[med-svn] [cufflinks] 04/10: Updated version 2.2.1+dfsg.1 from 'upstream/2.2.1+dfsg.1'

[Alex Mestiashvili]

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

commit dc67990d5cf171403cb0aa1b4ecb0079acc163f4
Merge: 532213d 5b2eb77
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Tue Sep 5 23:22:12 2017 +0200

    Updated version 2.2.1+dfsg.1 from 'upstream/2.2.1+dfsg.1'
    
    with Debian dir 01823d9eb39f32d3db7e36a48faef12a1cfb77c9

 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(-)

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