[med-svn] [seqan2] 01/02: Merge tag 'upstream/2.3.0_0.20161019_af07bc1+dfsg' into debian-experimental
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Oct 20 09:34:09 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to tag debian/2.3.0_0.20161019_af07bc1+dfsg-1
in repository seqan2.
commit d35474a11603dcc93d692ba2adb016a19bd660dd
Merge: 91b2729 97da30d
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Thu Oct 20 02:24:34 2016 -0700
Merge tag 'upstream/2.3.0_0.20161019_af07bc1+dfsg' into debian-experimental
Upstream version 2.3.0~0.20161019~af07bc1+dfsg
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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