[med-svn] [subread] branch upstream updated (e3249b5 -> 5ca905c)

[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  e3249b5   Imported Upstream version 1.5.1+dfsg
       new  5ca905c   New upstream version 1.5.2+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:
 README.txt                                |  56 +-
 doc/SubreadUsersGuide.tex                 | 166 +++---
 src/HelperFunctions.c                     | 169 ++++++
 src/HelperFunctions.h                     |   4 +
 src/Makefile.Linux                        |   5 +-
 src/SNPCalling.c                          |  62 +-
 src/core-bigtable.c                       |   2 +-
 src/core-bigtable.h                       |   2 +-
 src/core-indel.c                          | 931 +++++++++++++++++++++++-------
 src/core-indel.h                          |  19 +-
 src/core-interface-aligner.c              | 177 ++++--
 src/core-interface-subjunc.c              | 164 ++++--
 src/core-junction.c                       | 332 +++++------
 src/core-junction.h                       |   2 +
 src/core.c                                | 824 +++++++++++++++++---------
 src/core.h                                |  20 +-
 src/coverage_calc.c                       |  67 ++-
 src/gene-algorithms.c                     |  17 +-
 src/gene-value-index.c                    |  32 +-
 src/gene-value-index.h                    |   2 +-
 src/hashtable.c                           |  45 +-
 src/hashtable.h                           |  19 +-
 src/index-builder.c                       |  57 +-
 src/input-files.c                         | 239 +++++---
 src/input-files.h                         |  12 +-
 src/makefile.version                      |   2 +-
 src/propmapped.c                          |  35 +-
 src/readSummary.c                         | 402 +++++++------
 src/sambam-file.c                         |  47 +-
 src/sambam-file.h                         |   6 +-
 src/sorted-hashtable.c                    |  57 +-
 src/subread.h                             |  10 +-
 test/featureCounts/data/test-chralias.GTF |  23 +
 test/featureCounts/del4.FC                |   9 +
 test/featureCounts/del4.FC.summary        |  12 +
 35 files changed, 2809 insertions(+), 1219 deletions(-)
 create mode 100644 test/featureCounts/data/test-chralias.GTF
 create mode 100644 test/featureCounts/del4.FC
 create mode 100644 test/featureCounts/del4.FC.summary

-- 
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