[med-svn] [seqan] branch master updated (044c175 -> 3b1e926)
Andreas Tille
tille at debian.org
Wed Jan 20 10:39:37 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository seqan.
from 044c175 Rename seqan-doc doc-base document name
new 0dcf652 New minor upstream release
new 3e7c7b0 Imported Upstream version 2.0.1+dfsg
new 5c6394c Merge tag 'upstream/2.0.1+dfsg'
new f36ba41 Symlink to binaries only if these are part of the binary distribution
new 2097542 Depete outdated comment
new 309e9d0 Dox target does nothing and no *.html files will be created at all
new a1fbd62 Fix string quoting
new 716fb89 Location of file has changed
new 5c8838d Fix symlinks
new c7a9bb3 lintian override for false positive
new eed8e36 Remove swapfile right from the tarball rather than via patch
new 61466b0 Imported Upstream version 2.0.1+dfsg
new d4ce7a8 Merge tag 'upstream/2.0.1+dfsg'
new 3b1e926 More spelling issues
The 14 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 +-
debian/changelog | 5 +-
debian/copyright | 3 +-
debian/patches/0001-Remove-.swp-from-source.patch | Bin 41654 -> 0 bytes
debian/patches/series | 2 +-
debian/patches/spelling.patch | 115 ++
debian/rules | 53 +-
debian/seqan-apps.links | 21 -
debian/seqan-apps.lintian-overrides | 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
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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
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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
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.../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
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.../index/supermaxrepeats.cpp} | 0
.../index/textAt_indexText_saAt_indexRequire.cpp} | 0
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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
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.../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/alignment_gaps.cpp | 58 -
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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%)
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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%)
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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%)
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copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/file_io_overview/solution2.cpp.stdout (100%)
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create mode 100644 demos/tutorial/fragment_store/access_aligned_reads.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
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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
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create mode 100644 demos/tutorial/gff_and_gtf_io/example.gff
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copy demos/{index/index_iterator.cpp.stdout => tutorial/index_iterators/UNUSED_index_assignment3.cpp.stdout} (100%)
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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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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%)
rename demos/tutorial/{alignments/alignment_msa.cpp => multiple_sequence_alignment/msa.cpp} (100%)
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create mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_banded.cpp.stdout
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rename demos/tutorial/{alignments/alignment_pairwise_local.cpp => pairwise_sequence_alignment/alignment_local.cpp} (100%)
create mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp.stdout
rename demos/tutorial/{alignments/alignment_pairwise_local_assignment1.cpp => pairwise_sequence_alignment/alignment_local_assignment1.cpp} (100%)
create mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp.stdout
create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5.cpp
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create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp.stdout (100%)
create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp
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create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp
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create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp
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create mode 100644 demos/tutorial/parsing_command_line_arguments/assignment2_solution.cpp
