[med-svn] [cufflinks] branch master updated (25fe711 -> 6e5767c)

[Alex Mestiashvili]

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

      from  25fe711    d/copyright: UNRELEASED->unstable  d/control: fixed VCS-Browser field  d/rules: fixed description for man pages
       new  d68919a   d/control: cme fix dpkg-control
       new  55fd328   Imported Upstream version 2.2.1
       new  52933e8   Merge tag 'upstream/2.2.1'
       new  6e5767c    d/changelog: imported new upstream release  upload to unstable

The 4 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:
 Makefile.in          |   10 +-
 config.h.in          |    2 +-
 configure            | 8583 ++++++++++++++++++++++++++++----------------------
 configure.ac         |    2 +-
 debian/changelog     |    7 +
 debian/control       |   16 +-
 make_bin.sh          |    6 +-
 src/GBase.cpp        |    8 +-
 src/GFaSeqGet.h      |   24 +
 src/GStr.cpp         |   29 +-
 src/GStr.h           |   20 +-
 src/Makefile.in      |   10 +-
 src/abundances.cpp   |   10 +-
 src/common.cpp       |    6 +-
 src/common.h         |    1 +
 src/cuffdiff.cpp     |   58 +-
 src/cuffnorm.cpp     |  113 +-
 src/cuffquant.cpp    |    2 +-
 src/gff.cpp          |   25 +-
 src/gff.h            |   12 +-
 src/gff_utils.cpp    |   14 +-
 src/gtf_tracking.cpp |  112 +-
 src/gtf_tracking.h   |   17 +-
 src/replicates.cpp   |    4 +
 24 files changed, 5169 insertions(+), 3922 deletions(-)

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