[med-svn] [seqan] branch upstream updated (e8d90b2 -> 61466b0)
Andreas Tille
tille at debian.org
Wed Jan 20 10:39:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository seqan.
from e8d90b2 Imported Upstream version 2.0.0+dfsg
new 3e7c7b0 Imported Upstream version 2.0.1+dfsg
new 61466b0 Imported Upstream version 2.0.1+dfsg
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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 +
demos/{ => dox}/align/gaps_example.cpp | 0
demos/{ => dox}/align/gaps_example.cpp.stdout | 0
demos/{ => dox}/align/global_alignment_banded.cpp | 0
.../align/global_alignment_banded.cpp.stdout | 0
.../{ => dox}/align/global_alignment_unbanded.cpp | 0
.../align/global_alignment_unbanded.cpp.stdout | 0
demos/{ => dox}/align/integrate_align.cpp | 0
demos/{ => dox}/align/integrate_align.cpp.stdout | 0
demos/{ => dox}/align_extend/extend_alignment.cpp | 0
.../align_extend/extend_alignment.cpp.stdout | 0
.../align_profile/profile_seq_frac_score.cpp | 0
.../{ => dox}/align_profile/profile_seq_score.cpp | 0
demos/{ => dox}/align_split/split_alignment.cpp | 0
.../align_split/split_alignment.cpp.stdout | 0
demos/{ => dox}/arg_parse/argument_parser.cpp | 0
demos/{ => dox}/bam_io/bam_file_in.cpp | 0
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
demos/{ => dox}/basic/metaprogramming_math.cpp | 0
demos/{ => dox}/basic/metaprogramming_switch.cpp | 0
demos/{ => dox}/basic/simple_type_construction.cpp | 0
.../bed_io/UNUSED_bed_stream_read.cpp} | 0
demos/{ => dox}/consensus/consensus_alignment.cpp | 0
.../consensus/consensus_alignment.cpp.stdout | 0
demos/{ => dox}/find/finder_aho_corasick.cpp | 0
demos/{ => dox}/find/finder_index.cpp | 0
demos/{ => dox}/find/finder_index.cpp.stdout | 0
demos/{ => dox}/find/finder_online.cpp | 0
demos/{ => dox}/find/finder_online.cpp.stdout | 0
.../gff_io/UNUSED_gff_stream_read.cpp} | 0
.../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 +
.../graph_algorithms/dag_shortest_path.cpp.stdout | 0
demos/dox/graph_algorithms/depth_first_search.cpp | 50 +
.../graph_algorithms/depth_first_search.cpp.stdout | 0
demos/dox/graph_algorithms/dijkstra.cpp | 71 +
.../{ => dox}/graph_algorithms/dijkstra.cpp.stdout | 0
.../graph_algorithms/floyd_warshall_algorithm.cpp | 42 +
.../floyd_warshall_algorithm.cpp.stdout | 0
.../graph_algorithms/ford_fulkerson_algorithm.cpp | 40 +
.../ford_fulkerson_algorithm.cpp.stdout | 0
.../heaviest_increasing_subsequence.cpp | 0
demos/dox/graph_algorithms/kruskals_algorithm.cpp | 48 +
.../graph_algorithms/kruskals_algorithm.cpp.stdout | 0
.../longest_common_subsequence.cpp | 0
.../longest_increasing_subsequence.cpp | 0
demos/dox/graph_algorithms/prims_algorithm.cpp | 46 +
.../graph_algorithms/prims_algorithm.cpp.stdout | 0
.../strongly_connected_components.cpp | 41 +
.../strongly_connected_components.cpp.stdout | 0
demos/dox/graph_algorithms/topological_sort.cpp | 42 +
.../graph_algorithms/topological_sort.cpp.stdout | 0
demos/dox/graph_algorithms/transitive_closure.cpp | 34 +
.../graph_algorithms/transitive_closure.cpp.stdout | 0
demos/{ => dox}/graph_align/graph_align.cpp | 0
.../graph_types}/graph_algo_dijkstra.cpp | 0
.../graph_types}/graph_algo_dijkstra.cpp.stdout | 0
.../shape.cpp => dox/index/UNUSED_shape.cpp} | 0
.../index/UNUSED_shape_hash.cpp} | 0
.../index/UNUSED_shape_hash_next.cpp} | 0
.../index/begin_atEnd_representative.cpp} | 0
.../index/begin_atEnd_representative.cpp.stdout} | 0
.../index/begin_atEnd_representative_bottomUp.cpp} | 0
...egin_range_goDown_representative_repLength.cpp} | 0
.../index_counting.cpp => dox/index/counting.cpp} | 0
.../index/counting.cpp.stdout} | 0
...x_textAt_indexText_saAt_indexRequire.cpp.stdout | 0
