[med-svn] [rsem] branch master updated (d66fb92 -> 392a448)

[Michael Crusoe]

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misterc-guest pushed a change to branch master
in repository rsem.

      from  d66fb92   Upload to unstable
       new  421d375   fix build clean loop; VCS URL
       new  1e2dc5a   Imported Upstream version 1.2.26+dfsg
       new  c6a02ec   Merge tag 'upstream/1.2.26+dfsg'
       new  392a448   bump version

The 4 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:
 EBSeq/Makefile                       |   2 +-
 EBSeq/install                        |  15 +-
 EM.cpp                               |  13 +-
 GTFItem.h                            | 270 ++++++++++++++++++++---------------
 Gibbs.cpp                            |  63 ++++----
 README.md                            | 241 ++++++++++++++++++++++---------
 Transcript.h                         |  41 ++++--
 WHAT_IS_NEW                          |  26 ++++
 WriteResults.h                       |  27 +++-
 calcCI.cpp                           |  92 ++++++++----
 debian/changelog                     |   6 +
 debian/control                       |   5 +-
 debian/patches/series                |   1 +
 debian/patches/spelling              |  49 +++++++
 debian/rules                         |   4 +
 extractRef.cpp                       |  52 +++++--
 rsem-calculate-expression            |  36 ++++-
 rsem-gen-transcript-plots            |  11 +-
 rsem-gff3-to-gtf                     | 105 ++++++++++++++
 rsem-plot-model                      |  34 ++++-
 rsem-prepare-reference               |  53 +++++--
 rsem-refseq-extract-primary-assembly |  18 +++
 rsem-run-ebseq                       |   8 +-
 rsem_perl_utils.pm                   |   8 +-
 24 files changed, 860 insertions(+), 320 deletions(-)
 create mode 100644 debian/patches/spelling
 create mode 100755 rsem-gff3-to-gtf
 create mode 100755 rsem-refseq-extract-primary-assembly

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