[med-svn] [subread] branch upstream updated (5acf640 -> 8b7078e)

[Alex Mestiashvili]

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

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

      from  5acf640   Imported Upstream version 1.5.0-p1+dfsg
       new  8b7078e   Imported Upstream version 1.5.0-p2+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/SubreadUsersGuide.tex                          |   20 +-
 src/HelperFunctions.c                              |  148 +++
 src/HelperFunctions.h                              |    1 +
 src/Makefile                                       |    2 +-
 src/Makefile.Linux                                 |    8 +-
 src/SNPCalling.c                                   |   20 +-
 src/core-bigtable.c                                |   40 +-
 src/core-indel.c                                   |   19 +-
 src/core-interface-aligner.c                       |    2 +
 src/core-interface-subjunc.c                       |   20 +-
 src/core-junction.c                                | 1166 ++++++++++++++++----
 src/core.c                                         |  222 ++--
 src/core.h                                         |    3 +-
 src/coverage_calc.c                                |    4 +-
 src/gene-algorithms.c                              |   20 +-
 src/gene-algorithms.h                              |    2 +-
 src/gene-value-index.c                             |   16 +-
 src/global-reassembly.c                            |    5 +-
 src/index-builder.c                                |    2 +
 src/input-files.c                                  |   62 +-
 src/input-files.h                                  |    5 +-
 src/makefile.version                               |    6 +-
 src/propmapped.c                                   |    8 +-
 src/read-repair.c                                  |    6 +-
 src/readSummary.c                                  |  282 +++--
 src/removeDupReads.c                               |    6 +-
 src/sambam-file.c                                  |    6 +
 src/sambam-file.h                                  |    1 +
 src/subread.h                                      |    2 +-
 src/subtools.c                                     |    5 +-
 test/featureCounts/data/corner-EXON-ONLY.ora       |    9 +
 .../data/test-minimum-dup.ora.summary              |   12 -
 test/featureCounts/test_corner_cases.sh            |    1 +
 33 files changed, 1668 insertions(+), 463 deletions(-)
 create mode 100644 test/featureCounts/data/corner-EXON-ONLY.ora
 delete mode 100644 test/featureCounts/data/test-minimum-dup.ora.summary

-- 
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