demos/{ => dox}/index/find_repeats.cpp | 0
.../index_finder.cpp => dox/index/finder.cpp} | 0
.../index/finder.cpp.stdout} | 0
...getOccurrences_getFrequency_range_getFibre.cpp} | 0
...rrences_getFrequency_range_getFibre.cpp.stdout} | 0
.../index_iterator.cpp => dox/index/iterator.cpp} | 0
.../index/iterator.cpp.stdout} | 0
.../index/iterator_short.cpp} | 0
.../index/iterator_short.cpp.stdout} | 0
demos/dox/index/length_countSequences.cpp | 26 +
.../index/length_countSequences.cpp.stdout} | 0
.../index/maxrepeats.cpp} | 0
.../{index/index_mummy.cpp => dox/index/mummy.cpp} | 0
.../index/mummy.cpp.stdout} | 0
demos/{index/index_mums.cpp => dox/index/mums.cpp} | 0
.../index/node_predicate.cpp} | 0
demos/dox/index/open_save.cpp | 27 +
.../index/open_save.cpp.stdout} | 0
demos/{ => dox}/index/ref.fa | 0
demos/{ => dox}/index/shape_hash_init.cpp | 0
.../index_sufarray.cpp => dox/index/sufarray.cpp} | 0
.../index/sufarray.cpp.stdout} | 0
.../index/supermaxrepeats.cpp} | 0
.../index/textAt_indexText_saAt_indexRequire.cpp} | 0
.../textAt_indexText_saAt_indexRequire.cpp.stdout} | 0
demos/{ => dox}/misc/enumerate_strings.cpp | 0
demos/{ => dox}/misc/enumerate_strings.cpp.stdout | 0
demos/{ => dox}/misc/get_terminal_size.cpp | 0
demos/{ => dox}/misc/interval_tree_example.cpp | 0
demos/{ => dox}/misc/name_store_cache.cpp | 0
demos/{ => dox}/misc/name_store_cache.cpp.stdout | 0
demos/{ => dox/modifier}/cyclic_shape.cpp | 0
demos/{ => dox/modifier}/cyclic_shape.cpp.stdout | 0
demos/{ => dox/modifier}/cyclic_shape_snippets.cpp | 0
demos/{ => dox}/modifier/modified_string.cpp | 0
.../{ => dox}/modifier/modified_string.cpp.stdout | 0
.../modifier/modified_string_mod_view.cpp | 0
.../modifier/modified_string_mod_view.cpp.stdout | 0
.../{ => dox}/modifier/modified_string_nested.cpp | 0
.../modifier/modified_string_nested.cpp.stdout | 0
demos/dox/parallel/queue_example.cpp | 30 +
demos/{ => dox}/parallel/queue_example.cpp.stdout | 0
demos/{ => dox}/parallel/splitter_example.cpp | 0
.../{ => dox}/parallel/splitter_example.cpp.stdout | 0
demos/{ => dox}/pipe/pool_sorter.cpp | 0
demos/dox/random/random.cpp | 39 +
demos/{ => dox}/score/score.cpp | 0
demos/{ => dox}/score/score.cpp.stdout | 0
demos/{ => dox}/seeds/seeds_add_seed.cpp | 0
demos/{ => dox}/seeds/seeds_chaining.cpp | 0
demos/{ => dox}/seeds/seeds_chaining.cpp.stdout | 0
demos/{ => dox}/seeds/seeds_extension.cpp | 0
demos/{ => dox}/seeds/seeds_extension.cpp.stdout | 0
demos/{ => dox}/seq_io/example.fa | 0
demos/{ => dox}/seq_io/example.fa.fai | 0
demos/dox/seq_io/fai_index_example.cpp | 48 +
.../{ => dox}/seq_io/fai_index_example.cpp.stdout | 0
.../infix.cpp => dox/sequence/UNUSED_infix.cpp} | 0
.../prefix.cpp => dox/sequence/UNUSED_prefix.cpp} | 0
.../suffix.cpp => dox/sequence/UNUSED_suffix.cpp} | 0
demos/dox/sequence/segment.cpp | 120 ++
demos/{ => dox}/sequence/string.cpp | 0
demos/{ => dox}/sequence/string2.cpp | 0
demos/{ => dox}/sequence/string2.cpp.stdout | 0
demos/{ => dox}/sequence/stringset.cpp | 0
demos/{ => dox}/sequence/stringset.cpp.stdout | 0
demos/{ => dox}/statistics/background.fa | 0
demos/{ => dox}/statistics/build_markov_model.cpp | 0
demos/{ => dox}/statistics/load_markov_model.cpp | 0
demos/{ => dox}/statistics/zscore_example_mm.3 | 0
demos/{ => dox}/statistics/zscore_human_mm.3 | 0
demos/{ => dox}/store/store_example.cpp | 0
demos/dox/stream/lexical_cast.cpp | 53 +
demos/{ => dox}/stream/lexical_cast.cpp.stdout | 0
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 -
.../graph_algorithms/floyd_warshall_algorithm.cpp | 43 -
.../graph_algorithms/ford_fulkerson_algorithm.cpp | 41 -
demos/graph_algorithms/kruskals_algorithm.cpp | 49 -
demos/graph_algorithms/prims_algorithm.cpp | 47 -
