[med-svn] [cufflinks] branch upstream updated (a28a462 -> 9dea31c)

[Alex Mestiashvili]

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

      from  a28a462   Imported Upstream version 2.1.1
       new  9dea31c   Imported Upstream version 2.2.0

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               |    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(-)
 create mode 100644 ax_boost_serialization.m4
 create mode 100644 src/cuffnorm.cpp
 create mode 100644 src/cuffquant.cpp
 create mode 100644 src/tracking.cpp
 create mode 100644 src/tracking.h

-- 
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