[med-svn] [seqan] branch master updated (b539505 -> bcd7dab)
Andreas Tille
tille at debian.org
Tue Jul 26 07:12:06 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 b539505 Revert "More spelling issues"
new 812fe37 Revert "Imported Upstream version 2.0.1+dfsg"
new c5614d0 Revert "Remove swapfile right from the tarball rather than via patch"
new 397bc4e Revert "lintian override for false positive"
new 142ab66 Revert "Fix symlinks"
new dfeee2d Revert "Location of file has changed"
new 281f045 Revert "Fix string quoting"
new 7e815b2 Revert "Dox target does nothing and no *.html files will be created at all"
new 9e16195 Revert "Depete outdated comment"
new b40bd3d Revert "Symlink to binaries only if these are part of the binary distribution"
new 60a4224 Revert "Imported Upstream version 2.0.1+dfsg"
new 8121dba Revert "New minor upstream release"
new ec2b653 Revert "Rename seqan-doc doc-base document name"
new bf5d08a Revert "Fix erroneous duplication of Section in seqan-apps"
new b395044 Revert "Add swp removal patch to d/source/include-binaries"
new ba6d6eb Revert "Add debian hardening flags which cmake will use"
new 8206e1c Revert "Fix doc-base for seqan-doc"
new 4f5fd3a Revert "Remove a .swp file from the source with a patch"
new 8bb1c5e Revert "Add correct section for seqan-doc"
new c9c7232 Revert "Make seqan-doc.docs executable to use dh_exec"
new 317dbe4 Revert "Remove commenting out of find in d/rules"
new 90b2c3c Revert "Correct documentation make target name"
new 0df9c13 Revert "Fix typo in seqan-doc description (d/control)"
new bcd7dab Revert "Moved to Git"
The 23 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 | 6 +-
debian/control | 7 +-
debian/copyright | 3 +-
debian/patches/series | 2 +-
debian/patches/skip_splazers_test.patch | 44 +
debian/rules | 63 +-
debian/seqan-apps.links | 21 +
debian/seqan-apps.lintian-overrides | 2 -
debian/seqan-dev.doc-base | 22 +
debian/seqan-doc.doc-base | 22 -
debian/seqan-doc.docs | 0
debian/source/include-binaries | 1 -
demos/{dox => }/align/align.cpp | 0
demos/{dox => }/align/align.cpp.stdout | 0
demos/align/compute_alignment_stats.cpp | 66 +
demos/align/compute_alignment_stats.cpp.stdout | 50 +
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
demos/align_gaps_clipping.cpp | 74 +
.../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/alignment.cpp | 51 +
demos/alignment_local.cpp | 91 ++
demos/allocator.cpp | 28 +
demos/{unassigned_or_unused => }/alphabet.cpp | 0
.../annotation_converter.cpp | 0
demos/{unassigned_or_unused => }/arg_align.README | 0
demos/{unassigned_or_unused => }/arg_align.cpp | 0
demos/{dox => }/arg_parse/argument_parser.cpp | 0
demos/{dox => }/bam_io/bam_file_in.cpp | 0
demos/bam_io/bam_tags_dict.cpp | 36 +
demos/{dox => }/bam_io/bam_tags_dict.cpp.stdout | 0
demos/bam_library_size.cpp | 271 ++++
.../bam_print_alignments.cpp | 0
demos/{unassigned_or_unused => }/bamutil.cpp | 0
demos/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_stream_read.cpp} | 0
demos/benchmark_stream.cpp | 422 +++++
.../benchmark_stream_write.cpp | 0
demos/{dox => }/consensus/consensus_alignment.cpp | 0
.../consensus/consensus_alignment.cpp.stdout | 0
demos/{unassigned_or_unused => }/cuda/count.cu | 0
demos/{unassigned_or_unused => }/cuda/hello.cu | 0
demos/{unassigned_or_unused => }/cuda/mmap.cu | 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/align/compute_alignment_stats.cpp | 65 -
