[med-svn] [seqan] 03/14: Merge tag 'upstream/2.0.1+dfsg'
Andreas Tille
tille at debian.org
Wed Jan 20 10:39:39 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository seqan.
commit 5c6394cefb50992f5de2fe67dbabe10c2ee112bc
Merge: 0dcf652 3e7c7b0
Author: Andreas Tille <tille at debian.org>
Date: Mon Jan 18 15:05:51 2016 +0100
Merge tag 'upstream/2.0.1+dfsg'
Upstream version 2.0.1+dfsg
CHANGELOG.rst | 82 +
apps/alf/CMakeLists.txt | 2 +-
apps/bs_tools/CMakeLists.txt | 2 +-
apps/bs_tools/tests/run_tests.py | 31 +-
apps/dfi/CMakeLists.txt | 2 +-
apps/fiona/CMakeLists.txt | 2 +-
apps/fx_tools/CMakeLists.txt | 2 +-
apps/fx_tools/fx_bam_coverage.cpp | 34 +-
apps/gustaf/CMakeLists.txt | 2 +-
apps/insegt/CMakeLists.txt | 2 +-
apps/mason2/CMakeLists.txt | 2 +-
apps/mason2/mason_simulator.cpp | 83 +-
apps/mason2/simulate_illumina.cpp | 14 +-
apps/mason2/simulate_sanger.cpp | 14 +-
apps/mason2/tests/simulator.out1.sam | 52 +-
apps/mason2/tests/simulator.out2.sam | 100 +-
apps/mason2/tests/simulator.out4.sam | 26 +-
apps/mason2/tests/simulator.out7.sam | 50 +-
apps/mason2/tests/simulator.out8.sam | 1220 +++++++--------
apps/micro_razers/CMakeLists.txt | 2 +-
apps/ngs_roi/CMakeLists.txt | 2 +-
apps/pair_align/CMakeLists.txt | 8 +-
apps/param_chooser/CMakeLists.txt | 2 +-
apps/rabema/CMakeLists.txt | 2 +-
apps/rabema/curve_smoothing.h | 2 +-
apps/rabema/rabema_build_gold_standard.cpp | 2 +-
apps/razers/CMakeLists.txt | 2 +-
apps/razers2/CMakeLists.txt | 2 +-
apps/razers2/outputFormat.h | 4 +-
apps/razers3/CMakeLists.txt | 2 +-
apps/razers3/README | 82 +-
apps/rep_sep/CMakeLists.txt | 2 +-
apps/sak/CMakeLists.txt | 2 +-
apps/sam2matrix/CMakeLists.txt | 2 +-
apps/samcat/CMakeLists.txt | 2 +-
apps/searchjoin/CMakeLists.txt | 2 +-
apps/seqan_flexbar/CMakeLists.txt | 2 +-
apps/seqan_tcoffee/CMakeLists.txt | 2 +-
apps/seqan_tcoffee/tests/1aab.i.fasta | 110 +-
apps/seqan_tcoffee/tests/1ad2.i.fasta | 110 +-
apps/seqan_tcoffee/tests/2trx.i.fasta | 110 +-
apps/seqcons/CMakeLists.txt | 2 +-
apps/seqcons2/CMakeLists.txt | 2 +-
apps/sgip/CMakeLists.txt | 2 +-
apps/snp_store/CMakeLists.txt | 2 +-
apps/splazers/CMakeLists.txt | 7 +-
apps/splazers/razers_spliced.h | 4 +-
apps/stellar/CMakeLists.txt | 2 +-
apps/stellar/stellar.cpp | 7 +-
apps/tree_recon/CMakeLists.txt | 2 +-
apps/yara/CMakeLists.txt | 8 +-
apps/yara/bits_context.h | 4 +-
apps/yara/mapper.cpp | 11 +-
apps/yara/misc_options.h | 2 +-
apps/yara/tests/gold/adeno-reads_1.t1.sam | 2 +-
demos/align/compute_alignment_stats.cpp | 66 -
demos/align/compute_alignment_stats.cpp.stdout | 50 -
demos/align_gaps_clipping.cpp | 74 -
demos/alignment.cpp | 51 -
demos/alignment_local.cpp | 91 --
demos/allocator.cpp | 28 -
demos/bam_io/bam_tags_dict.cpp | 36 -
demos/bam_library_size.cpp | 271 ----
demos/basic/enable_if.cpp | 96 --
demos/benchmark_stream.cpp | 422 -----
demos/{ => dox}/align/align.cpp | 0
demos/{ => dox}/align/align.cpp.stdout | 0
demos/dox/align/compute_alignment_stats.cpp | 65 +
demos/dox/align/compute_alignment_stats.cpp.stdout | 52 +
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demos/{ => dox}/align/global_alignment_banded.cpp | 0
