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commit 7fcf128adddf089f09201690a90780845490a15a Merge: 20af6c2 8327bef Author: Michael R. Crusoe <michael.cru...@gmail.com> Date: Fri Jan 13 05:20:01 2017 -0800 Merge tag 'upstream/2.3.1+dfsg' into debian-experimental Upstream version 2.3.1+dfsg CHANGELOG.rst | 99 +++ CMakeLists.txt | 7 + CONTRIBUTING.rst | 5 + README.rst | 5 +- apps/alf/CMakeLists.txt | 4 +- apps/bs_tools/CMakeLists.txt | 4 +- apps/bs_tools/casbar.cpp | 1 + apps/dfi/CMakeLists.txt | 4 +- apps/fiona/CMakeLists.txt | 4 +- apps/fiona/compute_gain.cpp | 4 +- apps/fiona/error_rate_from_sam.cpp | 4 +- apps/fiona/fiona.cpp | 10 +- apps/fx_tools/CMakeLists.txt | 4 +- apps/gustaf/CMakeLists.txt | 4 +- apps/gustaf/msplazer.h | 6 +- apps/gustaf/msplazer_algorithms.h | 2 +- apps/gustaf/msplazer_main.h | 2 +- apps/gustaf/msplazer_out.h | 6 +- apps/gustaf/tests/pairedEnd_st1_l30.stdout | 2 +- apps/gustaf/tests/reference2_st1_l30.stdout | 2 +- apps/gustaf/tests/st1_l30.stdout | 2 +- apps/gustaf/tests/st1_l30_gth3.stdout | 2 +- apps/gustaf/tests/st1_l30_ith5.stdout | 2 +- apps/gustaf/tests/st1_l30_m.stdout | 2 +- apps/gustaf/tests/st2_l100.stdout | 2 +- apps/insegt/CMakeLists.txt | 4 +- apps/mason2/CMakeLists.txt | 4 +- apps/mason2/README.mason_splicing | 2 +- apps/mason2/mason_options.cpp | 8 +- apps/micro_razers/CMakeLists.txt | 4 +- apps/ngs_roi/CMakeLists.txt | 4 +- apps/ngs_roi/project_spliced.h | 2 +- apps/pair_align/CMakeLists.txt | 4 +- apps/pair_align/pair_align.cpp | 2 +- apps/param_chooser/CMakeLists.txt | 4 +- apps/rabema/CMakeLists.txt | 4 +- apps/rabema/README | 4 +- apps/rabema/rabema_build_gold_standard.cpp | 2 +- apps/rabema/rabema_evaluate.cpp | 10 +- apps/rabema/ref_id_mapping.h | 2 +- apps/razers/CMakeLists.txt | 4 +- apps/razers/razers.h | 2 +- apps/razers/razers_matepairs.h | 2 +- apps/razers3/CMakeLists.txt | 4 +- apps/razers3/razers.cpp | 2 +- apps/razers3/razers.h | 2 +- apps/razers3/razers_matepairs.h | 2 +- apps/razers3/razers_matepairs_parallel.h | 2 +- apps/razers3/razers_parallel.h | 2 +- apps/rep_sep/CMakeLists.txt | 4 +- apps/rep_sep/rep_sep.cpp | 2 +- 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.../index_iterators/iterator_solution2.cpp | 2 +- .../index_iterators/iterator_solution2.cpp.stdout | 31 +- ...ndex_assignment4.cpp => iterator_solution3.cpp} | 2 +- .../index_iterators/iterator_solution3.cpp.stdout | 17 + demos/tutorial/indices/fm_index.cpp | 29 + demos/tutorial/indices/fm_index.stdout | 0 .../tutorial_file_io/solution3.cpp | 4 +- dox/CMakeLists.txt | 47 +- dox/dox_only.sh | 4 +- dox/images/docs2/position_vs_id.png | Bin 0 -> 175321 bytes dox/pages/index.dox | 2 +- dox/pages/language_entities.dox | 2 +- dox/pages/suffix_array.dox | 2 +- dox/run.sh | 4 +- include/seqan/align/gaps_base.h | 2 +- include/seqan/align/gaps_iterator_array.h | 4 +- include/seqan/align/gaps_iterator_base.h | 2 +- include/seqan/align/global_alignment_unbanded.h | 4 +- include/seqan/align/local_alignment_unbanded.h | 2 +- include/seqan/arg_parse.h | 1 + include/seqan/arg_parse/arg_parse_argument.h | 189 ++++-- include/seqan/arg_parse/arg_parse_ctd_support.h | 34 +- include/seqan/arg_parse/arg_parse_doc.h | 179 ++++- include/seqan/arg_parse/arg_parse_option.h | 14 +- include/seqan/arg_parse/arg_parse_parse.h | 25 +- include/seqan/arg_parse/arg_parse_type_support.h | 62 +- include/seqan/arg_parse/arg_parse_version_check.h | 474 ++++++++++++++ include/seqan/arg_parse/argument_parser.h | 41 +- include/seqan/arg_parse/tool_doc.h | 61 +- include/seqan/bam_io/bam_alignment_record_util.h | 2 +- include/seqan/bam_io/bam_file.h | 7 +- include/seqan/bam_io/bam_header_record.h | 4 +- include/seqan/bam_io/write_bam.h | 51 +- include/seqan/bam_io/write_sam.h | 14 +- include/seqan/basic/aggregate_concept.h | 5 +- include/seqan/basic/fundamental_tags.h | 56 ++ include/seqan/basic/iterator_zip.h | 2 +- include/seqan/basic/metaprogramming_enable_if.h | 8 +- include/seqan/basic/metaprogramming_type.h | 2 +- include/seqan/basic/tuple_bit_compressed.h | 38 +- include/seqan/blast/blast_record.h | 99 ++- include/seqan/blast/blast_report_out.h | 18 +- include/seqan/blast/blast_tabular.h | 144 ++-- include/seqan/blast/blast_tabular_in.h | 73 ++- include/seqan/blast/blast_tabular_out.h | 145 +++- include/seqan/find/find_base.h | 4 +- include/seqan/find/find_begin.h | 2 +- include/seqan/gff_io/gff_io_base.h | 3 + include/seqan/index/find_index.h | 1 + include/seqan/index/index_esa_algs_multi.h | 22 +- include/seqan/index/index_esa_base.h | 5 +- include/seqan/index/index_esa_stree.h | 2 +- include/seqan/index/index_fm.h | 64 +- include/seqan/index/index_fm_dox.h | 2 +- include/seqan/index/index_fm_lf_table.h | 36 +- .../seqan/index/index_fm_rank_dictionary_base.h | 10 +- .../seqan/index/index_fm_rank_dictionary_levels.h | 727 +++++++++++++++------ include/seqan/index/index_fm_rank_dictionary_wt.h | 21 +- include/seqan/index/index_sa_qsort.h | 5 +- include/seqan/index/index_sa_stree.h | 4 +- include/seqan/index/index_wotd.h | 2 +- include/seqan/misc/bit_twiddling.h | 4 +- include/seqan/parallel/parallel_lock.h | 10 +- include/seqan/parallel/parallel_splitting.h | 2 +- include/seqan/pipe/pipe_edit_environment.h | 2 +- include/seqan/platform.h | 4 +- include/seqan/{arg_parse.h => rna_io.h} | 55 +- include/seqan/rna_io/bpseq_read_write.h | 240 +++++++ include/seqan/rna_io/connect_read_write.h | 302 +++++++++ include/seqan/rna_io/dot_bracket_read_write.h | 409 ++++++++++++ include/seqan/rna_io/ebpseq_read_write.h | 672 +++++++++++++++++++ .../seqan/rna_io/rna_header.h | 144 ++-- .../rna_io_context.h} | 151 +++-- include/seqan/rna_io/rna_record.h | 279 ++++++++ include/seqan/rna_io/rna_struct_file.h | 347 ++++++++++ include/seqan/rna_io/stockholm_read_write.h | 339 ++++++++++ include/seqan/rna_io/vienna_read_write.h | 280 ++++++++ include/seqan/seeds/banded_chain_alignment.h | 2 +- include/seqan/seq_io.h | 1 + include/seqan/seq_io/bam_sam.h | 554 ++++++++++++++++ include/seqan/seq_io/fai_index.h | 2 +- include/seqan/seq_io/fasta_fastq.h | 123 +--- include/seqan/seq_io/read_embl.h | 8 +- include/seqan/seq_io/read_genbank.h | 8 +- include/seqan/seq_io/sequence_file.h | 246 +++++-- include/seqan/sequence/sequence_interface.h | 2 +- include/seqan/sequence/string_cstyle.h | 12 +- include/seqan/sequence/string_set_base.h | 15 +- .../seqan/sequence/string_set_dependent_generous.h | 29 + .../seqan/sequence/string_set_dependent_tight.h | 55 +- include/seqan/statistics/statistics_base.h | 8 +- include/seqan/store/store_io_gff.h | 6 +- include/seqan/stream/file_stream.h | 4 +- include/seqan/stream/stream_base.h | 2 +- include/seqan/stream/tokenization.h | 45 +- include/seqan/tabix_io/tabix_index_tbi.h | 2 +- include/seqan/vcf_io/read_vcf.h | 48 +- include/seqan/version.h | 2 +- manual/attic/Tutorial/IndicesOld.rst | 2 +- .../Infrastructure/Contribute/GitWorkflow.rst | 70 +- .../Infrastructure/Use/CustomBuildSystem.rst | 32 + .../source/Infrastructure/Use/FindSeqAnCMake.rst | 29 +- manual/source/Intel-Logo-300x198.jpg | Bin 0 -> 41926 bytes .../Alignment/PairwiseSequenceAlignment.rst | 2 +- .../Tutorial/DataStructures/Indices/FMIndex.rst | 93 +++ .../DataStructures/Indices/IndexIterators.rst | 52 +- .../DataStructures/Indices/StringIndices.rst | 6 +- .../Tutorial/DataStructures/Indices/index.rst | 1 + .../Tutorial/DataStructures/Indices/preOrder.png | Bin 0 -> 35567 bytes .../GettingStarted/BackgroundAndMotivation.rst | 6 +- .../Tutorial/Workflows/GenerateKnimeNodes.rst | 12 +- .../Tutorial/Workflows/KnimeReadySeqAnApp.rst | 4 +- .../Tutorial/Workflows/UseSeqAnNodesInKnime.rst | 10 +- manual/source/deNBI_Logo_rgb.jpg | Bin 0 -> 110243 bytes manual/source/index.rst | 18 + tests/arg_parse/CMakeLists.txt | 20 +- tests/arg_parse/test_app.ctd | 14 +- tests/arg_parse/test_arg_parse.cpp | 17 +- tests/arg_parse/test_arg_parse.h | 51 ++ tests/arg_parse/test_arg_parse_argument.h | 94 +-- .../arg_parse/test_arg_parse_version_check.cpp | 75 ++- tests/arg_parse/test_arg_parse_version_check.h | 278 ++++++++ tests/basic/test_basic_allocator.h | 2 +- tests/basic/test_basic_simd_vector.h | 2 +- tests/consensus/test_consensus_realign.h | 2 +- tests/index/test_index_finder.cpp | 2 +- tests/index/test_index_fm_rank_dictionary.cpp | 14 +- tests/journaled_string_tree/test_delta_store.h | 8 +- tests/modifier/test_modifier_view.h | 2 +- tests/realign/test_realign.cpp | 2 +- tests/{arg_parse => rna_io}/CMakeLists.txt | 27 +- tests/rna_io/example.bpseq | 52 ++ tests/rna_io/example.ct | 74 +++ tests/rna_io/example.dbn | 3 + tests/rna_io/example.dbv | 9 + tests/rna_io/example.ebpseq | 39 ++ tests/rna_io/example.sth | 20 + .../version.h => tests/rna_io/test_rna_io.cpp | 34 +- tests/rna_io/test_rna_io.h | 472 +++++++++++++ tests/seq_io/CMakeLists.txt | 5 +- tests/seq_io/small_sequences.bam | Bin 0 -> 214 bytes tests/seq_io/small_sequences.sam | 5 + tests/seq_io/test_genbank.gbk | 90 +++ tests/seq_io/test_read_bam.h | 135 ++++ tests/seq_io/test_seq_io.cpp | 21 + tests/seq_io/test_tag_select_intersect.h | 108 +++ tests/seq_io/test_write_bam.h | 144 ++++ util/cmake/SeqAnBuildSystem.cmake | 100 +-- util/cmake/SetCPackSystemName.cmake | 2 + util/cmake/package.cmake | 8 +- util/cmake/{FindSeqAn.cmake => seqan-config.cmake} | 8 +- util/pkgconfig/seqan.pc.in | 3 +- util/raw_cmake_project/CMakeLists.txt | 2 +- 249 files changed, 8514 insertions(+), 1502 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqan2.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit