[med-svn] [seqan2] branch experimental updated (e738023 -> cbb003f)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Dec 8 12:43:14 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch experimental
in repository seqan2.
from e738023 catch up with fixes from unstable
adds 9f5dc02 New upstream version 2.3.2.000platform-issues8-6f85721+dfsg
adds 6831e00 Update upstream source from tag 'upstream/2.3.2.000platform-issues8-6f85721+dfsg'
adds cbb003f Another update from upstream
No new revisions were added by this update.
Summary of changes:
CMakeLists.txt | 6 +-
apps/alf/README | 8 +-
apps/bs_tools/bisar.h | 2 +-
apps/bs_tools/casbar.cpp | 10 +-
apps/bs_tools/casbar.h | 4 +-
apps/bs_tools/casbar_consensus_realign.h | 2 +-
apps/dfi/README | 14 +-
apps/fiona/compute_gain.cpp | 5 +-
apps/fiona/fiona.cpp | 36 ++--
apps/gustaf/README | 6 +-
apps/gustaf/create_stellarmatches_from_file.h | 6 +-
apps/gustaf/msplazer.h | 42 ++---
apps/gustaf/msplazer_algorithms.h | 10 +-
apps/gustaf/msplazer_out.h | 39 ++--
apps/insegt/README | 14 +-
apps/insegt/base.h | 6 +-
apps/insegt/create_gff.h | 4 +-
apps/insegt/fusion.h | 46 ++---
apps/insegt/overlap_module.h | 32 ++--
apps/mason2/external_split_merge.cpp | 6 +-
apps/mason2/external_split_merge.h | 6 +-
apps/mason2/fragment_generation.h | 2 +
apps/mason2/genomic_variants.cpp | 18 +-
apps/mason2/mason_materializer.cpp | 2 +-
apps/mason2/mason_simulator.cpp | 4 +-
apps/mason2/mason_splicing.cpp | 18 +-
apps/mason2/mason_variator.cpp | 28 +--
apps/micro_razers/README | 14 +-
apps/ngs_roi/CMakeLists.txt | 5 +
apps/ngs_roi/project_spliced.cpp | 6 +-
apps/ngs_roi/roi_feature_projection.cpp | 2 +-
apps/pair_align/lib/pair_align_lib.cpp | 2 +-
apps/rabema/rabema_build_gold_standard.cpp | 12 +-
apps/rabema/rabema_evaluate.cpp | 24 +--
apps/rabema/ref_id_mapping.h | 6 +-
apps/razers/README | 14 +-
apps/razers/outputFormat.h | 8 +-
apps/razers/razers.h | 10 +-
apps/razers/razers_matepairs.h | 10 +-
apps/razers/razers_spliced.h | 12 +-
apps/razers/readSimulator.h | 2 +-
apps/razers/tests/run_tests.py | 7 +
apps/razers3/README | 16 +-
apps/razers3/razers.h | 30 ++--
apps/razers3/razers_match_filter.h | 4 +-
apps/razers3/razers_matepairs.h | 10 +-
apps/razers3/razers_matepairs_parallel.h | 10 +-
apps/razers3/razers_paired_match_filter.h | 4 +-
apps/razers3/razers_parallel.h | 14 +-
apps/razers3/readSimulator.h | 2 +-
apps/sak/sak.cpp | 12 +-
apps/samcat/CMakeLists.txt | 5 +
apps/searchjoin/db.h | 26 +--
apps/sgip/sgip_base.h | 4 +-
apps/snp_store/README | 12 +-
apps/snp_store/snp_store.cpp | 10 +-
apps/snp_store/snp_store.h | 6 +-
apps/splazers/README | 15 +-
apps/splazers/outputFormat.h | 8 +-
apps/splazers/razers.h | 10 +-
apps/splazers/razers_matepairs.h | 8 +-
apps/splazers/razers_spliced.h | 24 +--
apps/splazers/readSimulator.h | 2 +-
apps/stellar/README | 8 +-
apps/stellar/stellar.cpp | 4 +-
apps/stellar/stellar.h | 8 +-
apps/stellar/stellar_extension.h | 6 +-
apps/stellar/stellar_types.h | 4 +-
apps/yara/bits_context.h | 2 +-
apps/yara/bits_matches.h | 4 +-
apps/yara/indexer.cpp | 8 +-
apps/yara/mapper.cpp | 8 +-
apps/yara/tests/run_tests.py | 11 +-
debian/changelog | 6 +
debian/patches/skip-seqan-revision | 2 +-
demos/blast/blast_in_lowlevel.cpp | 4 +-