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demos/dox/bam_io/bam_tags_dict.cpp | 36 +
demos/{ => dox}/bam_io/bam_tags_dict.cpp.stdout | 0
demos/dox/basic/enable_if.cpp | 96 ++
demos/{ => dox}/basic/metaprogramming_control.cpp | 0
demos/{ => dox}/basic/metaprogramming_logic.cpp | 0
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.../graph_algorithms/all_pairs_shortest_path.cpp | 43 +
.../all_pairs_shortest_path.cpp.stdout | 0
.../graph_algorithms/bellman_ford_algorithm.cpp | 46 +
.../bellman_ford_algorithm.cpp.stdout | 0
.../dox/graph_algorithms/breadth_first_search.cpp | 52 +
.../breadth_first_search.cpp.stdout | 0
demos/dox/graph_algorithms/dag_shortest_path.cpp | 43 +
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demos/dox/graph_algorithms/depth_first_search.cpp | 50 +
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demos/dox/graph_algorithms/dijkstra.cpp | 71 +
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.../heaviest_increasing_subsequence.cpp | 0
demos/dox/graph_algorithms/kruskals_algorithm.cpp | 48 +
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.../longest_common_subsequence.cpp | 0
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demos/dox/graph_algorithms/prims_algorithm.cpp | 46 +
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.../strongly_connected_components.cpp | 41 +
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demos/dox/graph_algorithms/topological_sort.cpp | 42 +
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demos/dox/graph_algorithms/transitive_closure.cpp | 34 +
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demos/{ => dox}/graph_align/graph_align.cpp | 0
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...egin_range_goDown_representative_repLength.cpp} | 0
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...x_textAt_indexText_saAt_indexRequire.cpp.stdout | 0
demos/{ => dox}/index/find_repeats.cpp | 0
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demos/dox/index/length_countSequences.cpp | 26 +
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demos/{index/index_mums.cpp => dox/index/mums.cpp} | 0
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demos/dox/index/open_save.cpp | 27 +
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demos/{ => dox}/index/ref.fa | 0
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demos/{ => dox}/misc/enumerate_strings.cpp | 0
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demos/dox/parallel/queue_example.cpp | 30 +
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demos/{ => dox}/pipe/pool_sorter.cpp | 0
demos/dox/random/random.cpp | 39 +
demos/{ => dox}/score/score.cpp | 0
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demos/{ => dox}/seeds/seeds_add_seed.cpp | 0
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.../infix.cpp => dox/sequence/UNUSED_infix.cpp} | 0
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demos/dox/sequence/segment.cpp | 120 ++
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demos/{ => dox}/sequence/string2.cpp | 0
