[med-svn] [jellyfish] branch upstream updated (91d6a38 -> 8daf559)

[Charles Plessy]

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plessy pushed a change to branch upstream
in repository jellyfish.

      from  91d6a38   Imported Upstream version 2.1.4
       new  e5b008d   Imported Upstream version 2.1.5
       new  79fce41   Imported Upstream version 2.2.0
       new  8daf559   Imported Upstream version 2.2.1

The 3 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 +++-
 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 +
 45 files changed, 1409 insertions(+), 82 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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