demos/dox/align/compute_alignment_stats.cpp.stdout | 52 -
demos/dox/bam_io/bam_tags_dict.cpp | 36 -
demos/dox/basic/enable_if.cpp | 96 --
.../graph_algorithms/all_pairs_shortest_path.cpp | 43 -
.../graph_algorithms/bellman_ford_algorithm.cpp | 46 -
.../dox/graph_algorithms/breadth_first_search.cpp | 52 -
demos/dox/graph_algorithms/dag_shortest_path.cpp | 43 -
demos/dox/graph_algorithms/depth_first_search.cpp | 50 -
demos/dox/graph_algorithms/dijkstra.cpp | 71 -
.../graph_algorithms/floyd_warshall_algorithm.cpp | 42 -
.../graph_algorithms/ford_fulkerson_algorithm.cpp | 40 -
demos/dox/graph_algorithms/kruskals_algorithm.cpp | 48 -
demos/dox/graph_algorithms/prims_algorithm.cpp | 46 -
.../strongly_connected_components.cpp | 41 -
demos/dox/graph_algorithms/topological_sort.cpp | 42 -
demos/dox/graph_algorithms/transitive_closure.cpp | 34 -
demos/dox/index/length_countSequences.cpp | 26 -
demos/dox/index/open_save.cpp | 27 -
demos/dox/parallel/queue_example.cpp | 30 -
demos/dox/random/random.cpp | 39 -
demos/dox/seq_io/fai_index_example.cpp | 48 -
demos/dox/sequence/segment.cpp | 120 --
demos/dox/stream/lexical_cast.cpp | 53 -
demos/{unassigned_or_unused => }/ecoln.out | 0
demos/{unassigned_or_unused => }/file_format.cpp | 0
.../{unassigned_or_unused => }/file_readwrite.cpp | 0
demos/{unassigned_or_unused => }/file_speed.cpp | 0
demos/{unassigned_or_unused => }/filter_sam.cpp | 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
demos/find_approx.cpp | 45 +
demos/find_exact.cpp | 35 +
demos/{unassigned_or_unused => }/find_wild.cpp | 0
demos/{unassigned_or_unused => }/gff2gtf.cpp | 0
.../gff_stream_read.cpp} | 0
.../graph_types => graph}/graph_algo_dijkstra.cpp | 0
.../graph_algo_dijkstra.cpp.stdout | 0
demos/graph_algorithms/all_pairs_shortest_path.cpp | 44 +
.../all_pairs_shortest_path.cpp.stdout | 0
demos/graph_algorithms/bellman_ford_algorithm.cpp | 47 +
.../bellman_ford_algorithm.cpp.stdout | 0
demos/graph_algorithms/breadth_first_search.cpp | 53 +
.../breadth_first_search.cpp.stdout | 0
demos/graph_algorithms/dag_shortest_path.cpp | 44 +
.../graph_algorithms/dag_shortest_path.cpp.stdout | 0
demos/graph_algorithms/depth_first_search.cpp | 51 +
.../graph_algorithms/depth_first_search.cpp.stdout | 0
demos/graph_algorithms/dijkstra.cpp | 72 +
.../{dox => }/graph_algorithms/dijkstra.cpp.stdout | 0
.../graph_algorithms/floyd_warshall_algorithm.cpp | 43 +
.../floyd_warshall_algorithm.cpp.stdout | 0
.../graph_algorithms/ford_fulkerson_algorithm.cpp | 41 +
.../ford_fulkerson_algorithm.cpp.stdout | 0
.../heaviest_increasing_subsequence.cpp | 0
demos/graph_algorithms/kruskals_algorithm.cpp | 49 +
.../graph_algorithms/kruskals_algorithm.cpp.stdout | 0
.../longest_common_subsequence.cpp | 0
.../longest_increasing_subsequence.cpp | 0
demos/graph_algorithms/prims_algorithm.cpp | 47 +
.../graph_algorithms/prims_algorithm.cpp.stdout | 0
.../strongly_connected_components.cpp | 42 +
.../strongly_connected_components.cpp.stdout | 0
demos/graph_algorithms/topological_sort.cpp | 43 +
.../graph_algorithms/topological_sort.cpp.stdout | 0
demos/graph_algorithms/transitive_closure.cpp | 35 +
.../graph_algorithms/transitive_closure.cpp.stdout | 0
demos/{dox => }/graph_align/graph_align.cpp | 0
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 -
...x_textAt_indexText_saAt_indexRequire.cpp.stdout | 0
demos/{dox => }/index/find_repeats.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
.../counting.cpp => index/index_counting.cpp} | 0