create mode 100644 demos/tutorial/parsing_command_line_arguments/assignment3_solution.cpp
create mode 100644 demos/tutorial/parsing_command_line_arguments/assignment4_solution.cpp
create mode 100644 demos/tutorial/parsing_command_line_arguments/assignment5_solution.cpp
create mode 100644 demos/tutorial/parsing_command_line_arguments/assignment6_solution.cpp
create mode 100644 demos/tutorial/parsing_command_line_arguments/example1.cpp
create mode 100644 demos/tutorial/parsing_command_line_arguments/example1_detailed.cpp
create mode 100644 demos/tutorial/parsing_command_line_arguments/example_with_modifyString.cpp
create mode 100644 demos/tutorial/parsing_command_line_arguments/example_with_own_function.cpp
create mode 100644 demos/tutorial/parsing_command_line_arguments/example_with_struct.cpp
create mode 100644 demos/tutorial/parsing_command_line_arguments/final_solution.cpp
rename demos/tutorial/{find/find_assignment1.cpp => pattern_matching/assignment1.cpp} (100%)
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/pattern_matching/assignment1.cpp.stdout (100%)
rename demos/tutorial/{find/find_assignment1_solution.cpp => pattern_matching/assignment1_solution.cpp} (100%)
create mode 100644 demos/tutorial/pattern_matching/assignment1_solution.cpp.stdout
rename demos/tutorial/{find/find_assignment2.cpp => pattern_matching/assignment2.cpp} (100%)
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rename demos/tutorial/{find/find_assignment2_solution.cpp => pattern_matching/assignment2_solution.cpp} (100%)
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rename demos/tutorial/{find/find_assignment3.cpp => pattern_matching/assignment3.cpp} (100%)
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rename demos/tutorial/{find => pattern_matching}/find_approx.cpp (100%)
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rename demos/tutorial/{find => pattern_matching}/find_index.cpp (100%)
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rename demos/tutorial/{index => q_gram_index}/index_assignment5.cpp (100%)
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rename demos/tutorial/{index => q_gram_index}/index_qgram_hash.cpp (100%)
create mode 100644 demos/tutorial/q_gram_index/index_qgram_hash.cpp.stdout
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delete mode 100644 demos/tutorial/read_mapping/CMakeLists.txt
delete mode 100644 demos/tutorial/read_mapping/nc_001454.fasta
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rename demos/tutorial/{realign => realignment}/ref.fa (100%)
create mode 100644 demos/tutorial/realignment/step1.cpp
rename demos/tutorial/{realign => realignment}/step1.cpp.stdout (100%)
create mode 100644 demos/tutorial/realignment/step2.cpp
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delete mode 100644 demos/tutorial/rnaseq/CMakeLists.txt
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create mode 100644 demos/tutorial/sam_and_bam_io/example.bam
create mode 100644 demos/tutorial/sam_and_bam_io/example.bam.bai
rename demos/tutorial/{bam_io => sam_and_bam_io}/example.sam (100%)
create mode 100644 demos/tutorial/sam_and_bam_io/example1.cpp
create mode 100644 demos/tutorial/sam_and_bam_io/example1.cpp.stdout
create mode 100644 demos/tutorial/sam_and_bam_io/example2.cpp
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create mode 100644 demos/tutorial/sam_and_bam_io/example7.cpp
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create mode 100644 demos/tutorial/sam_and_bam_io/solution1.cpp
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create mode 100644 demos/tutorial/sam_and_bam_io/solution3.cpp
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create mode 100644 demos/tutorial/seed_and_extend/example1.cpp.stdout
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create mode 100644 demos/tutorial/seed_and_extend/example5.cpp.stdout
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/seed_and_extend/example6.cpp.stdout (100%)
create mode 100644 demos/tutorial/seed_and_extend/example7.cpp.stdout
create mode 100644 demos/tutorial/seed_and_extend/example8.cpp.stdout
create mode 100644 demos/tutorial/seed_and_extend/solution1.cpp.stdout
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create mode 100644 demos/tutorial/seed_and_extend/solution4.cpp.stdout
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create mode 100644 demos/tutorial/seed_and_extend/solution7.cpp.stdout
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create mode 100644 demos/tutorial/sequence_io/example1.cpp.stdout
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create mode 100644 demos/tutorial/sequences/assignment_1_solution.cpp
