[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       new  9e16195   Revert "Depete outdated comment"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 -
 .../a_first_example/basic_code_detailed.cpp.stdout |    1 -
 .../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 -
 .../tutorial/a_first_example/solution_2.cpp.stdout |    1 -
 .../tutorial/a_first_example/solution_3.cpp.stdout |    1 -
 .../tutorial/a_first_example/solution_4.cpp.stdout |    1 -
 .../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 -
 .../graph_assignment1.cpp.stdout                   |   10 -
 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
 .../alignment_msa_assignment1.cpp.stdout}          |    0
 .../alignment_msa_consensus.cpp}                   |    0
 .../alignment_msa_consensus.cpp.stdout}            |    0
 .../alignments/alignment_pairwise_global.cpp       |   55 +
 .../alignments/alignment_pairwise_global2.cpp      |   45 +
 .../alignment_pairwise_global_assignment1.cpp      |   51 +
 .../alignment_pairwise_global_assignment2.cpp      |   30 +
 .../alignment_pairwise_local.cpp}                  |    0
 .../alignment_pairwise_local_assignment1.cpp}      |    0
 .../alignment_representation_ag.cpp}               |    0
 .../alignment_representation_ag_assignment1.cpp}   |    0
 .../pairwise_sequence_alignment_assignment5.cpp    |  136 ++
 ...irwise_sequence_alignment_assignment5_step1.cpp |   32 +
 ...irwise_sequence_alignment_assignment5_step2.cpp |   53 +
 ...irwise_sequence_alignment_assignment5_step3.cpp |   68 +
 ...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 +
 .../annotation_store/assignment_1_solution.cpp     |   26 +
 .../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 +
 demos/tutorial/bam_io/solution3.cpp                |   44 +
 demos/tutorial/bam_io/solution4.cpp                |   67 +
 demos/tutorial/bam_io/solution5.cpp                |   47 +
 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 +
 demos/tutorial/basics/allocator.cpp.stdout         |    6 -
 demos/tutorial/basics/show_alphabets.cpp.stdout    |    3 -
 demos/tutorial/basics/strings.cpp.stdout           |   28 -
 demos/tutorial/{metafunctions => basics}/swap.cpp  |    0
 demos/tutorial/bed_io/example.bed                  |    5 -
 demos/tutorial/bed_io/example1.cpp                 |    3 +-
 demos/tutorial/bed_io/example1.cpp.stdout          |    0
 demos/tutorial/bed_io/solution1.cpp                |    2 +-
 demos/tutorial/bed_io/solution1.cpp.stdout         |    0
 demos/tutorial/bed_io/solution2.cpp                |    2 +-
 demos/tutorial/bed_io/solution2.cpp.stdout         |    0
 demos/tutorial/bed_io/solution3.cpp.stdout         |    2 -
 demos/tutorial/blast_io/read_assignment.cpp.stdout |    0
 .../tutorial/blast_io/write_assignment.cpp.stdout  |    0
 .../with_positions.cpp                             |    0
 .../with_positions.cpp.stdout                      |    0
 .../without_positions.cpp                          |    0
 .../without_positions.cpp.stdout                   |    0
 .../custom_io}/NC_001405.fasta                     |    0
 .../custom_io}/NC_001460.fasta                     |    0
 .../custom_io}/blast_example.txt                   |    0
 .../custom_io}/example1.cpp                        |    0
 .../custom_io}/gff2_example.txt                    |    0
 .../custom_io}/newick_example.txt                  |    0
 .../custom_io}/parse_blastn.cpp                    |    0
 .../custom_io}/parse_gff2.cpp                      |    0
 .../custom_io}/reader_demo.cpp                     |    0
 .../custom_io}/solution1.cpp                       |    0
 .../custom_io}/solution2.cpp                       |    0
 .../custom_io}/solution3.cpp                       |    0
 .../custom_io}/solution4.cpp                       |    0
 .../example_join.cpp                               |    0
 .../example_journal_string_basic.cpp               |   47 +
 .../data_journaling/example_online_search.cpp      |  307 ++++
 .../example_online_search_assignment1_hint.cpp     |   58 +
 .../example_online_search_assignment2_hint.cpp     |   27 +
 .../example_online_search_assignment3_hint.cpp     |   30 +
 .../example_online_search_assignment4_hint.cpp     |   28 +
 .../solution_online_search_assignment1.cpp         |   62 +
 .../solution_online_search_assignment2.cpp         |  147 ++
 .../solution_online_search_assignment3.cpp         |  222 +++
 .../solution_online_search_assignment4.cpp         |  294 ++++
 .../solution_online_search_finder.cpp              |  251 +++
 .../file_io}/example1.cpp                          |    0
 .../file_io}/mmap_string_example.cpp               |    0
 .../file_io}/solution1.cpp                         |    0
 .../file_io}/solution2.cpp                         |    0
 .../file_io}/solution3.cpp                         |    0
 .../file_io}/stream_compression_formats.cpp        |    0
 demos/tutorial/file_io_overview/example.bam        |  Bin 365 -> 0 bytes
 demos/tutorial/file_io_overview/example.sam        |    9 -
 demos/tutorial/file_io_overview/example1.cpp       |   39 -
 .../tutorial/file_io_overview/example1.cpp.stdout  |    0
 demos/tutorial/file_io_overview/solution1.cpp      |   49 -