.../index_counting.cpp.stdout} | 0
.../index/finder.cpp => index/index_finder.cpp} | 0
.../index_finder.cpp.stdout} | 0
...getOccurrences_getFrequency_range_getFibre.cpp} | 0
...rrences_getFrequency_range_getFibre.cpp.stdout} | 0
.../iterator.cpp => index/index_iterator.cpp} | 0
.../index_iterator.cpp.stdout} | 0
.../index_iterator_short.cpp} | 0
.../index_iterator_short.cpp.stdout} | 0
demos/index/index_length_countSequences.cpp | 27 +
.../index_length_countSequences.cpp.stdout} | 0
.../{dox/index/mummy.cpp => index/index_mummy.cpp} | 0
.../index_mummy.cpp.stdout} | 0
demos/{dox/index/mums.cpp => index/index_mums.cpp} | 0
.../index_node_predicate.cpp} | 0
demos/index/index_open_save.cpp | 28 +
.../index_open_save.cpp.stdout} | 0
demos/index/index_qgram.cpp | 16 +
.../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 => }/index/ref.fa | 0
.../index/UNUSED_shape.cpp => index/shape.cpp} | 0
.../UNUSED_shape_hash.cpp => index/shape_hash.cpp} | 0
demos/{dox => }/index/shape_hash_init.cpp | 0
.../shape_hash_next.cpp} | 0
demos/index_counting.cpp | 36 +
demos/{unassigned_or_unused => }/index_find.cpp | 0
.../index_find_stringset.cpp | 0
demos/{unassigned_or_unused => }/index_lcp.cpp | 0
.../index/maxrepeats.cpp => index_maxrepeats.cpp} | 0
demos/{unassigned_or_unused => }/index_mums.cpp | 0
.../index_node_predicate.cpp | 0
.../index_qgram_counts.cpp | 0
.../{dox/index/sufarray.cpp => index_sufarray.cpp} | 0
.../index_supermaxrepeats.cpp | 0
demos/input_output/example.fa | 4 +
demos/input_output/seqfile_reader.cpp | 27 +
demos/input_output/seqfile_reader.cpp.stdout | 2 +
.../simple_rna_seq => }/interval_tree.cpp | 0
demos/{unassigned_or_unused => }/iterator.cpp | 0
demos/{unassigned_or_unused => }/knime_node.cpp | 0
demos/{unassigned_or_unused => }/lagan1.fasta | 0
demos/{unassigned_or_unused => }/lagan2.fasta | 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/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
.../modifier_modreverse.cpp | 0
.../modifier_modview.cpp | 0
.../{unassigned_or_unused => }/modifier_nested.cpp | 0
demos/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
.../parse_lm_stellar.cpp | 0
demos/{dox => }/pipe/pool_sorter.cpp | 0
demos/random/random.cpp | 42 +
.../{unassigned_or_unused => }/rooted_iterator.cpp | 0
demos/sam2svg.cpp | 222 +++
demos/{unassigned_or_unused => }/sample_seqs.cpp | 0
demos/{dox => }/score/score.cpp | 0
demos/{dox => }/score/score.cpp.stdout | 0
demos/{unassigned_or_unused => }/seeds.cpp | 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
.../segmentalignment.cpp | 0
demos/{dox => }/seq_io/example.fa | 0
demos/{dox => }/seq_io/example.fa.fai | 0
demos/seq_io/fai_index_example.cpp | 49 +
.../{dox => }/seq_io/fai_index_example.cpp.stdout | 0
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 +
.../UNUSED_infix.cpp => sequence/infix.cpp} | 0
.../UNUSED_prefix.cpp => sequence/prefix.cpp} | 0
demos/sequence/segment.cpp | 98 ++
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
.../UNUSED_suffix.cpp => sequence/suffix.cpp} | 0
demos/{unassigned_or_unused => }/sequence_1.fa | 0
demos/{unassigned_or_unused => }/sequence_2.fa | 0
.../{unassigned_or_unused => }/sequence_length.cpp | 0
.../soft_to_hard_masking.cpp | 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/stream/lexical_cast.cpp | 55 +
demos/{dox => }/stream/lexical_cast.cpp.stdout | 0
.../tutorial/a_first_example/basic_code.cpp.stdout | 1 -
