[med-svn] [subread] branch master updated (b750d4a -> 375b900)

[Alex Mestiashvili]

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

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

      from  b750d4a   Upload to unstable
       new  5ca905c   New upstream version 1.5.2+dfsg
       new  40cd25c   Merge tag 'upstream/1.5.2+dfsg'
       new  ee4a168   Refresh and update patches
       new  e9ae5f4   Add d/patches/typo.patch fixing a typo in featureCounts
       new  375b900   Update changelog, upload to unstable

The 5 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 +-
 debian/changelog                          |   8 +
 debian/patches/arch_specific_flags.patch  |  19 +-
 debian/patches/fix_ftbfs_kfreebsd.patch   |   4 +-
 debian/patches/series                     |   1 +
 debian/patches/typo.patch                 |  13 +
 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 +
 40 files changed, 2842 insertions(+), 1231 deletions(-)
 create mode 100644 debian/patches/typo.patch
 create mode 100644 test/featureCounts/data/test-chralias.GTF
 create mode 100644 test/featureCounts/del4.FC
 create mode 100644 test/featureCounts/del4.FC.summary

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/subread.git