[med-svn] [rsem] branch upstream updated (18fa866 -> 1e2dc5a)

[Michael Crusoe]

This is an automated email from the git hooks/post-receive script.

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

      from  18fa866   Imported Upstream version 1.2.23+dfsg
       new  1e2dc5a   Imported Upstream version 1.2.26+dfsg

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:
 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 ++++++++----
 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 +-
 19 files changed, 797 insertions(+), 318 deletions(-)
 create mode 100755 rsem-gff3-to-gtf
 create mode 100755 rsem-refseq-extract-primary-assembly

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