demos/dox/bam_io/bam_file_in.cpp | 2 +-
demos/dox/index/find_repeats.cpp | 2 +-
demos/dox/statistics/build_markov_model.cpp | 3 +-
demos/dox/statistics/load_markov_model.cpp | 3 +-
demos/dox/store/store_example.cpp | 4 +-
demos/tutorial/sam_and_bam_io/base.cpp | 6 +-
demos/tutorial/string_sets/example_iterators.cpp | 2 +-
demos/unassigned_or_unused/filter_sam.cpp | 2 +-
demos/unassigned_or_unused/sam2svg.cpp | 8 +-
.../tutorial_file_io/solution2.cpp | 61 -------
.../tutorial_file_io/solution3.cpp | 72 --------
.../stream_compression_formats.cpp | 12 +-
dox/CMakeLists.txt | 54 +-----
include/seqan/align/align_base.h | 13 +-
include/seqan/align/align_interface_wrapper.h | 3 +-
include/seqan/align/dp_algorithm_impl.h | 4 +-
include/seqan/align/dp_cell.h | 4 +-
include/seqan/align/dp_matrix_navigator.h | 2 +-
.../seqan/align/dp_matrix_navigator_score_matrix.h | 4 +-
.../dp_matrix_navigator_score_matrix_sparse.h | 4 +-
.../seqan/align/dp_matrix_navigator_trace_matrix.h | 6 +-
include/seqan/align/dp_profile.h | 14 +-
include/seqan/align/evaluate_alignment.h | 2 +-
include/seqan/align/gaps_anchor.h | 8 +-
include/seqan/align/gaps_base.h | 2 +-
include/seqan/align/gaps_iterator_anchor.h | 4 +-
.../align/global_alignment_myers_hirschberg_impl.h | 6 +-
include/seqan/align/global_alignment_myers_impl.h | 2 +-
.../local_alignment_banded_waterman_eggert_impl.h | 4 +-
.../align/local_alignment_waterman_eggert_impl.h | 8 +-
include/seqan/align_extend/align_extend.h | 10 +-
include/seqan/align_extend/dp_scout_xdrop.h | 8 +-
include/seqan/align_profile/add_to_profile.h | 6 +-
include/seqan/align_split/align_split_interface.h | 10 +-
include/seqan/bam_io/bam_alignment_record.h | 20 +--
include/seqan/bam_io/bam_file.h | 2 +-
include/seqan/bam_io/bam_header_record.h | 4 +-
include/seqan/bam_io/bam_index_bai.h | 62 +++----
include/seqan/bam_io/bam_sam_conversion.h | 4 +-
include/seqan/bam_io/bam_tags_dict.h | 6 +-
include/seqan/bam_io/read_bam.h | 6 +-
include/seqan/bam_io/read_sam.h | 2 +-
include/seqan/basic/allocator_interface.h | 40 ++---
include/seqan/basic/alphabet_adapt_builtins.h | 13 +-
include/seqan/basic/alphabet_concept.h | 24 +--
include/seqan/basic/alphabet_math.h | 28 +--
include/seqan/basic/alphabet_simple_type.h | 90 +++++++---
include/seqan/basic/array_construct_destruct.h | 4 +-
include/seqan/basic/basic_stream.h | 7 +-
include/seqan/basic/debug_test_system.h | 7 +-
include/seqan/basic/fundamental_concepts.h | 32 +++-
include/seqan/basic/fundamental_transport.h | 4 +-
include/seqan/basic/holder_tristate.h | 6 +-
include/seqan/basic/iterator_adaptor.h | 12 +-
include/seqan/basic/iterator_interface.h | 14 +-
include/seqan/basic/math_log_space_value.h | 2 +-
include/seqan/basic/pair_bit_compressed.h | 17 +-
include/seqan/basic/pair_packed.h | 16 +-
include/seqan/basic/proxy_base.h | 4 +-
include/seqan/consensus/consensus_base.h | 2 +-
include/seqan/consensus/consensus_library.h | 2 +-
include/seqan/consensus/consensus_realign.h | 2 +-
include/seqan/consensus/overlap_info_computation.h | 4 +-
include/seqan/consensus/overlapper.h | 2 +-
include/seqan/file/file_base.h | 1 +
include/seqan/file/file_page.h | 4 +-
include/seqan/find/find_bom.h | 1 +