.../strongly_connected_components.cpp | 42 -
demos/graph_algorithms/topological_sort.cpp | 43 -
demos/graph_algorithms/transitive_closure.cpp | 35 -
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 +-
demos/howto/scores/init_score.cpp.stdout | 22 +
demos/howto/scores/load_score.cpp | 11 +-
demos/howto/scores/load_score.cpp.stdout | 6 +
demos/index/index_length_countSequences.cpp | 27 -
demos/index/index_open_save.cpp | 28 -
demos/index/index_qgram.cpp | 16 -
demos/index_counting.cpp | 36 -
demos/input_output/example.fa | 4 -
demos/input_output/seqfile_reader.cpp | 27 -
demos/input_output/seqfile_reader.cpp.stdout | 2 -
demos/parallel/queue_example.cpp | 30 -
demos/random/random.cpp | 42 -
demos/sam2svg.cpp | 222 ---
demos/seq_io/fai_index_example.cpp | 49 -
demos/seq_io/sequence_stream_read.cpp | 68 -
demos/seq_io/sequence_stream_read.cpp.stdout | 1 -
demos/seq_io/sequence_stream_write.cpp | 17 -
demos/sequence/segment.cpp | 98 --
demos/stream/lexical_cast.cpp | 55 -
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demos/tutorial/alignments/CMakeLists.txt | 5 -
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demos/tutorial/alignments/alignment_gaps.cpp | 58 -
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include/seqan/graph_algorithms/bellman_ford.h | 4 +-
.../seqan/graph_algorithms/breadth_first_search.h | 4 +-
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include/seqan/parallel/parallel_splitting.h | 6 +-
include/seqan/pipe/pool_sorter.h | 2 +-
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include/seqan/store/store_io_ucsc.h | 0
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manual/requirements.txt | 3 +-
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manual/source/HowTo/ClipAlignments.rst | 2 +-
manual/source/HowTo/GenerateSeqAnKnimeNodes.rst | 2 +-
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manual/source/Infrastructure/Documentation.rst | 10 +
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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 +-
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manual/source/Tutorial/FirstStepsInSeqAn.rst | 562 -------
manual/source/Tutorial/FragmentStore.rst | 98 +-
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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 +-
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manual/source/Tutorial/PatternMatching.rst | 28 +-
manual/source/Tutorial/QgramIndex.rst | 217 +++
manual/source/Tutorial/Randomness.rst | 12 +-
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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 +
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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 +
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tests/gff_io/test_gff_io.h | 60 +
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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 +-
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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 +-
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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 +-
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util/py_lib/seqan/dox/test/test_dox_parser.py | 20 +
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1063 files changed, 19804 insertions(+), 22276 deletions(-)
delete mode 100644 demos/align/compute_alignment_stats.cpp
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delete mode 100644 demos/align_gaps_clipping.cpp
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delete mode 100644 demos/alignment_local.cpp
delete mode 100644 demos/allocator.cpp
delete mode 100644 demos/bam_io/bam_tags_dict.cpp
