[med-svn] [subread] branch upstream updated (91f65e5 -> ea3f671)

[Alex Mestiashvili]

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

      from  91f65e5   Imported Upstream version 1.4.6-p4+dfsg
       new  ea3f671   Imported Upstream version 1.4.6-p5+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:
 doc/MDSplot.png                                   |  Bin 0 -> 22947 bytes
 doc/SubreadUsersGuide.bib                         |   73 ++
 doc/SubreadUsersGuide.tex                         | 1219 +++++++++++++++++++++
 doc/indel.png                                     |  Bin 0 -> 108132 bytes
 doc/junction.png                                  |  Bin 0 -> 172344 bytes
 doc/seed-and-vote.png                             |  Bin 0 -> 112767 bytes
 doc/voom_mean_variance.png                        |  Bin 0 -> 99213 bytes
 src/HelperFunctions.c                             |   47 +-
 src/HelperFunctions.h                             |    2 +-
 src/core-junction.c                               |   24 +-
 src/coverage_calc.c                               |   18 +-
 src/makefile.version                              |    2 +-
 src/readSummary.c                                 |  669 ++++++-----
 src/subread.h                                     |    1 +
 test/featureCounts/result/test-minimum.FC         |    9 +
 test/featureCounts/result/test-minimum.FC.summary |   12 +
 16 files changed, 1768 insertions(+), 308 deletions(-)
 create mode 100644 doc/MDSplot.png
 create mode 100644 doc/SubreadUsersGuide.bib
 create mode 100644 doc/SubreadUsersGuide.tex
 create mode 100644 doc/indel.png
 create mode 100644 doc/junction.png
 create mode 100644 doc/seed-and-vote.png
 create mode 100644 doc/voom_mean_variance.png
 create mode 100644 test/featureCounts/result/test-minimum.FC
 create mode 100644 test/featureCounts/result/test-minimum.FC.summary

-- 
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