include/seqan/find/find_multiple_bfam.h | 1 +
include/seqan/find/find_myers_ukkonen.h | 6 +-
include/seqan/find/find_shiftand.h | 4 +-
include/seqan/find/find_shiftor.h | 2 +-
include/seqan/find/find_wumanber.h | 4 +-
include/seqan/gff_io/gff_io_base.h | 15 +-
include/seqan/graph_align/graph_impl_align.h | 8 +-
.../graph_msa/graph_align_tcoffee_guidetree.h | 2 +-
include/seqan/graph_types/graph_interface.h | 3 +-
include/seqan/index/find_backtracking.h | 2 +-
include/seqan/index/find_pigeonhole.h | 4 +-
include/seqan/index/index_base.h | 7 +-
include/seqan/index/index_childtab.h | 2 +-
include/seqan/index/index_fm_compressed_sa.h | 10 +-
include/seqan/index/index_fm_lf_table.h | 20 +--
.../seqan/index/index_fm_rank_dictionary_base.h | 4 +-
.../seqan/index/index_fm_rank_dictionary_levels.h | 6 +-
.../seqan/index/index_fm_rank_dictionary_naive.h | 2 +-
include/seqan/index/index_fm_rank_dictionary_wt.h | 2 +-
include/seqan/index/index_pizzachili.h | 4 +
include/seqan/index/index_qgram.h | 14 +-
include/seqan/index/index_sa_bwtwalk.h | 20 +--
include/seqan/index/index_sa_lss.h | 4 +-
include/seqan/index/index_sa_truncated.h | 8 +-
include/seqan/index/index_wotd.h | 8 +-
include/seqan/index/shape_threshold.h | 2 +-
include/seqan/journaled_string_tree/delta_map.h | 2 +-
.../journaled_string_tree/delta_map_iterator.h | 4 +-
.../journaled_string_tree_traverser_util.h | 12 +-
include/seqan/math/math_rational.h | 6 +-
include/seqan/misc/interval_tree.h | 12 +-
include/seqan/misc/name_store_cache.h | 25 ++-
include/seqan/modifier/modifier_padding.h | 14 +-
include/seqan/modifier/modifier_view.h | 4 +-
include/seqan/parse_lm/local_match_store.h | 22 +--
include/seqan/pipe/pipe_source.h | 2 +-
include/seqan/pipe/pool_base.h | 8 +-
include/seqan/platform.h | 27 ++-
include/seqan/realign/realign_base.h | 10 +-
include/seqan/rna_io/rna_record.h | 15 +-
include/seqan/seeds/banded_chain_alignment_impl.h | 10 +-
include/seqan/seeds/seeds_extension.h | 4 +-
include/seqan/seeds/seeds_global_chaining.h | 8 +-
include/seqan/seq_io/bam_sam.h | 6 +-
include/seqan/seq_io/sequence_file.h | 6 +-
include/seqan/sequence/adapt_stl_container.h | 3 +-
include/seqan/sequence/sequence_forwards.h | 3 +
include/seqan/sequence/string_cstyle.h | 3 +-
include/seqan/sequence/string_packed.h | 12 +-
include/seqan/sequence/string_packed_old.h | 2 +-
include/seqan/sequence/string_set_base.h | 5 +-
include/seqan/sequence/string_set_owner.h | 6 +
include/seqan/simd.h | 12 ++
include/seqan/simd/simd_base.h | 4 +
include/seqan/simd/simd_base_seqan_impl_avx2.h | 179 ++++++++++++------
include/seqan/simd/simd_base_seqan_impl_sse4.2.h | 165 ++++++++++++-----
include/seqan/simd/simd_base_seqan_interface.h | 12 ++
include/seqan/simd/simd_base_umesimd_impl.h | 11 ++
include/seqan/statistics/statistics_markov_model.h | 2 +-
include/seqan/store/store_align.h | 4 +-
include/seqan/store/store_all.h | 50 +++---
include/seqan/store/store_annotation.h | 4 +-
include/seqan/store/store_contig.h | 6 +-
include/seqan/store/store_io_sam.h | 6 +-
include/seqan/store/store_io_ucsc.h | 2 +-
include/seqan/store/store_matepair.h | 2 +-
include/seqan/store/store_read.h | 2 +-
include/seqan/stream.h | 6 +
include/seqan/stream/lexical_cast.h | 8 +-
