[med-svn] [jellyfish] branch master updated (538a54d -> fc62b54)

[Michael Crusoe]

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

misterc-guest pushed a change to branch master
in repository jellyfish.

      from  538a54d   Fix install target
       new  e526a4f   fix python bindings
       new  5d226e8   enable perl binding
       new  87fdddc   Imported Upstream version 2.2.5
       new  d4dd42a   Merge tag 'upstream/2.2.5' into test
       new  1b0c92f   Imported Upstream version 2.2.5
       new  92be8eb   Merge tag 'upstream/2.2.5' into test
       new  fc62b54   new upstream version

The 7 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:
 .travis.yml                                       |   6 +
 Makefile.am                                       |   6 +-
 README.md                                         |  39 ++++--
 configure.ac                                      |   2 +-
 debian/README.todo                                |   5 +
 debian/changelog                                  |  17 ++-
 debian/control                                    |  24 ++--
 debian/jellyfish-examples.lintian-overrides       |   1 +
 debian/libjellyfish-2.0-dev.install               |   1 +
 debian/libjellyfish-perl.install                  |   1 +
 debian/patches/drop-rpath                         |  88 ++++++++++++++
 debian/patches/modern-g++                         |  15 +++
 debian/patches/pkg-config-with-name               |  13 ++
 debian/patches/series                             |   4 +
 debian/patches/spelling                           |  13 ++
 debian/rules                                      |  42 +++++--
 include/jellyfish/generator_manager.hpp           |  45 ++++---
 include/jellyfish/mer_overlap_sequence_parser.hpp |   8 +-
 include/jellyfish/whole_sequence_parser.hpp       |  11 +-
 lib/generator_manager.cc                          |  22 ++--
 swig/Readme.md                                    |  95 ++++++++-------
 swig/jellyfish.i                                  |   1 +
 swig/perl5/t/test_string_mers.t                   |  30 +++++
 swig/python/test_string_mers.py                   |  39 ++++++
 swig/ruby/test_string_mers.rb                     |  36 ++++++
 swig/string_mers.i                                | 137 ++++++++++++++++++++++
 tests/swig_perl.sh                                |   2 +-
 tests/swig_python.sh                              |   2 +-
 tests/swig_ruby.sh                                |   2 +-
 unit_tests/test_mer_dna.cc                        |   3 +-
 unit_tests/test_stdio_filebuf.cc                  |   3 +-
 31 files changed, 590 insertions(+), 123 deletions(-)
 create mode 100644 .travis.yml
 create mode 100644 debian/README.todo
 create mode 100644 debian/jellyfish-examples.lintian-overrides
 create mode 100644 debian/libjellyfish-2.0-dev.install
 create mode 100644 debian/libjellyfish-perl.install
 create mode 100644 debian/patches/drop-rpath
 create mode 100644 debian/patches/modern-g++
 create mode 100644 debian/patches/pkg-config-with-name
 create mode 100644 debian/patches/spelling
 create mode 100644 swig/perl5/t/test_string_mers.t
 create mode 100644 swig/python/test_string_mers.py
 create mode 100644 swig/ruby/test_string_mers.rb

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