[med-svn] [cufflinks] branch master updated (af17562 -> 16304da)

[Alex Mestiashvili]

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

      from  af17562   Move debian/upstream to debian/upstream/metadata
       new  9dea31c   Imported Upstream version 2.2.0
       new  eaafd36   Merge tag 'upstream/2.2.0'
       new  27b51c3    d/patches: refreshed  d/changelog: imported new upstream version 2.2.0
       new  3d30643    d/rules: link to the serialization library "-lboost_serialization"  d/control: use canonical VCS-* fields, updated Standards-Version
       new  bb8cf0f    d/rules: attempt to generate man pages automatically  d/control: Build-Depends: add help2man
       new  22f4695    d/patches/gffread_show_usage.patch: fix buffer overflow in gffread  d/rules: separate rule for manpage for gffread as it doesn't return usage   message when executed without arguments  d/*.1: removed obsoleted manpages
       new  16304da    d/copyright: updated Source, Copyright years

The 7 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 +-
 debian/changelog                                |   23 +
 debian/compress_gtf.1                           |   19 -
 debian/control                                  |    9 +-
 debian/copyright                                |    4 +-
 debian/cuffcompare.1                            |   53 -
 debian/cuffdiff.1                               |   90 --
 debian/cufflinks.1                              |  240 ---
 debian/cufflinks.manpages                       |    1 -
 debian/cuffmerge.1                              |   33 -
 debian/gffread.1                                |  219 ---
 debian/gtf_to_sam.1                             |   14 -
 debian/patches/0001-fix_spelling.patch          |   18 +-
 debian/patches/0002-bam2samtools.patch          |    6 +-
 debian/patches/0003-fix_includes_path.patch     |   36 +-
 debian/patches/0004-fix-m64-usage-and-lfs.patch |    6 +-
 debian/patches/gffread_show_usage.patch         |  154 ++
 debian/patches/series                           |    1 +
 debian/rules                                    |   27 +-
 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 ++
 64 files changed, 7956 insertions(+), 2510 deletions(-)
 create mode 100644 ax_boost_serialization.m4
 delete mode 100644 debian/compress_gtf.1
 delete mode 100644 debian/cuffcompare.1
 delete mode 100644 debian/cuffdiff.1
 delete mode 100644 debian/cufflinks.1
 delete mode 100644 debian/cufflinks.manpages
 delete mode 100644 debian/cuffmerge.1
 delete mode 100644 debian/gffread.1
 delete mode 100644 debian/gtf_to_sam.1
 create mode 100644 debian/patches/gffread_show_usage.patch
 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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