include/seqan/stream/stream_compressor.h | 8 +-
include/seqan/stream/tokenization.h | 10 +-
include/seqan/system/file_async.h | 13 +-
include/seqan/tabix_io/tabix_index_tbi.h | 10 +-
.../Infrastructure/Use/CustomBuildSystem.rst | 25 +++
.../source/Infrastructure/Use/FindSeqAnCMake.rst | 24 +++
.../DataStructures/Indices/StringIndices.rst | 16 ++
tests/align/CMakeLists.txt | 6 +
tests/align/test_align_simd.h | 14 +-
.../test_alignment_algorithms_band_position.h | 34 ++--
tests/align/test_alignment_dp_cell.h | 2 +-
tests/align/test_alignment_dp_matrix_navigator.h | 24 +--
tests/arg_parse/test_arg_parse_ctd_support.h | 3 +-
tests/bam_io/test_bam_file.h | 26 +--
tests/bam_io/test_bam_index.h | 15 +-
tests/bam_io/test_bam_io.cpp | 2 +-
tests/bam_io/test_bam_sam_conversion.h | 11 +-
tests/bam_io/test_read_bam.h | 10 +-
tests/bam_io/test_write_bam.h | 6 +-
tests/basic/test_basic.cpp | 1 -
tests/basic/test_basic_alphabet.cpp | 6 +-
tests/basic/test_basic_alphabet.h | 50 +-----
tests/basic/test_basic_alphabet_adapt_builtins.h | 199 ---------------------
tests/basic/test_basic_alphabet_math.h | 29 +--
tests/basic/test_basic_alphabet_residue.h | 74 ++------
tests/basic/test_basic_concept.cpp | 4 +-
tests/basic/test_basic_concepts.h | 39 ++++
tests/basic/test_basic_exception.h | 6 +-
tests/basic/test_basic_iterator.h | 2 +-
tests/bed_io/test_bed_io.cpp | 8 +-
tests/blast/test_blast_input.h | 8 +-
tests/consensus/test_consensus.h | 27 +--
tests/consensus/test_consensus_realign.h | 5 +-
tests/gff_io/test_gff_io.h | 37 ++--
tests/index/test_index_creation.h | 6 +-
tests/index/test_index_helpers.h | 8 +-
tests/index/test_qgram_index.h | 23 +--
tests/index/test_sa_bwtwalk.h | 2 +-
tests/journaled_string_tree/test_delta_map.h | 14 +-
.../test_journaled_string_tree.h | 2 +-
tests/misc/test_misc.cpp | 6 +-
tests/parse_lm/test_parse_lm.h | 2 +-
tests/rna_io/CMakeLists.txt | 4 +-
tests/roi_io/test_roi_io.cpp | 8 +-
tests/score/test_score.cpp | 9 +-
tests/seeds/test_align_banded_chain_impl.cpp | 2 +-
tests/seq_io/test_fai_index.h | 24 +--
tests/seq_io/test_sequence_file.h | 36 ++--
tests/sequence/test_sequence.h | 53 ++----
tests/sequence/test_string_packed_extension.h | 4 +-
tests/sequence/test_string_set.h | 67 ++-----
tests/simd/CMakeLists.txt | 5 +-
tests/simd/test_simd_vector.h | 79 +++++---
tests/statistics/test_statistics_base.h | 3 +-
tests/store/test_store_io.h | 92 +++++-----
tests/store/test_store_io_bam.h | 10 +-
tests/stream/test_stream_lexical_cast.h | 4 +-
tests/stream/test_stream_tokenization.h | 60 +++----
tests/stream/test_stream_virtual_stream.h | 15 +-
tests/tabix_io/test_tabix_io.h | 11 +-
tests/translation/test_translation.h | 3 +-
tests/ucsc_io/test_ucsc_io.cpp | 24 +--
tests/vcf_io/test_vcf_io.h | 16 +-
util/cmake/SeqAnBuildSystem.cmake | 16 +-
util/cmake/SeqAnContribs.cmake | 113 +++++-------
util/cmake/SeqAnSimdUtility.cmake | 31 ++--
util/cmake/seqan-config.cmake | 14 +-
util/py_lib/CMakeLists.txt | 5 +
280 files changed, 1971 insertions(+), 2040 deletions(-)
delete mode 100644 demos/unassigned_or_unused/tutorial_file_io/solution2.cpp
delete mode 100644 demos/unassigned_or_unused/tutorial_file_io/solution3.cpp
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