/data/corner-EXON-ONLY.ora       |    9 +
 .../data/test-minimum-dup.ora.summary              |   12 -
 test/featureCounts/test_corner_cases.sh            |    1 +
 43 files changed, 1715 insertions(+), 516 deletions(-)
 create mode 100644 test/featureCounts/data/corner-EXON-ONLY.ora
 delete mode 100644 test/featureCounts/data/test-minimum-dup.ora.summary

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