[med-svn] [jellyfish] 04/07: Merge tag 'upstream/2.2.5' into test

[Michael Crusoe]

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

commit d4dd42a6e811d3d0460f0320a4ad2f9c0fe6a35f
Merge: 5d226e8 87fdddc
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Sat Mar 12 08:07:44 2016 -0800

    Merge tag 'upstream/2.2.5' into test
    
    Upstream version 2.2.5

 .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(-)

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