[med-svn] [jellyfish] branch master updated (3750540 -> 276072a)

[Charles Plessy]

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plessy pushed a change to branch master
in repository jellyfish.

      from  3750540   Replace unneeded dependency by @builddeps@
       new  e5b008d   Imported Upstream version 2.1.5
       new  0cd8047   Merge tag 'upstream/2.1.5'
       new  79fce41   Imported Upstream version 2.2.0
       new  b36cc95   Merge tag 'upstream/2.2.0'
       new  8daf559   Imported Upstream version 2.2.1
       new  9c87425   Merge tag 'upstream/2.2.1'
       new  276072a   New upstream release with new copyright and license statements.

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:
 .gitignore                                         |   1 -
 Makefile.am                                        |  16 +-
 README.md                                          |  31 +-
 configure.ac                                       |  59 +++-
 debian/changelog                                   |   6 +-
 debian/copyright                                   |  68 +++++
 examples/{count_in_file => jf_count_dump}/Makefile |   4 +-
 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/info_main_cmdline.yaggo               |   6 +-
 sub_commands/jellyfish.cc                          |   4 +
 sub_commands/mem_main_cmdline.yaggo                |   6 +-
 swig/Makefile.am                                   |  68 +++++
 swig/Readme.md                                     |  30 +-
 swig/perl5/t/test_mer_file.t                       |  12 +-
 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 +
 47 files changed, 1482 insertions(+), 83 deletions(-)
 copy examples/{count_in_file => jf_count_dump}/Makefile (83%)
 create mode 100644 examples/jf_count_dump/README
 create mode 100644 examples/jf_count_dump/jf_count_dump.cc
 create mode 100644 examples/swig/README.md
 create mode 100644 examples/swig/dump.pl
 create mode 100644 examples/swig/dump.py
 create mode 100644 examples/swig/dump.rb
 create mode 100644 examples/swig/query.pl
 create mode 100644 examples/swig/query.py
 create mode 100644 examples/swig/query.rb
 create mode 100644 jellyfish.spec.in
 create mode 100644 m4/m4-ax_perl_ext.m4
 create mode 100644 m4/m4-ax_pkg_swig.m4
 create mode 100644 m4/m4-ax_python_devel.m4
 create mode 100644 m4/m4-ax_ruby_ext.m4
 create mode 100644 m4/m4-ax_swig_enable_cxx.m4
 create mode 100644 m4/m4-ax_swig_python.m4
 create mode 100644 swig/Makefile.am
 create mode 100644 swig/string_mers.i
 create mode 100644 tests/swig_perl.sh
 create mode 100644 tests/swig_python.sh
 create mode 100644 tests/swig_ruby.sh

-- 
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