[med-svn] [seqan] branch master updated (bcd7dab -> 7fe81c3)
Andreas Tille
tille at debian.org
Tue Jul 26 07:20:59 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 bcd7dab Revert "Moved to Git"
new c801d94 Revert "Imported Upstream version 2.0.0+dfsg"
new 4d8986a Revert "Revert "Imported Upstream version 2.0.0+dfsg""
new 10bffb5 Revert "Revert "Moved to Git""
new ab6de15 Revert "Revert "Fix typo in seqan-doc description (d/control)""
new 5dfc303 Revert "Revert "Correct documentation make target name""
new 0e26e1f Revert "Revert "Remove commenting out of find in d/rules""
new dd2baf1 Revert "Revert "Make seqan-doc.docs executable to use dh_exec""
new 0fc9957 Revert "Revert "Add correct section for seqan-doc""
new ac86550 Revert "Revert "Remove a .swp file from the source with a patch""
new 2208219 Revert "Revert "Fix doc-base for seqan-doc""
new 8716f37 Revert "Revert "Add debian hardening flags which cmake will use""
new e57ee1e Revert "Revert "Add swp removal patch to d/source/include-binaries""
new 0b7d594 Revert "Revert "Fix erroneous duplication of Section in seqan-apps""
new 845fcad Revert "Revert "Rename seqan-doc doc-base document name""
new 8703670 Revert "Revert "New minor upstream release""
new b63f133 Revert "Revert "Imported Upstream version 2.0.1+dfsg""
new 5732762 Revert "Revert "Symlink to binaries only if these are part of the binary distribution""
new 4bcec67 Revert "Revert "Depete outdated comment""
new 2170e54 Revert "Revert "Dox target does nothing and no *.html files will be created at all""
new ca74d90 Revert "Revert "Fix string quoting""
new 0fac073 Revert "Revert "Location of file has changed""
new 795e6bf Revert "Revert "Fix symlinks""
new 7d2b61b Revert "Revert "lintian override for false positive""
new 77496ec Revert "Revert "Remove swapfile right from the tarball rather than via patch""
new fa6b571 Revert "Revert "Imported Upstream version 2.0.1+dfsg""
new 129b25e Revert "Revert "More spelling issues""
new 1caac13 Revert "Revert "Tried to create docs but failed""
new 8718dd1 Revert "Revert "The new version should work with gcc-6 according to https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-January/038560.html""
new c140731 Revert "The new version should work with gcc-6 according to https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-January/038560.html"
new 50b262e Revert "Tried to create docs but failed"
new 7fe81c3 Revert "More spelling issues"
The 31 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/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 -
.../basic_code.cpp | 0
.../tutorial/a_first_example/basic_code.cpp.stdout | 1 +
.../basic_code_detailed.cpp | 0
.../a_first_example/basic_code_detailed.cpp.stdout | 1 +
.../code_encapsulation.cpp | 0
.../a_first_example/code_encapsulation.cpp.stdout | 1 +
.../final_result.cpp | 0
.../a_first_example/final_result.cpp.stdout | 10 +
.../solution_1.cpp | 0
.../tutorial/a_first_example/solution_1.cpp.stdout | 1 +
.../solution_2.cpp | 0
.../tutorial/a_first_example/solution_2.cpp.stdout | 1 +
.../solution_3.cpp | 0
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.../solution_4.cpp | 0
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.../solution_5.cpp | 0
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.../solution_6.cpp | 0
.../tutorial/a_first_example/solution_6.cpp.stdout | 10 +
.../align.cpp} | 0
.../alignment_representation/align.cpp.stdout | 42 +
.../align_assignmen1.cpp} | 0
.../align_assignment1.cpp.stdout | 1 +
.../graph.cpp} | 0
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.../graph_assignment1.cpp} | 0
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demos/tutorial/alignments/CMakeLists.txt | 5 -
demos/tutorial/alignments/alignment_example.png | Bin 8633 -> 0 bytes
demos/tutorial/alignments/alignment_gaps.cpp | 58 -
.../alignment_global_assignment4_part1.cpp | 40 -
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.../alignments/alignment_local_waterman_eggert.cpp | 32 -
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.../pairwise_sequence_alignment_assignment5.cpp | 136 --
...irwise_sequence_alignment_assignment5_step1.cpp | 32 -
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.../alphabet_assignment_1_solution.cpp.stdout | Bin 0 -> 183 bytes
.../annotation_store/assignment_1_hint.cpp | 22 -
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demos/tutorial/bam_io/example1.cpp | 27 -
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demos/tutorial/bam_io/example3.cpp | 32 -
demos/tutorial/bam_io/example7.cpp | 100 --
demos/tutorial/bam_io/solution1.cpp | 39 -
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demos/tutorial/base_io/solution1.cpp | 57 -
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demos/tutorial/basics/CMakeLists.txt | 5 -
demos/tutorial/basics/allocator.cpp.stdout | 6 +
demos/tutorial/basics/show_alphabets.cpp.stdout | 3 +
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.../solution_online_search_finder.cpp | 251 ---
