[med-svn] [subread] branch master updated (e53d446 -> 5d6bf61)

[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  e53d446   Update changelog, upload to unstable
       new  61c423e   Update d/watch
       new  139eabe   Bump Standards-Version to 4.1.1
       new  e99d951   New upstream version 1.6.0+dfsg
       new  08ecce9   Update upstream source from tag 'upstream/1.6.0+dfsg'
       new  c6636a1   Update d/subread.install, add sublong and txUnique binaries
       new  4fdd026   Add man page generation for sublong binary
       new  e8f51b3   Use conditional variable assignment operator for DEB_HOST_ARCH
       new  3c94c26   Drop autopkgtest testsuite from d/control as we have d/tests/control
       new  25e97fe   Update arch_specific_flags patch, fix Makefile for sublong
       new  5d6bf61   Update chnagelog, upload to unstable

The 10 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                                   |   15 +
 debian/control                                     |    3 +-
 debian/filter.pl                                   |    2 +
 debian/patches/arch_specific_flags.patch           |   16 +
 debian/rules                                       |    5 +-
 debian/subread.install                             |    4 +-
 debian/watch                                       |    2 +-
 doc/SubreadUsersGuide.tex                          |   53 +-
 src/Makefile.FreeBSD                               |   13 +-
 src/Makefile.Linux                                 |   11 +-
 src/Makefile.MacOS                                 |   10 +-
 src/core-interface-aligner.c                       |    5 +-
 src/core-interface-subjunc.c                       |    3 +-
 src/core-junction.c                                |   66 +-
 src/core.c                                         |   57 +-
 src/gene-algorithms.c                              |   29 +-
 src/gene-value-index.c                             |   48 +-
 src/input-files.c                                  |  131 +-
 src/longread-mapping/LRMbase-index.c               |  285 +++
 src/longread-mapping/LRMbase-index.h               |   38 +
 src/longread-mapping/LRMchro-event.c               | 1241 ++++++++++++
 src/longread-mapping/LRMchro-event.h               |   40 +
 src/longread-mapping/LRMconfig.h                   |  389 ++++
 src/longread-mapping/LRMfile-io.c                  |  673 +++++++
 src/longread-mapping/LRMfile-io.h                  |   55 +
 src/longread-mapping/LRMhelper.c                   |   77 +
 src/{SNPCalling.h => longread-mapping/LRMhelper.h} |   24 +-
 src/longread-mapping/LRMsorted-hashtable.c         |  534 ++++++
 src/longread-mapping/LRMsorted-hashtable.h         |   44 +
 src/longread-mapping/Makefile                      |   23 +
 src/{ => longread-mapping}/hashtable.c             |   59 +-
 src/{ => longread-mapping}/hashtable.h             |    9 +-
 src/longread-mapping/longread-mapping-one.c        | 1231 ++++++++++++
 src/longread-mapping/longread-mapping.c            | 2012 ++++++++++++++++++++
 src/{ => longread-mapping}/seek-zlib.c             |   37 +-
 src/longread-mapping/seek-zlib.h                   |   86 +
 src/makefile.version                               |    2 +-
 src/propmapped.c                                   |   13 +-
 src/readSummary.c                                  |  257 ++-
 src/subread.h                                      |   23 +-
 40 files changed, 7367 insertions(+), 258 deletions(-)
 create mode 100644 src/longread-mapping/LRMbase-index.c
 create mode 100644 src/longread-mapping/LRMbase-index.h
 create mode 100644 src/longread-mapping/LRMchro-event.c
 create mode 100644 src/longread-mapping/LRMchro-event.h
 create mode 100644 src/longread-mapping/LRMconfig.h
 create mode 100644 src/longread-mapping/LRMfile-io.c
 create mode 100644 src/longread-mapping/LRMfile-io.h
 create mode 100644 src/longread-mapping/LRMhelper.c
 copy src/{SNPCalling.h => longread-mapping/LRMhelper.h} (51%)
 create mode 100644 src/longread-mapping/LRMsorted-hashtable.c
 create mode 100644 src/longread-mapping/LRMsorted-hashtable.h
 create mode 100644 src/longread-mapping/Makefile
 copy src/{ => longread-mapping}/hashtable.c (93%)
 copy src/{ => longread-mapping}/hashtable.h (98%)
 create mode 100644 src/longread-mapping/longread-mapping-one.c
 create mode 100644 src/longread-mapping/longread-mapping.c
 copy src/{ => longread-mapping}/seek-zlib.c (88%)
 create mode 100644 src/longread-mapping/seek-zlib.h

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