[med-svn] [jellyfish] 02/06: Update upstream source from tag 'upstream/2.2.7'

[Andreas Tille]

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tille pushed a commit to branch master
in repository jellyfish.

commit 069075a75d790bcefe5a69d34121708f0492928a
Merge: a6924ce 37545be
Author: Andreas Tille <tille at debian.org>
Date:   Mon Feb 5 22:20:52 2018 +0100

    Update upstream source from tag 'upstream/2.2.7'
    
    Update to upstream version '2.2.7'
    with Debian dir 560af915e95d9e2ff8ec0ae402352c095fe74cee

 .gitignore                                        |   1 +
 .travis.yml                                       |   5 +
 Makefile.am                                       |  18 +-
 README.md                                         |   6 +
 config.rpath                                      | 545 ++++++++++++++++++++++
 configure.ac                                      |  24 +-
 examples/count_in_file/Makefile                   |   3 +-
 examples/jf_count_dump/Makefile                   |   3 +-
 examples/query_per_sequence/Makefile              |   3 +-
 include/jellyfish/mer_overlap_sequence_parser.hpp | 111 +++--
 include/jellyfish/parser_common.hpp               |  61 +++
 include/jellyfish/sam_format.hpp                  | 105 +++++
 include/jellyfish/stream_manager.hpp              | 106 ++++-
 include/jellyfish/whole_sequence_parser.hpp       | 108 +++--
 jellyfish/fastq2sam.cc                            |  47 ++
 jellyfish/fastq2sam_cmdline.yaggo                 |   8 +
 m4/m4-ax_check_compile_flag.m4                    |  74 +++
 m4/m4-ax_ext.m4                                   | 303 ++++++++++++
 m4/m4-ax_gcc_x86_avx_xgetbv.m4                    |  79 ++++
 m4/m4-ax_gcc_x86_cpuid.m4                         |  89 ++++
 sub_commands/count_main.cc                        | 102 ++--
 sub_commands/count_main_cmdline.yaggo             |  10 +
 swig/mer_file.i                                   |   4 +-
 tests/bloom_filter.sh                             |  29 +-
 tests/compat.sh.in                                |   1 +
 tests/generate_sequence.sh                        |   6 +
 tests/large_key.sh                                |   6 +-
 tests/quality_filter.sh                           |   6 +
 tests/sam.sh                                      |  45 ++
 unit_tests/test_mer_dna.cc                        |   1 -
 unit_tests/test_mer_dna_bloom_counter.cc          |  20 +-
 unit_tests/test_mer_iterator.cc                   |   6 +-
 unit_tests/test_mer_overlap_sequence_parser.cc    |   7 +-
 unit_tests/test_whole_sequence_parser.cc          |   6 +-
 34 files changed, 1791 insertions(+), 157 deletions(-)

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