[med-svn] [jellyfish1] 03/12: Merge tag 'upstream/2.2.0'

[Andreas Tille]

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tille pushed a commit to tag debian/2.2.3-1
in repository jellyfish1.

commit b36cc9587b514ed3ed316e040b670921951e850c
Merge: 0cd8047 79fce41
Author: Charles Plessy <plessy at debian.org>
Date:   Wed Jun 17 18:05:47 2015 +0900

    Merge tag 'upstream/2.2.0'
    
    Upstream version 2.2.0
    
    # gpg: Signature made Wed 17 Jun 2015 18:05:43 JST using RSA key ID B3443334
    # gpg: Good signature from "Charles Plessy <plessy at riken.jp>"

 .gitignore                                        |   1 -
 Makefile.am                                       |  16 +-
 README.md                                         |  31 ++-
 configure.ac                                      |  59 +++-
 examples/jf_count_dump/Makefile                   |   7 +
 examples/jf_count_dump/README                     |  52 ++++
 examples/jf_count_dump/jf_count_dump.cc           |  80 ++++++
 examples/swig/README.md                           |   1 +
 examples/swig/dump.pl                             |   8 +
 examples/swig/dump.py                             |   8 +
 examples/swig/dump.rb                             |   9 +
 examples/swig/query.pl                            |   8 +
 examples/swig/query.py                            |   9 +
 examples/swig/query.rb                            |   9 +
 include/jellyfish/bloom_filter.hpp                |   1 +
 include/jellyfish/generator_manager.hpp           |   2 +-
 include/jellyfish/large_hash_array.hpp            |   2 +-
 include/jellyfish/mer_overlap_sequence_parser.hpp |  29 +-
 include/jellyfish/rectangular_binary_matrix.hpp   |   4 +-
 include/jellyfish/simple_circular_buffer.hpp      |   1 +
 include/jellyfish/whole_sequence_parser.hpp       |  15 +-
 jellyfish.spec.in                                 |  83 ++++++
 lib/generator_manager.cc                          |  11 +-
 m4/.gitignore                                     |   3 +-
 m4/m4-ax_perl_ext.m4                              | 135 +++++++++
 m4/m4-ax_pkg_swig.m4                              | 135 +++++++++
 m4/m4-ax_python_devel.m4                          | 324 ++++++++++++++++++++++
 m4/m4-ax_ruby_ext.m4                              | 102 +++++++
 m4/m4-ax_swig_enable_cxx.m4                       |  53 ++++
 m4/m4-ax_swig_python.m4                           |  64 +++++
 sub_commands/jellyfish.cc                         |   4 +
 swig/Makefile.am                                  |  68 +++++
 swig/Readme.md                                    |  30 +-
 swig/perl5/t/test_mer_file.t                      |  12 +-
 swig/python/__init__.py                           |   1 +
 swig/python/test_mer_file.py                      |  10 +-
 swig/ruby/test_mer_file.rb                        |  10 +-
 swig/string_mers.i                                |   6 +
 tests/compat.sh.in                                |   8 +
 tests/swig_perl.sh                                |  17 ++
 tests/swig_python.sh                              |  17 ++
 tests/swig_ruby.sh                                |  19 ++
 unit_tests/test_mer_overlap_sequence_parser.cc    |  12 +
 unit_tests/test_whole_sequence_parser.cc          |   7 +
 44 files changed, 1411 insertions(+), 72 deletions(-)

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