[med-svn] [seqan2] 04/05: Merge tag 'upstream/2.3.0_0.20161011_73a5aaf+dfsg' into debian-experimental

[Michael Crusoe]

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misterc-guest pushed a commit to branch debian-experimental
in repository seqan2.

commit 922aa9c1efcfdadf14a58a2cdef6b3a9fe95224c
Merge: 52afd09 6f07e3e
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Tue Oct 11 08:52:15 2016 -0700

    Merge tag 'upstream/2.3.0_0.20161011_73a5aaf+dfsg' into debian-experimental
    
    Upstream version 2.3.0~0.20161011~73a5aaf+dfsg

 CONTRIBUTING.rst                                   |   2 +-
 apps/bs_tools/tests/run_tests.py                   |   6 +-
 apps/fiona/index_qgram_parallel.h                  |  44 ++---
 apps/razers3/razers_match_filter.h                 |   8 +-
 include/seqan/align.h                              |   2 +-
 include/seqan/align/align_interface_wrapper.h      |   2 +-
 include/seqan/align/dp_align_simd_helper.h         |   2 +-
 .../align/global_alignment_myers_hirschberg_impl.h |   1 -
 include/seqan/arg_parse.h                          |   4 +
 include/seqan/arg_parse/arg_parse_doc.h            |  56 +++++-
 include/seqan/basic/basic_allocator.h              |   1 -
 include/seqan/basic/basic_simd_vector.h            |  48 +++--
 include/seqan/file/file_page.h                     |  42 ++---
 include/seqan/file/string_external.h               | 200 ++++++++++-----------
 include/seqan/graph_algorithms.h                   |   2 +
 .../seqan/graph_algorithms/depth_first_search.h    | 101 +++++++----
 .../strongly_connected_compnents.h                 |  29 +++
 include/seqan/graph_msa/graph_align_tcoffee_io.h   |   2 +-
 .../seqan/graph_msa/graph_align_tcoffee_library.h  |  71 ++++----
 include/seqan/index/index_bidirectional.h          |  41 ++---
 include/seqan/index/index_bidirectional_stree.h    | 153 +++++++++++++---
 include/seqan/index/index_bifm.h                   |   2 +
 include/seqan/index/index_bifm_stree.h             |   4 +-
 include/seqan/modifier/modifier_padding.h          |  12 ++
 include/seqan/parallel/parallel_lock.h             |   4 +-
 include/seqan/score.h                              |   2 +-
 include/seqan/stream/file_stream.h                 |  24 +--
 include/seqan/stream/formatted_file.h              |  20 +++
 include/seqan/stream/stream_base.h                 |   9 +-
 include/seqan/tabix_io/tabix_index_tbi.h           |   3 +
 include/seqan/version.h                            |   2 +-
 .../Infrastructure/Use/CustomBuildSystem.rst       |   4 +
 manual/source/Infrastructure/Use/Install.rst       |  44 ++---
 manual/source/index.rst                            |   2 +-
 tests/bam_io/test_bam_file.h                       |  42 +++++
 tests/bam_io/test_bam_io.cpp                       |   4 +
 tests/basic/test_basic_simd_vector.cpp             |   6 +-
 tests/basic/test_basic_simd_vector.h               |   7 +-
 tests/bed_io/test_bed_io.cpp                       |  42 +++++
 tests/gff_io/test_gff_io.cpp                       |   4 +
 tests/gff_io/test_gff_io.h                         |  38 ++++
 tests/graph_msa/test_graph_tcoffee.h               |   2 +-
 tests/index/test_index_bifm.cpp                    |  58 +++---
 tests/roi_io/test_roi_io.cpp                       |  42 +++++
 tests/seq_io/test_seq_io.cpp                       |   4 +
 tests/seq_io/test_sequence_file.h                  |  42 +++++
 tests/vcf_io/test_vcf_io.cpp                       |   3 +
 tests/vcf_io/test_vcf_io.h                         |  38 ++++
 util/cmake/FindSeqAn.cmake                         |  22 ++-
 49 files changed, 921 insertions(+), 382 deletions(-)

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