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demos/{ => dox}/statistics/background.fa | 0
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demos/{ => dox}/statistics/zscore_human_mm.3 | 0
demos/{ => dox}/store/store_example.cpp | 0
demos/dox/stream/lexical_cast.cpp | 53 +
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demos/{ => dox}/vcf_io/example.vcf | 0
demos/find_approx.cpp | 45 -
demos/find_exact.cpp | 35 -
demos/graph_algorithms/all_pairs_shortest_path.cpp | 44 -
demos/graph_algorithms/bellman_ford_algorithm.cpp | 47 -
demos/graph_algorithms/breadth_first_search.cpp | 53 -
demos/graph_algorithms/dag_shortest_path.cpp | 44 -
demos/graph_algorithms/depth_first_search.cpp | 51 -
demos/graph_algorithms/dijkstra.cpp | 72 -
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demos/graph_algorithms/prims_algorithm.cpp | 47 -
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demos/graph_algorithms/topological_sort.cpp | 43 -
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demos/graph_hmm.cpp | 98 --
demos/graph_hmm_silent.cpp | 118 --
demos/howto/align_gaps_clipping.cpp | 72 +
demos/howto/scores/init_score.cpp | 83 +-
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demos/howto/scores/load_score.cpp | 11 +-
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demos/index/index_length_countSequences.cpp | 27 -
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demos/sam2svg.cpp | 222 ---
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include/seqan/basic/debug_test_system.h | 42 +-
include/seqan/basic/fundamental_tags.h | 28 +-
include/seqan/basic/iterator_adapt_std.h | 52 +-
include/seqan/basic/iterator_adaptor.h | 10 +-
include/seqan/basic/iterator_counting.h | 7 +-
include/seqan/basic/iterator_interface.h | 72 +-
include/seqan/basic/iterator_range.h | 0
include/seqan/basic/metaprogramming_control.h | 10 +-
include/seqan/basic/metaprogramming_enable_if.h | 8 +-
include/seqan/basic/metaprogramming_logic.h | 44 +-
include/seqan/basic/metaprogramming_math.h | 6 +-
.../seqan/consensus/consensus_aligner_interface.h | 4 +-
include/seqan/consensus/consensus_builder.h | 5 +-
include/seqan/find/find_ahocorasick.h | 2 +-
include/seqan/find/find_base.h | 8 +-
include/seqan/find/find_set_horspool.h | 2 +
include/seqan/gff_io/gff_io_base.h | 7 +-
.../graph_algorithms/all_pairs_shortest_path.h | 4 +-
include/seqan/graph_algorithms/bellman_ford.h | 4 +-
.../seqan/graph_algorithms/breadth_first_search.h | 4 +-
.../seqan/graph_algorithms/depth_first_search.h | 4 +-
include/seqan/graph_algorithms/dijkstra.h | 4 +-
include/seqan/graph_algorithms/floyd_warshall.h | 4 +-
include/seqan/graph_algorithms/ford_fulkerson.h | 4 +-
.../graph_algorithms/graph_algorithm_lis_his.h | 6 +-
include/seqan/graph_algorithms/kruskal.h | 4 +-
include/seqan/graph_algorithms/prim.h | 4 +-
.../graph_algorithms/single_source_shortest_path.h | 4 +-
.../strongly_connected_compnents.h | 4 +-
include/seqan/graph_algorithms/topological_sort.h | 4 +-
.../seqan/graph_algorithms/transitive_closure.h | 4 +-
