[med-svn] [jellyfish] branch upstream updated (7784a23 -> 37545be)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository jellyfish.

      from  7784a23   Imported Upstream version 2.2.6
       new  37545be   New upstream version 2.2.7

The 1 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 +
 .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 +++--
 lib/err.cc => include/jellyfish/parser_common.hpp |  48 +-
 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, 1769 insertions(+), 166 deletions(-)
 create mode 100644 config.rpath
 copy lib/err.cc => include/jellyfish/parser_common.hpp (50%)
 create mode 100644 include/jellyfish/sam_format.hpp
 create mode 100644 jellyfish/fastq2sam.cc
 create mode 100644 jellyfish/fastq2sam_cmdline.yaggo
 create mode 100644 m4/m4-ax_check_compile_flag.m4
 create mode 100644 m4/m4-ax_ext.m4
 create mode 100644 m4/m4-ax_gcc_x86_avx_xgetbv.m4
 create mode 100644 m4/m4-ax_gcc_x86_cpuid.m4
 create mode 100644 tests/sam.sh

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