delete mode 100644 demos/bam_library_size.cpp
delete mode 100644 demos/basic/enable_if.cpp
delete mode 100644 demos/benchmark_stream.cpp
rename demos/{ => dox}/align/align.cpp (100%)
rename demos/{ => dox}/align/align.cpp.stdout (100%)
create mode 100644 demos/dox/align/compute_alignment_stats.cpp
create mode 100644 demos/dox/align/compute_alignment_stats.cpp.stdout
rename demos/{ => dox}/align/gaps_example.cpp (100%)
rename demos/{ => dox}/align/gaps_example.cpp.stdout (100%)
rename demos/{ => dox}/align/global_alignment_banded.cpp (100%)
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rename demos/{ => dox}/align/global_alignment_unbanded.cpp (100%)
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rename demos/{ => dox}/align_extend/extend_alignment.cpp (100%)
rename demos/{ => dox}/align_extend/extend_alignment.cpp.stdout (100%)
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rename demos/{ => dox}/align_split/split_alignment.cpp (100%)
rename demos/{ => dox}/align_split/split_alignment.cpp.stdout (100%)
rename demos/{ => dox}/arg_parse/argument_parser.cpp (100%)
rename demos/{ => dox}/bam_io/bam_file_in.cpp (100%)
create mode 100644 demos/dox/bam_io/bam_tags_dict.cpp
rename demos/{ => dox}/bam_io/bam_tags_dict.cpp.stdout (100%)
create mode 100644 demos/dox/basic/enable_if.cpp
rename demos/{ => dox}/basic/metaprogramming_control.cpp (100%)
rename demos/{ => dox}/basic/metaprogramming_logic.cpp (100%)
rename demos/{ => dox}/basic/metaprogramming_math.cpp (100%)
rename demos/{ => dox}/basic/metaprogramming_switch.cpp (100%)
rename demos/{ => dox}/basic/simple_type_construction.cpp (100%)
rename demos/{bed_io/bed_stream_read.cpp => dox/bed_io/UNUSED_bed_stream_read.cpp} (100%)
rename demos/{ => dox}/consensus/consensus_alignment.cpp (100%)
rename demos/{ => dox}/consensus/consensus_alignment.cpp.stdout (100%)
rename demos/{ => dox}/find/finder_aho_corasick.cpp (100%)
rename demos/{ => dox}/find/finder_index.cpp (100%)
rename demos/{ => dox}/find/finder_index.cpp.stdout (100%)
rename demos/{ => dox}/find/finder_online.cpp (100%)
rename demos/{ => dox}/find/finder_online.cpp.stdout (100%)
rename demos/{gff_io/gff_stream_read.cpp => dox/gff_io/UNUSED_gff_stream_read.cpp} (100%)
create mode 100644 demos/dox/graph_algorithms/all_pairs_shortest_path.cpp
rename demos/{ => dox}/graph_algorithms/all_pairs_shortest_path.cpp.stdout (100%)
create mode 100644 demos/dox/graph_algorithms/bellman_ford_algorithm.cpp
rename demos/{ => dox}/graph_algorithms/bellman_ford_algorithm.cpp.stdout (100%)
create mode 100644 demos/dox/graph_algorithms/breadth_first_search.cpp
rename demos/{ => dox}/graph_algorithms/breadth_first_search.cpp.stdout (100%)
create mode 100644 demos/dox/graph_algorithms/dag_shortest_path.cpp
rename demos/{ => dox}/graph_algorithms/dag_shortest_path.cpp.stdout (100%)
create mode 100644 demos/dox/graph_algorithms/depth_first_search.cpp
rename demos/{ => dox}/graph_algorithms/depth_first_search.cpp.stdout (100%)
create mode 100644 demos/dox/graph_algorithms/dijkstra.cpp
rename demos/{ => dox}/graph_algorithms/dijkstra.cpp.stdout (100%)
create mode 100644 demos/dox/graph_algorithms/floyd_warshall_algorithm.cpp
rename demos/{ => dox}/graph_algorithms/floyd_warshall_algorithm.cpp.stdout (100%)
create mode 100644 demos/dox/graph_algorithms/ford_fulkerson_algorithm.cpp
rename demos/{ => dox}/graph_algorithms/ford_fulkerson_algorithm.cpp.stdout (100%)
rename demos/{ => dox}/graph_algorithms/heaviest_increasing_subsequence.cpp (100%)
create mode 100644 demos/dox/graph_algorithms/kruskals_algorithm.cpp
rename demos/{ => dox}/graph_algorithms/kruskals_algorithm.cpp.stdout (100%)
rename demos/{ => dox}/graph_algorithms/longest_common_subsequence.cpp (100%)