include/seqan/graph_align/graph_impl_align.h | 2 +-
include/seqan/graph_types/graph_interface.h | 4 +-
include/seqan/index/index_base.h | 34 +-
include/seqan/index/index_esa_base.h | 4 +-
include/seqan/index/index_esa_stree.h | 22 +-
include/seqan/index/index_fm.h | 9 +-
include/seqan/index/index_fm_rank_dictionary_wt.h | 3 +-
include/seqan/index/index_qgram_openaddressing.h | 60 +
include/seqan/index/index_sa_qsort.h | 2 +-
include/seqan/index/index_shims.h | 4 +-
include/seqan/index/repeat_base.h | 2 +-
include/seqan/index/shape_base.h | 2 +-
include/seqan/index/shape_threshold.h | 0
include/seqan/misc/edit_environment.h | 4 +-
include/seqan/misc/interval_tree.h | 2 +-
include/seqan/misc/name_store_cache.h | 4 +-
include/seqan/misc/terminal.h | 2 +-
include/seqan/modifier/cyclic_shape.h | 14 +-
include/seqan/modifier/modifier_cyclic_shape.h | 6 +-
include/seqan/modifier/modifier_iterator.h | 87 +-
include/seqan/modifier/modifier_reverse.h | 23 +-
include/seqan/modifier/modifier_string.h | 67 +-
include/seqan/modifier/modifier_view.h | 89 +-
include/seqan/parallel/parallel_macros.h | 4 +-
include/seqan/parallel/parallel_queue.h | 4 +-
include/seqan/parallel/parallel_splitting.h | 6 +-
include/seqan/pipe/pool_sorter.h | 2 +-
include/seqan/platform.h | 9 +
include/seqan/platform/platform_windows.h | 7 +
include/seqan/random/ext_MersenneTwister.h | 0
include/seqan/random/random_base.h | 2 +-
include/seqan/realign/realign_base.h | 4 +-
.../reduced_aminoacid_murphy10_base.h | 2 +-
.../reduced_aminoacid_murphy10_tables.h | 8 +-
include/seqan/score/score_base.h | 4 +-
include/seqan/score/score_matrix_data.h | 757 ++++-----
include/seqan/score/score_simple.h | 9 +
include/seqan/seeds/banded_chain_alignment_impl.h | 1 +
.../seqan/seeds/banded_chain_alignment_traceback.h | 7 +
include/seqan/seeds/seeds_global_chaining.h | 6 +-
include/seqan/seeds/seeds_seed_base.h | 6 +-
include/seqan/seeds/seeds_seed_set_base.h | 2 +-
include/seqan/seq_io/fai_index.h | 4 +-
include/seqan/seq_io/fasta_fastq.h | 17 +-
include/seqan/sequence/adapt_std_list.h | 9 +
include/seqan/sequence/adapt_std_string.h | 15 +
include/seqan/sequence/segment_base.h | 6 +-
include/seqan/sequence/segment_infix.h | 8 +
include/seqan/sequence/segment_prefix.h | 9 +
include/seqan/sequence/segment_suffix.h | 8 +
include/seqan/sequence/string_array.h | 16 +
include/seqan/sequence/string_base.h | 10 +-
include/seqan/sequence/string_set_base.h | 76 +-
include/seqan/sequence/string_set_concat_direct.h | 67 +-
include/seqan/sequence/string_set_owner.h | 15 +
include/seqan/statistics/statistics_markov_model.h | 4 +-
include/seqan/store/store_all.h | 4 +-
include/seqan/store/store_io.h | 43 +
include/seqan/store/store_io_gff.h | 30 +-
include/seqan/store/store_io_sam.h | 27 -
include/seqan/store/store_io_ucsc.h | 0
include/seqan/stream.h | 13 +
include/seqan/stream/buffered_stream.h | 19 +-
include/seqan/stream/file_stream.h | 5 +-
include/seqan/stream/formatted_file.h | 18 +-
include/seqan/stream/iostream_bgzf.h | 923 +++++++++++
include/seqan/stream/iostream_bzip2.h | 302 ++++
