[med-svn] [jellyfish] branch upstream updated (efe89cc -> 1b0c92f)

[Michael Crusoe]

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

      from  efe89cc   Imported Upstream version 2.2.4
       new  87fdddc   Imported Upstream version 2.2.5
       new  1b0c92f   Imported Upstream version 2.2.5

The 2 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 +-
 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 +-
 19 files changed, 388 insertions(+), 101 deletions(-)
 create mode 100644 .travis.yml
 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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