[med-svn] [cufflinks] 02/07: Merge tag 'upstream/2.2.0'

[Alex Mestiashvili]

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

commit eaafd361325ad12e42628f4e8900f6620bf4c2ef
Merge: af17562 9dea31c
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Apr 11 13:01:34 2014 +0200

    Merge tag 'upstream/2.2.0'
    
    Upstream version 2.2.0

 Makefile.in               |    8 +-
 ax_boost_serialization.m4 |  135 ++++
 config.h.in               |    3 +
 configure                 |  473 +++++++++++-
 configure.ac              |    6 +-
 make_bin.sh               |   21 +-
 src/Makefile.am           |   29 +-
 src/Makefile.in           |   72 +-
 src/abundances.cpp        |  911 ++++++++++++++++++----
 src/abundances.h          |  264 +++++--
 src/assemble.h            |    2 +-
 src/biascorrection.cpp    |   18 +-
 src/biascorrection.h      |    2 +-
 src/bundles.cpp           |  179 ++++-
 src/bundles.h             |   91 ++-
 src/clustering.cpp        |   18 +-
 src/common.cpp            |   50 +-
 src/common.h              |  256 +++++-
 src/compress_gtf.cpp      |   27 +-
 src/cuffcompare.cpp       |   59 +-
 src/cuffdiff.cpp          |  703 ++++++++---------
 src/cufflinks.cpp         |  109 +--
 src/cuffnorm.cpp          | 1892 +++++++++++++++++++++++++++++++++++++++++++++
 src/cuffquant.cpp         | 1623 ++++++++++++++++++++++++++++++++++++++
 src/differential.cpp      |  609 +++++----------
 src/differential.h        |  127 +--
 src/filters.cpp           |   10 +-
 src/filters.h             |    4 +-
 src/genes.cpp             |    2 +-
 src/gff.cpp               |  438 +++++++----
 src/gff.h                 |  146 ++--
 src/gff_utils.cpp         |   95 ++-
 src/gff_utils.h           |    6 +-
 src/gffread.cpp           |  266 ++++---
 src/gtf_to_sam.cpp        |   19 +-
 src/gtf_tracking.cpp      |   34 +-
 src/gtf_tracking.h        |    6 +-
 src/hits.cpp              |  173 +++++
 src/hits.h                |  146 +++-
 src/replicates.cpp        |  113 ++-
 src/replicates.h          |  102 ++-
 src/rounding.h            |   25 +-
 src/scaffolds.cpp         |   14 +-
 src/scaffolds.h           |   10 +-
 src/tracking.cpp          |   99 +++
 src/tracking.h            |  118 +++
 46 files changed, 7712 insertions(+), 1801 deletions(-)

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