[med-svn] [seqan2] branch debian-experimental updated (275acf8 -> 91b2729)

[Michael Crusoe]

This is an automated email from the git hooks/post-receive script.

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

      from  275acf8   Try patch from upstream to fix kfreebsd/hurd builds
       new  d45d8d2   bump version
       new  a7057cf   switch to upstream's patch
       new  52afd09   Restrict archs for now.
      adds  6f07e3e   New upstream version 2.3.0~0.20161011~73a5aaf+dfsg
       new  922aa9c   Merge tag 'upstream/2.3.0_0.20161011_73a5aaf+dfsg' into debian-experimental
       new  91b2729   test upstream's develop branch

The 5 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:
 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 +-
 debian/changelog                                   |   6 +-
 debian/patches/pthread-linking                     |  14 --
 debian/patches/series                              |   1 -
 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 ++-
 52 files changed, 924 insertions(+), 400 deletions(-)
 delete mode 100644 debian/patches/pthread-linking

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