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.../a_first_example/code_encapsulation.cpp.stdout | 1 -
.../a_first_example/final_result.cpp.stdout | 10 -
.../tutorial/a_first_example/solution_1.cpp.stdout | 1 -
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.../tutorial/a_first_example/solution_5.cpp.stdout | 3 -
.../tutorial/a_first_example/solution_6.cpp.stdout | 10 -
.../alignment_representation/align.cpp.stdout | 42 -
.../align_assignment1.cpp.stdout | 1 -
.../alignment_representation/graph.cpp.stdout | 11 -
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demos/tutorial/alignments/CMakeLists.txt | 5 +
.../align.cpp => alignments/alignment2_align.cpp} | 0
.../alignment_align_assignment1.cpp} | 0
.../alignment_banded.cpp | 0
.../tutorial/alignments}/alignment_example.png | Bin
demos/tutorial/alignments/alignment_gaps.cpp | 58 +
.../alignment_global_assignment1.cpp | 0
.../alignment_global_assignment2.cpp | 0
.../alignment_global_assignment3.cpp | 0
.../alignment_global_assignment4_part1.cpp | 40 +
.../alignment_global_assignment4_part2.cpp | 50 +
.../alignment_global_overlap.cpp | 0
.../alignment_global_specialised.cpp | 0
.../alignment_global_standard.cpp | 0
.../alignments/alignment_local_standard.cpp | 30 +
.../alignments/alignment_local_waterman_eggert.cpp | 32 +
.../msa.cpp => alignments/alignment_msa.cpp} | 0
.../alignment_msa.cpp.stdout} | 0
.../alignment_msa_assignment1.cpp} | 0
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.../alignment_msa_consensus.cpp} | 0
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.../alignments/alignment_pairwise_global.cpp | 55 +
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.../alignment_pairwise_local.cpp} | 0
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.../alignment_representation_ag.cpp} | 0
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.../pairwise_sequence_alignment_assignment5.cpp | 136 ++
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...irwise_sequence_alignment_assignment5_step4.cpp | 89 ++
...irwise_sequence_alignment_assignment5_step5.cpp | 101 ++
...irwise_sequence_alignment_assignment5_step6.cpp | 124 ++
.../alphabet_assignment_1_solution.cpp.stdout | Bin 183 -> 0 bytes
.../annotation_store/assignment_1_hint.cpp | 22 +
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.../annotation_store/assignment_2_solution.cpp | 40 +
.../annotation_store/assignment_3_solution.cpp | 28 +
.../annotation_store/assignment_4_solution.cpp | 50 +
.../assignment_annotations.gtf | 0
.../{sam_and_bam_io => bam_io}/example.sam | 0
demos/tutorial/bam_io/example1.cpp | 27 +
demos/tutorial/bam_io/example2.cpp | 21 +
demos/tutorial/bam_io/example3.cpp | 32 +
demos/tutorial/bam_io/example7.cpp | 100 ++
demos/tutorial/bam_io/solution1.cpp | 39 +
demos/tutorial/bam_io/solution2.cpp | 41 +
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demos/tutorial/bam_io/solution6.cpp | 40 +
demos/tutorial/bam_io/solution7.cpp | 43 +
demos/tutorial/base_io/example1.cpp | 38 +
demos/tutorial/base_io/solution1.cpp | 57 +
demos/tutorial/base_io/solution2.cpp | 65 +
demos/tutorial/base_io/solution3.cpp | 73 +
demos/tutorial/basics/CMakeLists.txt | 5 +
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manual/source/Tutorial/AlignmentRepresentation.rst | 30 +-
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manual/source/Tutorial/Metafunctions.rst | 20 +-
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