[med-svn] [tophat] branch master updated (06a8ddb -> e872e3f)

[Alex Mestiashvili]

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

      from  06a8ddb   upload to unstable renamed patch name due to the typo  hardening4samtols.patch -> hardening4samtools.patch
       new  6f808e1   Imported Upstream version 2.0.14+dfsg
       new  b8c2097   Merge tag 'upstream/2.0.14+dfsg'
       new  e872e3f   d/changelog: new upstream version d/patches/fix_includes_path.patch: refresh

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Summary of changes:
 Makefile.in                            |   493 +-
 aclocal.m4                             |   812 ++-
 ar-lib                                 |   270 +
 config.h.in                            |    10 +-
 configure                              | 10208 +++++++++++++++----------------
 configure.ac                           |    10 +-
 debian/changelog                       |     6 +
 debian/patches/fix_includes_path.patch |     8 +-
 src/Makefile.am                        |    24 +-
 src/Makefile.in                        |   524 +-
 src/bam_merge_impl.cpp                 |    29 +-
 src/common.cpp                         |    12 +
 src/reads.cpp                          |    26 +-
 src/reads.h                            |   129 +-
 src/tophat-fusion-post                 |     2 +-
 src/tophat.py                          |    15 +-
 src/tophat_reports.cpp                 |    37 +-
 17 files changed, 6606 insertions(+), 6009 deletions(-)
 create mode 100755 ar-lib

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