demos/tutorial/file_io_overview/example.bam | Bin 0 -> 365 bytes
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demos/tutorial/find/CMakeLists.txt | 5 -
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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%)
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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
create mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment2.cpp
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create mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment3.cpp
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create mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment4.cpp
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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
rename demos/tutorial/{basics => metafunctions}/swap.cpp (100%)
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delete mode 100644 demos/tutorial/mini_bowtie/mini_bowtie.cpp
delete mode 100755 demos/tutorial/mini_bowtie/nc_001454.fasta
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rename demos/tutorial/modifiers/{modifier_modcomplementdna.cpp => UNUSED_modcomplementdna.cpp} (100%)
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%)
rename demos/tutorial/{alignments/alignment_msa.cpp.stdout => multiple_sequence_alignment/msa.cpp.stdout} (100%)
rename demos/tutorial/{alignments => pairwise_sequence_alignment}/alignment_banded.cpp (100%)
create mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_banded.cpp.stdout
rename demos/tutorial/{alignments => pairwise_sequence_alignment}/alignment_global_assignment1.cpp (100%)
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rename demos/tutorial/{alignments => pairwise_sequence_alignment}/alignment_global_assignment2.cpp (100%)
create mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment2.cpp.stdout
rename demos/tutorial/{alignments => pairwise_sequence_alignment}/alignment_global_assignment3.cpp (100%)
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create mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_global_standard.cpp.stdout
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
create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5.cpp.stdout
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
create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp.stdout
create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp
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create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp
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create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp
create mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp.stdout
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%)
create mode 100644 demos/tutorial/pattern_matching/assignment2.cpp.stdout
rename demos/tutorial/{find/find_assignment2_solution.cpp => pattern_matching/assignment2_solution.cpp} (100%)
create mode 100644 demos/tutorial/pattern_matching/assignment2_solution.cpp.stdout
rename demos/tutorial/{find/find_assignment3.cpp => pattern_matching/assignment3.cpp} (100%)
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rename demos/tutorial/{find/find_assignment3_solution.cpp => pattern_matching/assignment3_solution.cpp} (100%)
create mode 100644 demos/tutorial/pattern_matching/assignment3_solution.cpp.stdout
rename demos/tutorial/{find => pattern_matching}/find_approx.cpp (100%)
create mode 100644 demos/tutorial/pattern_matching/find_approx.cpp.stdout
rename demos/tutorial/{find => pattern_matching}/find_exact.cpp (100%)
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rename demos/tutorial/{find => pattern_matching}/find_index.cpp (100%)
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rename demos/tutorial/{find => pattern_matching}/find_index_multiple.cpp (100%)
create mode 100644 demos/tutorial/pattern_matching/find_index_multiple.cpp.stdout
rename demos/tutorial/{index => q_gram_index}/index_assignment5.cpp (100%)
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rename demos/tutorial/{index => q_gram_index}/index_assignment6.cpp (100%)
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rename demos/tutorial/{index => q_gram_index}/index_qgram.cpp (100%)
create mode 100644 demos/tutorial/q_gram_index/index_qgram.cpp.stdout
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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create mode 100644 demos/tutorial/randomness/examples.cpp
create mode 100644 demos/tutorial/randomness/examples.cpp.stdout
delete mode 100644 demos/tutorial/read_mapping/CMakeLists.txt
delete mode 100644 demos/tutorial/read_mapping/nc_001454.fasta
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delete mode 100644 demos/tutorial/read_mapping/reads_hamming.fasta
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delete mode 100644 demos/tutorial/realign/step2.cpp
