[med-svn] [seqan2] branch upstream-develop updated (6f07e3e -> 97da30d)

[Michael Crusoe]

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

misterc-guest pushed a change to branch upstream-develop
in repository seqan2.

      from  6f07e3e   New upstream version 2.3.0~0.20161011~73a5aaf+dfsg
      adds  97da30d   New upstream version 2.3.0~0.20161019~af07bc1+dfsg

No new revisions were added by this update.

Summary of changes:
 apps/alf/CMakeLists.txt                           |  4 +-
 apps/bs_tools/CMakeLists.txt                      |  8 +--
 apps/bs_tools/casbar.h                            | 14 ++---
 apps/bs_tools/casbar_score.h                      |  2 +
 apps/dfi/CMakeLists.txt                           |  4 +-
 apps/dfi/dfi.cpp                                  |  2 +
 apps/fiona/CMakeLists.txt                         | 10 ++--
 apps/fx_tools/CMakeLists.txt                      |  4 +-
 apps/gustaf/CMakeLists.txt                        |  4 +-
 apps/insegt/CMakeLists.txt                        |  4 +-
 apps/mason2/CMakeLists.txt                        |  8 +--
 apps/micro_razers/CMakeLists.txt                  |  4 +-
 apps/ngs_roi/CMakeLists.txt                       |  6 ++-
 apps/pair_align/CMakeLists.txt                    |  4 +-
 apps/param_chooser/CMakeLists.txt                 |  4 +-
 apps/rabema/CMakeLists.txt                        |  6 ++-
 apps/razers/CMakeLists.txt                        |  4 +-
 apps/razers/readSimulator.h                       |  2 +
 apps/razers3/CMakeLists.txt                       | 10 ++--
 apps/razers3/readSimulator.h                      |  2 +
 apps/rep_sep/CMakeLists.txt                       |  4 +-
 apps/sak/CMakeLists.txt                           |  4 +-
 apps/sam2matrix/CMakeLists.txt                    |  4 +-
 apps/samcat/CMakeLists.txt                        |  8 +--
 apps/searchjoin/CMakeLists.txt                    |  6 ++-
 apps/seqan_tcoffee/CMakeLists.txt                 |  4 +-
 apps/seqcons2/CMakeLists.txt                      |  6 ++-
 apps/sgip/CMakeLists.txt                          |  4 +-
 apps/snp_store/CMakeLists.txt                     |  8 +--
 apps/splazers/CMakeLists.txt                      |  4 +-
 apps/splazers/readSimulator.h                     |  2 +
 apps/stellar/CMakeLists.txt                       |  4 +-
 apps/tree_recon/CMakeLists.txt                    |  4 +-
 apps/yara/CMakeLists.txt                          | 10 ++--
 include/seqan/bam_io/cigar.h                      | 19 ++++---
 include/seqan/blast/blast_tabular_in.h            |  1 +
 include/seqan/graph_align/graph_impl_align.h      | 12 +++++
 include/seqan/graph_types/graph_impl_automaton.h  | 55 +++++++++++++++++++
 include/seqan/graph_types/graph_impl_directed.h   | 64 ++++++++++++++++++++++-
 include/seqan/graph_types/graph_impl_hmm.h        | 12 +++++
 include/seqan/graph_types/graph_impl_tree.h       | 12 +++++
 include/seqan/graph_types/graph_impl_undirected.h | 50 ++++++++++++++++++
 include/seqan/graph_types/graph_interface.h       | 14 +++++
 include/seqan/index/pump_extender7.h              | 24 ++++-----
 include/seqan/index/shape_threshold.h             |  2 +
 include/seqan/journaled_set/score_biaffine.h      | 31 ++++++++---
 include/seqan/parallel/parallel_lock.h            | 24 ++++++---
 include/seqan/pipe/pipe_edit_environment.h        |  2 +
 include/seqan/platform.h                          | 13 +++++
 include/seqan/seeds/banded_chain_alignment_impl.h | 19 ++++++-
 tests/align/CMakeLists.txt                        |  4 +-
 tests/align_extend/CMakeLists.txt                 |  4 +-
 tests/align_profile/CMakeLists.txt                |  4 +-
 tests/align_split/CMakeLists.txt                  |  4 +-
 tests/alignment_free/CMakeLists.txt               |  4 +-
 tests/arg_parse/CMakeLists.txt                    |  4 +-
 tests/bam_io/CMakeLists.txt                       |  6 ++-
 tests/basic/CMakeLists.txt                        |  4 +-
 tests/bed_io/CMakeLists.txt                       |  4 +-
 tests/blast/CMakeLists.txt                        |  4 +-
 tests/consensus/CMakeLists.txt                    |  4 +-
 tests/consensus_v2/CMakeLists.txt                 |  4 +-
 tests/find/CMakeLists.txt                         |  4 +-
 tests/gff_io/CMakeLists.txt                       |  4 +-
 tests/graph_algorithms/CMakeLists.txt             |  4 +-
 tests/graph_align/CMakeLists.txt                  |  4 +-
 tests/graph_align/test_graph_impl_align.h         | 10 ++++
 tests/graph_msa/CMakeLists.txt                    |  4 +-
 tests/graph_types/CMakeLists.txt                  |  4 +-
 tests/graph_types/test_graph_types_types.cpp      | 58 +++++++++++++++++++-
 tests/index/CMakeLists.txt                        |  6 ++-
 tests/journaled_set/CMakeLists.txt                |  4 +-
 tests/journaled_string_tree/CMakeLists.txt        |  6 ++-
 tests/map/CMakeLists.txt                          |  4 +-
 tests/misc/CMakeLists.txt                         |  4 +-
 tests/modifier/CMakeLists.txt                     |  4 +-
 tests/modifier_cyclic_shape/CMakeLists.txt        |  4 +-
 tests/multiple_translation_units/CMakeLists.txt   |  4 +-
 tests/parallel/CMakeLists.txt                     |  6 ++-
 tests/parse_lm/CMakeLists.txt                     |  4 +-
 tests/pipe/CMakeLists.txt                         |  4 +-
 tests/platform/CMakeLists.txt                     |  4 +-
 tests/random/CMakeLists.txt                       |  4 +-
 tests/realign/CMakeLists.txt                      |  4 +-
 tests/reduced_aminoacid/CMakeLists.txt            |  4 +-
 tests/roi_io/CMakeLists.txt                       |  4 +-
 tests/score/CMakeLists.txt                        |  4 +-
 tests/seeds/CMakeLists.txt                        |  4 +-
 tests/seeds/test_align_banded_chain_impl.cpp      | 18 +++++++
 tests/seq_io/CMakeLists.txt                       |  8 +--
 tests/sequence/CMakeLists.txt                     |  4 +-
 tests/sequence_journaled/CMakeLists.txt           |  4 +-
 tests/simple_intervals_io/CMakeLists.txt          |  4 +-
 tests/statistics/CMakeLists.txt                   |  4 +-
 tests/store/CMakeLists.txt                        |  6 ++-
 tests/stream/CMakeLists.txt                       |  8 +--
 tests/swift_local/CMakeLists.txt                  |  4 +-
 tests/tabix_io/CMakeLists.txt                     |  6 ++-
 tests/translation/CMakeLists.txt                  |  6 ++-
 tests/ucsc_io/CMakeLists.txt                      |  4 +-
 tests/vcf_io/CMakeLists.txt                       |  4 +-
 util/cmake/SeqAnBuildSystem.cmake                 | 17 ++++--
 102 files changed, 692 insertions(+), 157 deletions(-)

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