[med-svn] [cufflinks] branch upstream updated (9dea31c -> 55fd328)

[Alex Mestiashvili]

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

      from  9dea31c   Imported Upstream version 2.2.0
       new  55fd328   Imported Upstream version 2.2.1

The 1 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 +-
 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 +
 22 files changed, 5154 insertions(+), 3914 deletions(-)

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