rename demos/{ => dox}/graph_algorithms/longest_increasing_subsequence.cpp (100%)
create mode 100644 demos/dox/graph_algorithms/prims_algorithm.cpp
rename demos/{ => dox}/graph_algorithms/prims_algorithm.cpp.stdout (100%)
create mode 100644 demos/dox/graph_algorithms/strongly_connected_components.cpp
rename demos/{ => dox}/graph_algorithms/strongly_connected_components.cpp.stdout (100%)
create mode 100644 demos/dox/graph_algorithms/topological_sort.cpp
rename demos/{ => dox}/graph_algorithms/topological_sort.cpp.stdout (100%)
create mode 100644 demos/dox/graph_algorithms/transitive_closure.cpp
rename demos/{ => dox}/graph_algorithms/transitive_closure.cpp.stdout (100%)
rename demos/{ => dox}/graph_align/graph_align.cpp (100%)
rename demos/{graph => dox/graph_types}/graph_algo_dijkstra.cpp (100%)
rename demos/{graph => dox/graph_types}/graph_algo_dijkstra.cpp.stdout (100%)
rename demos/{index/shape.cpp => dox/index/UNUSED_shape.cpp} (100%)
rename demos/{index/shape_hash.cpp => dox/index/UNUSED_shape_hash.cpp} (100%)
rename demos/{index/shape_hash_next.cpp => dox/index/UNUSED_shape_hash_next.cpp} (100%)
rename demos/{index/index_begin_atEnd_representative.cpp => dox/index/begin_atEnd_representative.cpp} (100%)
rename demos/{index/index_begin_atEnd_representative.cpp.stdout => dox/index/begin_atEnd_representative.cpp.stdout} (100%)
rename demos/{index/index_begin_atEnd_representative_bottomUp.cpp => dox/index/begin_atEnd_representative_bottomUp.cpp} (100%)
rename demos/{index/index_begin_range_goDown_representative_repLength.cpp => dox/index/begin_range_goDown_representative_repLength.cpp} (100%)
rename demos/{index/index_counting.cpp => dox/index/counting.cpp} (100%)
rename demos/{index/index_counting.cpp.stdout => dox/index/counting.cpp.stdout} (100%)
rename demos/{ => dox}/index/demo_index_index_textAt_indexText_saAt_indexRequire.cpp.stdout (100%)
rename demos/{ => dox}/index/find_repeats.cpp (100%)
rename demos/{index/index_finder.cpp => dox/index/finder.cpp} (100%)
rename demos/{index/index_finder.cpp.stdout => dox/index/finder.cpp.stdout} (100%)
rename demos/{index/index_getOccurrences_getFrequency_range_getFibre.cpp => dox/index/getOccurrences_getFrequency_range_getFibre.cpp} (100%)
rename demos/{index/index_getOccurrences_getFrequency_range_getFibre.cpp.stdout => dox/index/getOccurrences_getFrequency_range_getFibre.cpp.stdout} (100%)
rename demos/{index/index_iterator.cpp => dox/index/iterator.cpp} (100%)
copy demos/{index/index_iterator.cpp.stdout => dox/index/iterator.cpp.stdout} (100%)
rename demos/{index/index_iterator_short.cpp => dox/index/iterator_short.cpp} (100%)
rename demos/{index/index_iterator_short.cpp.stdout => dox/index/iterator_short.cpp.stdout} (100%)
create mode 100644 demos/dox/index/length_countSequences.cpp
rename demos/{index/index_length_countSequences.cpp.stdout => dox/index/length_countSequences.cpp.stdout} (100%)
rename demos/{index_maxrepeats.cpp => dox/index/maxrepeats.cpp} (100%)
rename demos/{index/index_mummy.cpp => dox/index/mummy.cpp} (100%)
rename demos/{index/index_mummy.cpp.stdout => dox/index/mummy.cpp.stdout} (100%)
rename demos/{index/index_mums.cpp => dox/index/mums.cpp} (100%)
rename demos/{index/index_node_predicate.cpp => dox/index/node_predicate.cpp} (100%)
create mode 100644 demos/dox/index/open_save.cpp
rename demos/{index/index_open_save.cpp.stdout => dox/index/open_save.cpp.stdout} (100%)
rename demos/{ => dox}/index/ref.fa (100%)
rename demos/{ => dox}/index/shape_hash_init.cpp (100%)
rename demos/{index/index_sufarray.cpp => dox/index/sufarray.cpp} (100%)
rename demos/{index/index_sufarray.cpp.stdout => dox/index/sufarray.cpp.stdout} (100%)