rename demos/tutorial/{realign => realignment}/reads.sam (100%)
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
rename demos/tutorial/{realign => realignment}/step2.cpp.stdout (100%)
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
create mode 100644 demos/tutorial/sam_and_bam_io/example7.cpp.stdout
create mode 100644 demos/tutorial/sam_and_bam_io/solution1.cpp
create mode 100644 demos/tutorial/sam_and_bam_io/solution1.cpp.stdout
create mode 100644 demos/tutorial/sam_and_bam_io/solution2.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
create mode 100644 demos/tutorial/seed_and_extend/example2.cpp.stdout
create mode 100644 demos/tutorial/seed_and_extend/example3.cpp.stdout
create mode 100644 demos/tutorial/seed_and_extend/example4.cpp.stdout
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
create mode 100644 demos/tutorial/seed_and_extend/solution2.cpp.stdout
create mode 100644 demos/tutorial/seed_and_extend/solution3.cpp.stdout
create mode 100644 demos/tutorial/seed_and_extend/solution4.cpp.stdout
create mode 100644 demos/tutorial/seed_and_extend/solution5.cpp.stdout
copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/seed_and_extend/solution6.cpp.stdout (100%)
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_3_solution.cpp
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rename demos/tutorial/sequences/{lexical_assignment_solution.cpp => assignment_4_solution.cpp} (100%)
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%)
create mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment4.cpp
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
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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
rename demos/{ => tutorial/simple_rna_seq}/interval_tree.cpp (100%)
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
delete mode 100644 demos/tutorial/store/store_access_aligned_reads2.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
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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%)
rename demos/{tutorial/file_io => unassigned_or_unused/tutorial_file_io}/solution1.cpp (100%)
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
delete mode 100644 demos/vcf_io/vcf_stream_read.cpp.stdout
mode change 100755 => 100644 include/seqan/basic/iterator_range.h
mode change 100755 => 100644 include/seqan/index/shape_threshold.h
mode change 100755 => 100644 include/seqan/misc/name_store_cache.h
mode change 100755 => 100644 include/seqan/random/ext_MersenneTwister.h
delete mode 100644 include/seqan/statistics/.statistics_markov_model.h.swp
mode change 100755 => 100644 include/seqan/store/store_io_ucsc.h
create mode 100644 include/seqan/stream/iostream_bgzf.h
create mode 100644 include/seqan/stream/iostream_bzip2.h
create mode 100644 include/seqan/stream/iostream_bzip2_impl.h
create mode 100644 include/seqan/stream/iostream_zip.h
create mode 100644 include/seqan/stream/iostream_zip_impl.h
create mode 100644 include/seqan/stream/iostream_zutil.h
delete mode 100644 include/seqan/stream/zipstream/bgzfstream.h
delete mode 100644 include/seqan/stream/zipstream/bgzfstream_impl.h
delete mode 100644 include/seqan/stream/zipstream/bzip2stream.h
delete mode 100644 include/seqan/stream/zipstream/bzip2stream_impl.h
delete mode 100644 include/seqan/stream/zipstream/zipstream.h
delete mode 100644 include/seqan/stream/zipstream/zipstream_impl.h
delete mode 100644 include/seqan/stream/zipstream/zutil.h
delete mode 100644 manual/source/HowTo/knime_node_app.zip
create mode 100644 manual/source/Tutorial/AFirstExample.rst
delete mode 100644 manual/source/Tutorial/AnnotationStore.rst
create mode 100644 manual/source/Tutorial/FileIOOverview.rst
delete mode 100644 manual/source/Tutorial/FirstStepsInSeqAn.rst
rename manual/source/Tutorial/{TemplateSubclassing.rst => GenericProgramming.rst} (100%)
create mode 100644 manual/source/Tutorial/GenomeAnnotations.rst
create mode 100644 manual/source/Tutorial/GffAndGtfIO.rst
delete mode 100644 manual/source/Tutorial/GffGtfIO.rst
delete mode 100644 manual/source/Tutorial/IndexQGram.rst
delete mode 100644 manual/source/Tutorial/InputOutputOverview.rst
delete mode 100644 manual/source/Tutorial/JournalSet.rst
create mode 100644 manual/source/Tutorial/JournaledSet.rst
delete mode 100644 manual/source/Tutorial/MiniBowtie.rst
create mode 100644 manual/source/Tutorial/QgramIndex.rst
create mode 100644 manual/source/Tutorial/SamAndBamIO.rst
delete mode 100644 manual/source/Tutorial/SamBamIO.rst
delete mode 100644 manual/source/Tutorial/SimpleReadMapping.rst
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
delete mode 100755 util/py_lib/seqan/dox/tpl/lib/bootstrap-multiselect/js/bootstrap-3.0.0.min.js
delete mode 100644 util/py_lib/seqan/dox/tpl/lib/bootstrap-multiselect/js/jquery-2.0.3.min.js
delete mode 100644 util/py_lib/seqan/dox/tpl/lib/bootstrap-multiselect/js/prettify.js
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