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create mode 100644 demos/tutorial/sequences/assignment_4_solution.cpp.stdout
create mode 100644 demos/tutorial/sequences/assignment_5_solution.cpp
create mode 100644 demos/tutorial/sequences/assignment_5_solution.cpp.stdout
rename demos/tutorial/sequences/{segments_assignment_2_solution.cpp => assignment_6_solution.cpp} (100%)
delete mode 100644 demos/tutorial/sequences/segments_assignment_hint.cpp
delete mode 100644 demos/tutorial/sequences/segments_assignment_solution.cpp
delete mode 100644 demos/tutorial/sequences/string_assignment_1_solution.cpp
create mode 100644 demos/tutorial/sequences_in_depth/assignment_exact_generous_solution.cpp.stdout
create mode 100644 demos/tutorial/sequences_in_depth/example_overflow.cpp
create mode 100644 demos/tutorial/sequences_in_depth/example_overflow.cpp.stdout
create mode 100644 demos/tutorial/simple_rna_seq/example.gtf
create mode 100644 demos/tutorial/simple_rna_seq/example.sam
create mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment1.cpp
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/simple_rna_seq/genequant_assignment1.cpp.stdout (100%)
create mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment2.cpp
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/simple_rna_seq/genequant_assignment2.cpp.stdout (100%)
create mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment3.cpp
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/simple_rna_seq/genequant_assignment3.cpp.stdout (100%)
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copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/simple_rna_seq/genequant_assignment4.cpp.stdout (100%)
create mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment5.cpp
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/simple_rna_seq/genequant_assignment5.cpp.stdout (100%)
create mode 100644 demos/tutorial/simple_rna_seq/genequant_solution1.cpp
create mode 100644 demos/tutorial/simple_rna_seq/genequant_solution1.cpp.stdout
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create mode 100644 demos/tutorial/simple_rna_seq/genequant_solution5.cpp
create mode 100644 demos/tutorial/simple_rna_seq/genequant_solution5.cpp.stdout
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create mode 100644 demos/tutorial/simple_rna_seq/interval_tree.cpp.stdout
delete mode 100644 demos/tutorial/store/CMakeLists.txt
delete mode 100644 demos/tutorial/store/store_access_aligned_reads.cpp
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create mode 100644 demos/tutorial/string_sets/assignment_1_solution.cpp.stdout
create mode 100644 demos/tutorial/string_sets/assignment_2_solution.cpp.stdout
create mode 100644 demos/tutorial/string_sets/assignment_3_workshop_solution.cpp.stdout
delete mode 100644 demos/tutorial/string_sets/assignment_3b_workshop_solution.cpp
create mode 100644 demos/tutorial/string_sets/assignment_4_workshop_solution.cpp.stdout
create mode 100644 demos/tutorial/vcf_io/example.vcf
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/vcf_io/example1.cpp.stdout (100%)
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/vcf_io/solution1.cpp.stdout (100%)
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/vcf_io/solution2.cpp.stdout (100%)
create mode 100644 demos/tutorial/vcf_io/solution3.cpp.stdout
rename demos/{ => unassigned_or_unused}/alphabet.cpp (100%)
rename demos/{ => unassigned_or_unused}/annotation_converter.cpp (100%)
rename demos/{ => unassigned_or_unused}/arg_align.README (100%)
rename demos/{ => unassigned_or_unused}/arg_align.cpp (100%)
create mode 100644 demos/unassigned_or_unused/bam_library_size.cpp
rename demos/{ => unassigned_or_unused}/bam_print_alignments.cpp (100%)
rename demos/{ => unassigned_or_unused}/bamutil.cpp (100%)
create mode 100644 demos/unassigned_or_unused/benchmark_stream.cpp
rename demos/{ => unassigned_or_unused}/benchmark_stream_write.cpp (100%)
rename demos/{ => unassigned_or_unused}/cuda/count.cu (100%)
rename demos/{ => unassigned_or_unused}/cuda/hello.cu (100%)
rename demos/{ => unassigned_or_unused}/cuda/mmap.cu (100%)
rename demos/{ => unassigned_or_unused}/ecoln.out (100%)
rename demos/{ => unassigned_or_unused}/file_format.cpp (100%)
rename demos/{ => unassigned_or_unused}/file_readwrite.cpp (100%)
rename demos/{ => unassigned_or_unused}/file_speed.cpp (100%)
rename demos/{ => unassigned_or_unused}/filter_sam.cpp (100%)
rename demos/{ => unassigned_or_unused}/find_wild.cpp (100%)
rename demos/{ => unassigned_or_unused}/gff2gtf.cpp (100%)
create mode 100644 demos/unassigned_or_unused/graph_hmm_silent.cpp
