[med-svn] [rsem] branch upstream updated (1e2dc5a -> 1f68569)

[Michael Crusoe]

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

      from  1e2dc5a   Imported Upstream version 1.2.26+dfsg
      adds  4e68d2a   Imported Upstream version 1.2.27+dfsg
      adds  1f68569   Imported Upstream version 1.2.28+dfsg

No new revisions were added by this update.

Summary of changes:
 .gitignore                   |   6 +-
 BamConverter.h               | 133 ++++++------
 BamWriter.h                  | 111 +++++-----
 EBSeq/rsem-for-ebseq-find-DE |   2 +-
 EM.cpp                       |  27 +--
 GTFItem.h                    |  74 ++++---
 Gibbs.cpp                    |   2 +
 Makefile                     |  78 ++++---
 README.md                    |  68 +++---
 SamParser.h                  | 331 +++++++++---------------------
 Transcript.h                 |   6 +-
 WHAT_IS_NEW                  |  18 ++
 bam2wig.cpp                  |   4 +-
 bc_aux.h                     |   8 +-
 buildReadIndex.cpp           |   2 +
 calcCI.cpp                   |   2 +
 convert-sam-for-rsem         |  83 +++-----
 extractRef.cpp               |   2 +
 getUnique.cpp                |  29 +--
 parseIt.cpp                  |  44 ++--
 preRef.cpp                   |   2 +
 rsem-calculate-expression    | 478 ++++++++++++++++++++++---------------------
 rsem-gen-transcript-plots    | 210 +++++++++++--------
 rsem-gff3-to-gtf             |  18 +-
 rsem-plot-transcript-wiggles |  24 ++-
 rsem-prepare-reference       |   4 +-
 rsem-run-ebseq               |   8 +-
 rsem_perl_utils.pm           |  10 +-
 samValidator.cpp             | 169 ++++++++-------
 sam_rsem_aux.h               |  48 -----
 sam_rsem_cvt.h               |  92 ---------
 sam_utils.h                  | 234 +++++++++++++++++++++
 scanForPairedEndReads.cpp    | 138 +++++++------
 simulation.cpp               |   2 +
 synthesisRef.cpp             |   2 +
 tbam2gbam.cpp                |  11 +-
 utils.h                      |   2 +-
 wiggle.cpp                   | 106 +++++-----
 38 files changed, 1313 insertions(+), 1275 deletions(-)
 delete mode 100644 sam_rsem_aux.h
 delete mode 100644 sam_rsem_cvt.h
 create mode 100644 sam_utils.h

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