[med-svn] [subread] branch master updated (375b900 -> e53d446)

[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  375b900   Update changelog, upload to unstable
       new  1e72188   Bump Standards-Version to 4.0.0
       new  9d897ea   New upstream version 1.5.3+dfsg
       new  490dbe4   Updated version 1.5.3+dfsg from 'upstream/1.5.3+dfsg'
       new  8dbd32f   Refresh and update paches
       new  412c5e8   Update filter for man pages, update descriptions for tools
       new  e53d446   Update changelog, upload to unstable

The 6 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:
 debian/changelog                         |   30 +-
 debian/control                           |   14 +-
 debian/filter.pl                         |   19 +-
 debian/patches/arch_specific_flags.patch |    8 +-
 debian/patches/fix_ftbfs_kfreebsd.patch  |    6 +-
 debian/rules                             |   13 +-
 doc/SubreadUsersGuide.tex                |  159 +--
 src/HelperFunctions.c                    |   42 +-
 src/HelperFunctions.h                    |    4 +-
 src/Makefile.FreeBSD                     |   11 +-
 src/Makefile.Linux                       |   29 +-
 src/Makefile.MacOS                       |    6 +-
 src/core-indel.c                         |   37 +-
 src/core-interface-aligner.c             |   37 +-
 src/core-interface-subjunc.c             |   39 +-
 src/core-junction.c                      |   29 +-
 src/core-junction.h                      |    3 +
 src/core.c                               |  373 ++++---
 src/core.h                               |   23 +-
 src/hashtable.c                          |   70 +-
 src/hashtable.h                          |    5 +-
 src/input-files.c                        |  574 ++++++++---
 src/input-files.h                        |   15 +-
 src/makefile.version                     |    2 +-
 src/read-repair.c                        |    2 +-
 src/readSummary.c                        | 1620 +++++++++++++++++++++---------
 src/sambam-file.c                        |  184 +++-
 src/sambam-file.h                        |    4 +-
 src/subread.h                            |    6 +-
 src/tx-unique.c                          |  443 ++++++++
 src/tx-unique.h                          |   37 +
 test/subread-align/subread-align-test.sh |    4 +-
 32 files changed, 2817 insertions(+), 1031 deletions(-)
 create mode 100644 src/tx-unique.c
 create mode 100644 src/tx-unique.h

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