include/seqan/stream/iostream_bzip2_impl.h | 429 ++++++
include/seqan/stream/iostream_zip.h | 383 +++++
include/seqan/stream/iostream_zip_impl.h | 386 +++++
include/seqan/stream/iostream_zutil.h | 229 +++
include/seqan/stream/lexical_cast.h | 4 +-
include/seqan/stream/stream_base.h | 14 +-
include/seqan/stream/stream_compressor.h | 2 +-
include/seqan/stream/tokenization.h | 2 +-
include/seqan/stream/virtual_stream.h | 187 ++-
include/seqan/stream/zipstream/bgzfstream.h | 969 ------------
include/seqan/stream/zipstream/bgzfstream_impl.h | 203 ---
include/seqan/stream/zipstream/bzip2stream.h | 305 ----
include/seqan/stream/zipstream/bzip2stream_impl.h | 430 ------
include/seqan/stream/zipstream/zipstream.h | 665 --------
include/seqan/stream/zipstream/zipstream_impl.h | 675 --------
include/seqan/stream/zipstream/zutil.h | 226 ---
include/seqan/translation/translation.h | 9 +-
include/seqan/ucsc_io/ucsc_file.h | 2 +-
include/seqan/vcf_io/vcf_io_context.h | 28 +
include/seqan/version.h | 2 +-
manual/requirements.txt | 3 +-
.../BuildManual/UsingTheSeqAnBuildSystem.rst | 8 +-
manual/source/HowTo/ClipAlignments.rst | 2 +-
manual/source/HowTo/GenerateSeqAnKnimeNodes.rst | 2 +-
manual/source/HowTo/UseSeqAnNodesInKnime.rst | 2 +-
.../source/HowTo/WorkWithCustomScoreMatrices.rst | 137 +-
manual/source/HowTo/knime_node_app.zip | Bin 4697 -> 0 bytes
manual/source/HowTo/workflow_plugin_dir.zip | Bin 5912 -> 808808 bytes
manual/source/Infrastructure/Documentation.rst | 10 +
manual/source/StyleGuide/Cpp.rst | 32 +-
manual/source/StyleGuide/DoxApiDocs.rst | 24 +-
manual/source/Tutorial.rst | 25 +-
manual/source/Tutorial/AFirstExample.rst | 563 +++++++
manual/source/Tutorial/AlignmentRepresentation.rst | 30 +-
manual/source/Tutorial/AnnotationStore.rst | 366 -----
manual/source/Tutorial/BackgroundAndMotivation.rst | 149 +-
manual/source/Tutorial/BedIO.rst | 8 +-
manual/source/Tutorial/ConsensusAlignment.rst | 14 +-
manual/source/Tutorial/FileIOOverview.rst | 232 +++
manual/source/Tutorial/FirstStepsInSeqAn.rst | 562 -------
manual/source/Tutorial/FragmentStore.rst | 98 +-
...plateSubclassing.rst => GenericProgramming.rst} | 0
manual/source/Tutorial/GenomeAnnotations.rst | 315 ++++
manual/source/Tutorial/GettingStarted.rst | 2 +-
manual/source/Tutorial/GffAndGtfIO.rst | 214 +++
manual/source/Tutorial/GffGtfIO.rst | 243 ---
manual/source/Tutorial/IndexIterators.rst | 38 +-
manual/source/Tutorial/IndexQGram.rst | 217 ---
manual/source/Tutorial/IndexedFastaIO.rst | 10 +-
manual/source/Tutorial/Indices.rst | 12 +-
manual/source/Tutorial/InputOutputOverview.rst | 227 ---
manual/source/Tutorial/Iterators.rst | 10 +-
manual/source/Tutorial/JournalSet.rst | 668 --------
manual/source/Tutorial/JournaledSet.rst | 655 ++++++++
manual/source/Tutorial/Metafunctions.rst | 20 +-
manual/source/Tutorial/MiniBowtie.rst | 358 -----
manual/source/Tutorial/Modifiers.rst | 8 +-
.../source/Tutorial/MultipleSequenceAlignment.rst | 20 +-
.../source/Tutorial/PairwiseSequenceAlignment.rst | 97 +-
.../Tutorial/ParsingCommandLineArguments.rst | 891 +----------
manual/source/Tutorial/PatternMatching.rst | 28 +-