rename demos/{index/index_supermaxrepeats.cpp => dox/index/supermaxrepeats.cpp} (100%)
rename demos/{index/index_textAt_indexText_saAt_indexRequire.cpp => dox/index/textAt_indexText_saAt_indexRequire.cpp} (100%)
rename demos/{index/index_textAt_indexText_saAt_indexRequire.cpp.stdout => dox/index/textAt_indexText_saAt_indexRequire.cpp.stdout} (100%)
rename demos/{ => dox}/misc/enumerate_strings.cpp (100%)
rename demos/{ => dox}/misc/enumerate_strings.cpp.stdout (100%)
rename demos/{ => dox}/misc/get_terminal_size.cpp (100%)
rename demos/{ => dox}/misc/interval_tree_example.cpp (100%)
rename demos/{ => dox}/misc/name_store_cache.cpp (100%)
rename demos/{ => dox}/misc/name_store_cache.cpp.stdout (100%)
rename demos/{ => dox/modifier}/cyclic_shape.cpp (100%)
rename demos/{ => dox/modifier}/cyclic_shape.cpp.stdout (100%)
rename demos/{ => dox/modifier}/cyclic_shape_snippets.cpp (100%)
rename demos/{ => dox}/modifier/modified_string.cpp (100%)
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rename demos/{ => dox}/modifier/modified_string_mod_view.cpp (100%)
copy demos/{ => dox}/modifier/modified_string_mod_view.cpp.stdout (100%)
rename demos/{ => dox}/modifier/modified_string_nested.cpp (100%)
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create mode 100644 demos/dox/parallel/queue_example.cpp
rename demos/{ => dox}/parallel/queue_example.cpp.stdout (100%)
rename demos/{ => dox}/parallel/splitter_example.cpp (100%)
rename demos/{ => dox}/parallel/splitter_example.cpp.stdout (100%)
rename demos/{ => dox}/pipe/pool_sorter.cpp (100%)
create mode 100644 demos/dox/random/random.cpp
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rename demos/tutorial/{alignments/alignment2_align.cpp => alignment_representation/align.cpp} (100%)
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rename demos/tutorial/{alignments/alignment_align_assignment1.cpp => alignment_representation/align_assignmen1.cpp} (100%)
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rename demos/tutorial/{alignments/alignment_representation_ag.cpp => alignment_representation/graph.cpp} (100%)
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rename demos/tutorial/{alignments/alignment_representation_ag_assignment1.cpp => alignment_representation/graph_assignment1.cpp} (100%)
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create mode 100644 demos/tutorial/basics/show_alphabets.cpp.stdout
create mode 100644 demos/tutorial/basics/strings.cpp.stdout
create mode 100644 demos/tutorial/bed_io/example.bed
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/bed_io/example1.cpp.stdout (100%)
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/bed_io/solution1.cpp.stdout (100%)
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/bed_io/solution2.cpp.stdout (100%)
create mode 100644 demos/tutorial/bed_io/solution3.cpp.stdout
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/blast_io/read_assignment.cpp.stdout (100%)
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/blast_io/write_assignment.cpp.stdout (100%)
rename demos/tutorial/{consensus => consensus_alignment}/with_positions.cpp (100%)
rename demos/tutorial/{consensus => consensus_alignment}/with_positions.cpp.stdout (100%)
rename demos/tutorial/{consensus => consensus_alignment}/without_positions.cpp (100%)
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create mode 100644 demos/tutorial/file_io_overview/example.bam
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create mode 100644 demos/tutorial/file_io_overview/solution1.cpp
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/file_io_overview/solution1.cpp.stdout (100%)
create mode 100644 demos/tutorial/file_io_overview/solution2.cpp
