[med-svn] [cufflinks] branch master updated (3a4814f -> 92ce41b)

[Alex Mestiashvili]

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

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

      from  3a4814f   add a closes to the previous changelog entry
       new  03c0ac2   Update d/watch
       new  532213d   Update d/copyright, add Files-Excluded section
      adds  70257e8   Imported Upstream version 2.2.1
       new  5b2eb77   New upstream version 2.2.1+dfsg.1
       new  dc67990   Updated version 2.2.1+dfsg.1 from 'upstream/2.2.1+dfsg.1'
       new  e839c3e   Update d/rules, use variables provided by /usr/share/dpkg/default.mk
       new  b2684cc   Add patch fixing ftbfs with gcc-7, thanks to Jeff Epler <jepler at unpythonic.net>
       new  e016a8c   Update 0003-fix_includes_path.patch
       new  5f4e165   Update 0001-fix_spelling.patch
       new  7ea311c   Bump Standards-Version, use https for copyrigth-format, add Upstream-Name
       new  92ce41b   Update changelog, 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:
 Makefile.in                                 |   624 --
 aclocal.m4                                  |  1031 ---
 autogen.sh                                  |    21 +
 ax_openmp.m4                                |   101 +
 boost.m4                                    |    87 +
 build-aux/config.guess                      |  1463 ----
 build-aux/config.sub                        |  1579 ----
 build-aux/depcomp                           |   530 --
 build-aux/install-sh                        |   323 -
 build-aux/missing                           |   360 -
 config.h.in                                 |   112 -
 configure                                   | 10836 --------------------------
 debian/changelog                            |    26 +-
 debian/control                              |     2 +-
 debian/copyright                            |    12 +-
 debian/patches/0001-fix_spelling.patch      |    32 +-
 debian/patches/0003-fix_includes_path.patch |    12 +-
 debian/patches/fix_gcc-7_ftbfs.patch        |    85 +
 debian/patches/series                       |     1 +
 debian/rules                                |    18 +-
 debian/watch                                |     7 +-
 make_bin.sh                                 |     6 +-
 src/LICENSE                                 |    18 +
 src/Makefile.in                             |  1624 ----
 src/biascorrection.cpp                      |     2 +-
 src/bundles.cpp                             |    39 +-
 src/bundles.h                               |    25 +-
 src/common.h                                |    10 +
 src/compress_gtf.cpp                        |     6 -
 src/cuffcluster.cpp                         |   942 +++
 src/cuffcompare.cpp                         |     7 -
 src/cuffdiff.cpp                            |    12 +-
 src/cuffdiff_to_gct.py                      |   108 +
 src/cufflinks.cpp                           |     8 +-
 src/cuffnorm.cpp                            |   701 +-
 src/cuffquant.cpp                           |    10 +-
 src/differential.cpp                        |   169 +-
 src/differential.h                          |   729 +-
 src/gtf_reads.cpp                           |   187 +
 src/gtf_to_sam.cpp                          |     6 -
 src/hits.cpp                                |     8 +-
 src/hits.h                                  |     2 +-
 src/replicates.cpp                          |    53 +-
 src/replicates.h                            |     4 +-
 version.m4                                  |     1 +
 45 files changed, 2519 insertions(+), 19420 deletions(-)
 delete mode 100644 Makefile.in
 delete mode 100644 aclocal.m4
 create mode 100755 autogen.sh
 create mode 100644 ax_openmp.m4
 create mode 100644 boost.m4
 delete mode 100755 build-aux/config.guess
 delete mode 100755 build-aux/config.sub
 delete mode 100755 build-aux/depcomp
 delete mode 100755 build-aux/install-sh
 delete mode 100755 build-aux/missing
 delete mode 100644 config.h.in
 delete mode 100755 configure
 create mode 100644 debian/patches/fix_gcc-7_ftbfs.patch
 create mode 100644 src/LICENSE
 delete mode 100644 src/Makefile.in
 create mode 100644 src/cuffcluster.cpp
 create mode 100755 src/cuffdiff_to_gct.py
 create mode 100644 src/gtf_reads.cpp
 create mode 100644 version.m4

-- 
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