manual/source/Tutorial/QgramIndex.rst | 217 +++
manual/source/Tutorial/Randomness.rst | 12 +-
manual/source/Tutorial/Realignment.rst | 8 +-
manual/source/Tutorial/SamAndBamIO.rst | 342 +++++
manual/source/Tutorial/SamBamIO.rst | 332 ----
manual/source/Tutorial/SequenceIO.rst | 54 +-
manual/source/Tutorial/Sequences.rst | 243 +--
manual/source/Tutorial/SequencesInDepth.rst | 19 +-
manual/source/Tutorial/SimpleReadMapping.rst | 161 --
manual/source/Tutorial/SimpleRnaSeq.rst | 64 +-
manual/source/Tutorial/StringSets.rst | 4 +-
manual/source/Tutorial/VcfIO.rst | 27 +-
manual/source/Tutorial/WritingTests.rst | 1 +
manual/source/conf.py | 33 +-
tests/align/test_evaluate_alignment.h | 6 +-
tests/bam_io/CMakeLists.txt | 4 +-
tests/bam_io/test_bam_file.h | 2 +-
tests/bam_io/test_bam_index.h | 45 +-
tests/bam_io/test_bam_io.cpp | 5 +-
tests/basic/test_basic_alphabet_residue.h | 31 +-
tests/find/test_find.cpp | 4 +-
tests/gff_io/example_with_comments.gff | 6 +
tests/gff_io/test_gff_io.cpp | 9 +-
tests/gff_io/test_gff_io.h | 60 +
tests/modifier/test_modifier.cpp | 3 +-
tests/modifier/test_modifier_string.h | 85 +-
tests/modifier/test_modifier_view.h | 2 +-
tests/parallel/test_parallel.cpp | 6 +-
tests/reduced_aminoacid/test_reduced_aminoacid.cpp | 3 +-
tests/reduced_aminoacid/test_reduced_aminoacid.h | 143 +-
tests/score/BLOSUM30 | 55 +-
tests/score/BLOSUM45 | 55 +-
tests/score/BLOSUM62 | 55 +-
tests/score/BLOSUM80 | 55 +-
tests/score/PAM120 | 55 +-
tests/score/PAM200 | 55 +-
tests/score/PAM250 | 55 +-
tests/score/PAM40 | 55 +-
tests/score/VTML200I | 55 +-
tests/seeds/test_align_banded_chain_impl.cpp | 26 +
tests/seq_io/test_sequence_file.h | 15 +-
tests/sequence/CMakeLists.txt | 4 +
tests/sequence/test_sequence.h | 6 +-
tests/sequence/test_string_set.h | 1607 +++++++++++---------
tests/sequence/test_stringset_v2.cpp | 47 +
tests/store/example.gff | 2 +-
util/cmake/CMakeFindJavaCommon.cmake | 40 +
util/cmake/FindJava.cmake | 228 +++
util/cmake/FindOpenMP.cmake | 9 +-
util/cmake/FindSeqAn.cmake | 14 +-
util/cmake/SeqAnBuildSystem.cmake | 27 +-
util/cmake/package.cmake | 2 +-
util/makefile_project/src/main.cpp | 11 +-
util/py_lib/seqan/auto_build.py | 2 +-
util/py_lib/seqan/dox/dox_parser.py | 24 +-
util/py_lib/seqan/dox/dox_tokens.py | 3 +-
util/py_lib/seqan/dox/proc_doc.py | 38 +
util/py_lib/seqan/dox/raw_doc.py | 35 +
util/py_lib/seqan/dox/test/test_dox_parser.py | 20 +
util/py_lib/seqan/dox/test/test_proc_doc.py | 25 +
util/py_lib/seqan/dox/test/test_raw_doc.py | 22 +
util/py_lib/seqan/dox/tpl/function.html | 9 +-
.../js/bootstrap-3.0.0.min.js | 6 -
.../bootstrap-multiselect/js/jquery-2.0.3.min.js | 6 -
.../tpl/lib/bootstrap-multiselect/js/prettify.js | 28 -
util/py_lib/seqan/dox/tpl/list.html | 2 +-
util/py_lib/seqan/dox/tpl/macro.html | 10 +-
util/py_lib/seqan/dox/tpl/sections.html | 81 +-
util/py_lib/seqan/dox/write_html.py | 3 +-
util/skel/test_template/test.h | 1 +
util/travis/linux-cibuild.cmake | 18 +-
1062 files changed, 19915 insertions(+), 22276 deletions(-)
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