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misterc-guest pushed a commit to branch debian-experimental
in repository seqan2.
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 +-
apps/sak/CMakeLists.txt | 4 +-
apps/sak/README | 2 +-
apps/sam2matrix/CMakeLists.txt | 4 +-
apps/samcat/CMakeLists.txt | 4 +-
apps/samcat/README | 2 +-
apps/samcat/README.md | 2 +-
apps/samcat/samcat.cpp | 2 +-
apps/searchjoin/CMakeLists.txt | 4 +-
apps/seqan_tcoffee/CMakeLists.txt | 4 +-
apps/seqcons2/CMakeLists.txt | 4 +-
apps/seqcons2/seqcons.cpp | 2 +-
apps/seqcons2/seqcons_options.cpp | 4 +-
apps/seqcons2/seqcons_options.h | 2 +-
.../tests/alns1.contig_consensus.sam.stderr | 2 +-
.../tests/alns1.contig_consensus.txt.stderr | 2 +-
apps/seqcons2/tests/alns1.nop.sam.stderr | 2 +-
apps/seqcons2/tests/alns1.nop.txt.stderr | 2 +-
.../tests/alns1.overlap_consensus.sam.stderr | 2 +-
.../tests/alns1.overlap_consensus.txt.stderr | 2 +-
apps/seqcons2/tests/alns1.pos_consensus.sam.stderr | 2 +-
apps/seqcons2/tests/alns1.pos_consensus.txt.stderr | 2 +-
apps/seqcons2/tests/alns1.realign.sam.stderr | 2 +-
apps/seqcons2/tests/alns1.realign.txt.stderr | 2 +-
apps/seqcons2/tests/seqs1.align_consensus.stderr | 2 +-
apps/seqcons2/tests/seqs1.nop.stderr | 2 +-
apps/seqcons2/tests/seqs1.overlap_consensus.stderr | 2 +-
.../tests/seqs2.align_consensus.sam.stderr | 2 +-
.../tests/seqs2.align_consensus.txt.stderr | 2 +-
apps/sgip/CMakeLists.txt | 4 +-
apps/sgip/sgip.cpp | 24 +-
apps/snp_store/CMakeLists.txt | 4 +-
apps/splazers/CMakeLists.txt | 4 +-
apps/stellar/CMakeLists.txt | 4 +-
apps/stellar/README | 2 +-
apps/stellar/stellar.cpp | 2 +-
apps/tree_recon/CMakeLists.txt | 4 +-
apps/yara/CMakeLists.txt | 4 +-
demos/tutorial/basics/strings.cpp | 4 +-
demos/tutorial/blast_io/write_assignment.cpp | 2 +-
.../index_iterators/UNUSED_index_assignment3.cpp | 26 -
.../UNUSED_index_assignment3.cpp.stdout | 16 -
.../index_iterators/index_assignment4.cpp.stdout | 14 -
.../index_iterators/index_bidirectional_search.cpp | 36 +
.../index_bidirectional_search.cpp.stdout | 4 +
.../index_iterators/iterator_assignment2.cpp | 2 +-
.../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(-)
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