[med-svn] [cufflinks] branch upstream updated (70257e8 -> 5b2eb77)

[Alex Mestiashvili]

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

      from  70257e8   Imported Upstream version 2.2.1
       new  5b2eb77   New upstream version 2.2.1+dfsg.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            |   624 ---
 aclocal.m4             |  1031 -----
 autogen.sh             |    21 +
 ax_openmp.m4           |   101 +
 boost.m4               |    87 +
 build-aux/config.guess |  1463 -------
 build-aux/config.sub   |  1579 -------
 build-aux/depcomp      |   530 ---
 build-aux/install-sh   |   323 --
 build-aux/missing      |   360 --
 config.h.in            |   112 -
 configure              | 10836 -----------------------------------------------
 make_bin.sh            |     6 +-
 src/LICENSE            |    18 +
 src/Makefile.in        |  1624 -------
 src/biascorrection.cpp |     2 +-
 src/bundles.cpp        |    39 +-
 src/bundles.h          |    25 +-
 src/common.h           |    10 +
 src/compress_gtf.cpp   |     6 -
 src/cuffcluster.cpp    |   942 ++++
 src/cuffcompare.cpp    |     7 -
 src/cuffdiff.cpp       |    12 +-
 src/cuffdiff_to_gct.py |   108 +
 src/cufflinks.cpp      |     8 +-
 src/cuffnorm.cpp       |   701 +--
 src/cuffquant.cpp      |    10 +-
 src/differential.cpp   |   169 +-
 src/differential.h     |   729 +++-
 src/gtf_reads.cpp      |   187 +
 src/gtf_to_sam.cpp     |     6 -
 src/hits.cpp           |     8 +-
 src/hits.h             |     2 +-
 src/replicates.cpp     |    53 +-
 src/replicates.h       |     4 +-
 version.m4             |     1 +
 36 files changed, 2366 insertions(+), 19378 deletions(-)
 delete mode 100644 Makefile.in
 delete mode 100644 aclocal.m4
 create mode 100755 autogen.sh
 create mode 100644 ax_openmp.m4
 create mode 100644 boost.m4
 delete mode 100755 build-aux/config.guess
 delete mode 100755 build-aux/config.sub
 delete mode 100755 build-aux/depcomp
 delete mode 100755 build-aux/install-sh
 delete mode 100755 build-aux/missing
 delete mode 100644 config.h.in
 delete mode 100755 configure
 create mode 100644 src/LICENSE
 delete mode 100644 src/Makefile.in
 create mode 100644 src/cuffcluster.cpp
 create mode 100755 src/cuffdiff_to_gct.py
 create mode 100644 src/gtf_reads.cpp
 create mode 100644 version.m4

-- 
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