[med-svn] [jellyfish] branch master updated (a6924ce -> 746d4a7)

[Andreas Tille]

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tille pushed a change to branch master
in repository jellyfish.

      from  a6924ce   Really apply portability patch
       new  37545be   New upstream version 2.2.7
       new  069075a   Update upstream source from tag 'upstream/2.2.7'
       new  9cba69e   New upstream version
       new  5ec87d0   cme fix dpkg-control
       new  251b452   debhelper 11
       new  746d4a7   Fix changelog and upload to unstable

The 6 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 +-
 debian/changelog                                  |   8 +
 debian/compat                                     |   2 +-
 debian/control                                    |   4 +-
 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 +-
 37 files changed, 1780 insertions(+), 169 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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