rename demos/{ => unassigned_or_unused}/index_find.cpp (100%)
rename demos/{ => unassigned_or_unused}/index_find_stringset.cpp (100%)
rename demos/{ => unassigned_or_unused}/index_lcp.cpp (100%)
rename demos/{ => unassigned_or_unused}/index_mums.cpp (100%)
rename demos/{ => unassigned_or_unused}/index_node_predicate.cpp (100%)
rename demos/{ => unassigned_or_unused}/index_qgram_counts.cpp (100%)
rename demos/{ => unassigned_or_unused}/index_sufarray.cpp (100%)
rename demos/{ => unassigned_or_unused}/index_supermaxrepeats.cpp (100%)
rename demos/{ => unassigned_or_unused}/iterator.cpp (100%)
rename demos/{ => unassigned_or_unused}/knime_node.cpp (100%)
rename demos/{ => unassigned_or_unused}/lagan1.fasta (100%)
rename demos/{ => unassigned_or_unused}/lagan2.fasta (100%)
rename demos/{tutorial/read_mapping => unassigned_or_unused}/minimapper.cpp (100%)
rename demos/{ => unassigned_or_unused}/modifier_modreverse.cpp (100%)
rename demos/{tutorial/modifiers => unassigned_or_unused}/modifier_modview.cpp (100%)
rename demos/{tutorial/modifiers => unassigned_or_unused}/modifier_nested.cpp (100%)
rename demos/{ => unassigned_or_unused}/parse_lm_stellar.cpp (100%)
rename demos/{ => unassigned_or_unused}/rooted_iterator.cpp (100%)
create mode 100644 demos/unassigned_or_unused/sam2svg.cpp
rename demos/{ => unassigned_or_unused}/sample_seqs.cpp (100%)
rename demos/{ => unassigned_or_unused}/seeds.cpp (100%)
rename demos/{ => unassigned_or_unused}/segmentalignment.cpp (100%)
rename demos/{ => unassigned_or_unused}/sequence_1.fa (100%)
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rename demos/{ => unassigned_or_unused}/sequence_length.cpp (100%)
rename demos/{ => unassigned_or_unused}/soft_to_hard_masking.cpp (100%)
rename demos/{tutorial/file_io => unassigned_or_unused/tutorial_file_io}/example1.cpp (100%)
rename demos/{tutorial/file_io => unassigned_or_unused/tutorial_file_io}/mmap_string_example.cpp (100%)
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rename demos/{tutorial/file_io => unassigned_or_unused/tutorial_file_io}/solution2.cpp (100%)
rename demos/{tutorial/file_io => unassigned_or_unused/tutorial_file_io}/solution3.cpp (100%)
rename demos/{tutorial/file_io => unassigned_or_unused/tutorial_file_io}/stream_compression_formats.cpp (100%)
rename demos/{tutorial/sequence => unassigned_or_unused/tutorial_sequence}/CMakeLists.txt (100%)
rename demos/{tutorial/sequence => unassigned_or_unused/tutorial_sequence}/count_characters.cpp (100%)
rename demos/{tutorial/sequence => unassigned_or_unused/tutorial_sequence}/count_generic_characters.cpp (100%)
rename demos/{tutorial/sequence => unassigned_or_unused/tutorial_sequence}/replace_as.cpp (100%)
rename demos/{tutorial/sequence => unassigned_or_unused/tutorial_sequence}/sequence_all_strings.cpp (100%)
rename demos/{tutorial/sequence => unassigned_or_unused/tutorial_sequence}/sequence_iterator_demo.cpp (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/NC_001405.fasta (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/NC_001460.fasta (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/blast_example.txt (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/example1.cpp (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/gff2_example.txt (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/newick_example.txt (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/parse_blastn.cpp (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/parse_gff2.cpp (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/reader_demo.cpp (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/solution1.cpp (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/solution2.cpp (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/solution3.cpp (100%)
rename demos/{tutorial/custom_io => unassigned_or_unused/tutorials_custim_io}/solution4.cpp (100%)
delete mode 100644 demos/vcf_io/vcf_stream_read.cpp
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create mode 100644 include/seqan/stream/iostream_bzip2.h
create mode 100644 include/seqan/stream/iostream_bzip2_impl.h
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rename manual/source/Tutorial/{TemplateSubclassing.rst => GenericProgramming.rst} (100%)
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create mode 100644 manual/source/Tutorial/GffAndGtfIO.rst
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create mode 100644 tests/gff_io/example_with_comments.gff
create mode 100644 tests/sequence/test_stringset_v2.cpp
create mode 100644 util/cmake/CMakeFindJavaCommon.cmake
create mode 100644 util/cmake/FindJava.cmake
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