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/file_io_overview/solution2.cpp.stdout (100%)
create mode 100644 demos/tutorial/file_io_overview/solution3.cpp
create mode 100644 demos/tutorial/file_io_overview/solution3.cpp.stdout
delete mode 100644 demos/tutorial/find/CMakeLists.txt
create mode 100644 demos/tutorial/fragment_store/access_aligned_reads.cpp
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create mode 100644 demos/tutorial/fragment_store/access_aligned_reads2.cpp
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create mode 100644 demos/tutorial/fragment_store/display_aligned_reads.cpp
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rename demos/tutorial/{store/ex1.sam => fragment_store/example.sam} (100%)
create mode 100644 demos/tutorial/generic_programming/template_subclassing.cpp.stdout
create mode 100644 demos/tutorial/genome_annotations/assignment_1_hint.cpp
create mode 100644 demos/tutorial/genome_annotations/assignment_1_hint.cpp.stdout
create mode 100644 demos/tutorial/genome_annotations/assignment_1_solution.cpp
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create mode 100644 demos/tutorial/genome_annotations/assignment_4_solution.cpp
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rename demos/tutorial/{annotation_store => genome_annotations}/assignment_annotations.gtf (100%)
create mode 100644 demos/tutorial/genome_annotations/base.cpp
create mode 100644 demos/tutorial/genome_annotations/base.cpp.stdout
create mode 100644 demos/tutorial/genome_annotations/example.gtf
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create mode 100644 demos/tutorial/gff_and_gtf_io/example.gff
create mode 100644 demos/tutorial/gff_and_gtf_io/example1.cpp
create mode 100644 demos/tutorial/gff_and_gtf_io/example1.cpp.stdout
create mode 100644 demos/tutorial/gff_and_gtf_io/example2.cpp
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create mode 100644 demos/tutorial/gff_and_gtf_io/solution1.cpp
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create mode 100644 demos/tutorial/gff_and_gtf_io/solution3.cpp.stdout
delete mode 100644 demos/tutorial/gff_io/example1.cpp
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create mode 100644 demos/tutorial/graph/graph_dijkstra.cpp.stdout
create mode 100644 demos/tutorial/graph/graph_hmm.cpp.stdout
create mode 100644 demos/tutorial/graph/solution_1.cpp.stdout
delete mode 100644 demos/tutorial/index/CMakeLists.txt
rename demos/tutorial/{index/index_assignment3.cpp => index_iterators/UNUSED_index_assignment3.cpp} (100%)
copy demos/{index/index_iterator.cpp.stdout => tutorial/index_iterators/UNUSED_index_assignment3.cpp.stdout} (100%)
rename demos/tutorial/{index => index_iterators}/index_assignment1.cpp (100%)
create mode 100644 demos/tutorial/index_iterators/index_assignment1.cpp.stdout
rename demos/tutorial/{index => index_iterators}/index_assignment2.cpp (100%)
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rename demos/tutorial/{index => index_iterators}/index_property_maps.cpp (100%)
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rename demos/tutorial/{index => index_iterators}/index_search.cpp (100%)
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rename demos/tutorial/{index => index_iterators}/iterator_solution1.cpp (100%)
create mode 100644 demos/tutorial/index_iterators/iterator_solution1.cpp.stdout
rename demos/tutorial/{index => index_iterators}/iterator_solution2.cpp (100%)
rename demos/{index/index_iterator.cpp.stdout => tutorial/index_iterators/iterator_solution2.cpp.stdout} (100%)
rename demos/tutorial/{index/indices_assignment_1.cpp => indices/assignment_1.cpp} (100%)
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/indices/assignment_1.cpp.stdout (100%)
rename demos/tutorial/{index/indices_assignment_2.cpp => indices/assignment_2.cpp} (100%)
create mode 100644 demos/tutorial/indices/assignment_2.cpp.stdout
rename demos/tutorial/iterators/{iterators_assignment_1_solution.cpp => assignment_1_solution.cpp} (100%)
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rename demos/tutorial/iterators/{iterators_assignment_2_solution.cpp => assignment_2_solution.cpp} (100%)
create mode 100644 demos/tutorial/iterators/assignment_2_solution.cpp.stdout
create mode 100644 demos/tutorial/iterators/assignment_3_workshop_solution.cpp
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create mode 100644 demos/tutorial/iterators/sequence_iterator_demo.cpp.stdout
rename demos/tutorial/{data_journaling => journaled_set}/example_join.cpp (100%)
create mode 100644 demos/tutorial/journaled_set/example_join.cpp.stdout
create mode 100644 demos/tutorial/journaled_set/example_journal_string_basic.cpp
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create mode 100644 demos/tutorial/journaled_set/example_online_search.cpp
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create mode 100644 demos/tutorial/journaled_set/example_online_search_assignment1_hint.cpp
create mode 100644 demos/tutorial/journaled_set/example_online_search_assignment1_hint.cpp.stdout
copy {manual/source/Tutorial => demos/tutorial/journaled_set}/sequences.fasta (100%)
create mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment1.cpp
create mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment1.cpp.stdout
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create mode 100644 demos/tutorial/journaled_set/solution_online_search_finder.cpp
create mode 100644 demos/tutorial/journaled_set/solution_online_search_finder.cpp.stdout
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delete mode 100644 demos/tutorial/mini_bowtie/mini_bowtie.cpp
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create mode 100644 demos/tutorial/modifiers/UNUSED_modcomplementdna.cpp.stdout
rename demos/{modifier_modview.cpp => tutorial/modifiers/UNUSED_modview.cpp} (100%)
rename demos/{modifier/modified_string_mod_view.cpp.stdout => tutorial/modifiers/UNUSED_modview.cpp.stdout} (100%)
rename demos/{modifier_nested.cpp => tutorial/modifiers/UNUSED_nested.cpp} (100%)
rename demos/{modifier/modified_string_nested.cpp.stdout => tutorial/modifiers/UNUSED_nested.cpp.stdout} (100%)
create mode 100644 demos/tutorial/modifiers/assignment1.cpp.stdout
create mode 100644 demos/tutorial/modifiers/assignment1_solution.cpp.stdout
rename demos/tutorial/modifiers/{modifier_modreverse.cpp => modreverse.cpp} (100%)
create mode 100644 demos/tutorial/modifiers/modreverse.cpp.stdout
rename demos/tutorial/{alignments/alignment_msa_assignment1.cpp => multiple_sequence_alignment/assignment1.cpp} (100%)
rename demos/tutorial/{alignments/alignment_msa_assignment1.cpp.stdout => multiple_sequence_alignment/assignment1.cpp.stdout} (100%)
rename demos/tutorial/{alignments/alignment_msa_consensus.cpp => multiple_sequence_alignment/consensus.cpp} (100%)
rename demos/tutorial/{alignments/alignment_msa_consensus.cpp.stdout => multiple_sequence_alignment/consensus.cpp.stdout} (100%)
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rename demos/tutorial/{find/find_assignment1_solution.cpp => pattern_matching/assignment1_solution.cpp} (100%)
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create mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment1.cpp
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rename demos/{tutorial/read_mapping => unassigned_or_unused}/minimapper.cpp (100%)
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