 .../tutorial/file_io_overview/solution1.cpp.stdout |    0
 demos/tutorial/file_io_overview/solution2.cpp      |   56 -
 .../tutorial/file_io_overview/solution2.cpp.stdout |    0
 demos/tutorial/file_io_overview/solution3.cpp      |   56 -
 .../tutorial/file_io_overview/solution3.cpp.stdout |    9 -
 demos/tutorial/find/CMakeLists.txt                 |    5 +
 .../{pattern_matching => find}/find_approx.cpp     |    0
 .../assignment1.cpp => find/find_assignment1.cpp}  |    0
 .../find_assignment1_solution.cpp}                 |    0
 .../assignment2.cpp => find/find_assignment2.cpp}  |    0
 .../find_assignment2_solution.cpp}                 |    0
 .../assignment3.cpp => find/find_assignment3.cpp}  |    0
 .../find_assignment3_solution.cpp}                 |    0
 .../{pattern_matching => find}/find_exact.cpp      |    0
 .../{pattern_matching => find}/find_index.cpp      |    0
 .../find_index_multiple.cpp                        |    0
 .../basic_code.cpp                                 |    0
 .../basic_code_detailed.cpp                        |    0
 .../code_encapsulation.cpp                         |    0
 .../final_result.cpp                               |    0
 .../solution_1.cpp                                 |    0
 .../solution_2.cpp                                 |    0
 .../solution_3.cpp                                 |    0
 .../solution_4.cpp                                 |    0
 .../solution_5.cpp                                 |    0
 .../solution_6.cpp                                 |    0
 .../fragment_store/access_aligned_reads.cpp        |   63 -
 .../fragment_store/access_aligned_reads.cpp.stdout |   20 -
 .../fragment_store/access_aligned_reads2.cpp       |   66 -
 .../access_aligned_reads2.cpp.stdout               |   20 -
 .../fragment_store/display_aligned_reads.cpp       |   34 -
 .../display_aligned_reads.cpp.stdout               |   37 -
 .../template_subclassing.cpp.stdout                |    5 -
 .../genome_annotations/assignment_1_hint.cpp       |   23 -
 .../assignment_1_hint.cpp.stdout                   |    1 -
 .../genome_annotations/assignment_1_solution.cpp   |   29 -
 .../assignment_1_solution.cpp.stdout               |    2 -
 .../genome_annotations/assignment_2_solution.cpp   |   42 -
 .../assignment_2_solution.cpp.stdout               |    4 -
 .../genome_annotations/assignment_3_solution.cpp   |   29 -
 .../assignment_3_solution.cpp.stdout               |    6 -
 .../genome_annotations/assignment_4_solution.cpp   |   51 -
 .../assignment_4_solution.cpp.stdout               |    3 -
 demos/tutorial/genome_annotations/base.cpp         |   69 -
 demos/tutorial/genome_annotations/base.cpp.stdout  |    7 -
 demos/tutorial/genome_annotations/example.gtf      |    4 -
 demos/tutorial/getting_started/CMakeLists.txt      |    5 +
 .../tutorial/getting_started/cmd_dir_build_src.png |  Bin 0 -> 23654 bytes
 .../eclipse_convert_to_cpp_project.png             |  Bin 0 -> 43575 bytes
 .../getting_started/eclipse_hello_world.png        |  Bin 0 -> 4847 bytes
 .../eclipse_import_build_project.png               |  Bin 0 -> 87749 bytes
 .../eclipse_new_repository_location.png            |  Bin 0 -> 58449 bytes
 .../eclipse_preference_build_on_launch.png         |  Bin 0 -> 54319 bytes
 .../getting_started/eclipse_required_plugins.png   |  Bin 0 -> 113708 bytes
 .../getting_started/eclipse_run_configurations.png |  Bin 0 -> 56172 bytes
 .../getting_started/mingw_installation.png         |  Bin 0 -> 45348 bytes
 .../getting_started/repository_overview.pptx       |  Bin 0 -> 120459 bytes
 .../getting_started/repository_overview/Folie1.jpg |  Bin 0 -> 100850 bytes
 .../getting_started/win_command_arguments.jpg      |  Bin 0 -> 127597 bytes
 demos/tutorial/getting_started/win_new_file.jpg    |  Bin 0 -> 79513 bytes
 demos/tutorial/getting_started/win_save_file.jpg   |  Bin 0 -> 74650 bytes
 .../getting_started/win_solution_explorer.png      |  Bin 0 -> 39118 bytes
 .../getting_started/win_start_up_project.png       |  Bin 0 -> 42641 bytes
 demos/tutorial/getting_started/win_tortoise.png    |  Bin 0 -> 9686 bytes
 demos/tutorial/getting_started/xcode/base_sdk.png  |  Bin 0 -> 292747 bytes
 .../getting_started/xcode/base_sdk_selection.png   |  Bin 0 -> 19604 bytes
 .../xcode}/download-command-line-tools.png         |  Bin
 .../getting_started/xcode/first_app_new.png        |  Bin 0 -> 308287 bytes
 .../getting_started/xcode/first_app_old.png        |  Bin 0 -> 381585 bytes
 .../getting_started/xcode}/razers2_built.png       |  Bin
 .../getting_started/xcode}/razers2_selection.png   |  Bin
 .../xcode/test_stream_selection.png                |  Bin 0 -> 18397 bytes
 .../getting_started/xcode}/xcode_startup.png       |  Bin
 demos/tutorial/getting_started/xcode_first_app.jpg |  Bin 0 -> 145898 bytes
 .../getting_started/xcode_start_up_view.png        |  Bin 0 -> 81291 bytes
 demos/tutorial/gff_and_gtf_io/example.gff          |   23 -
 demos/tutorial/gff_and_gtf_io/example1.cpp         |   26 -
 demos/tutorial/gff_and_gtf_io/example1.cpp.stdout  |   23 -
 demos/tutorial/gff_and_gtf_io/example2.cpp         |   26 -
 demos/tutorial/gff_and_gtf_io/example2.cpp.stdout  |   23 -
 demos/tutorial/gff_and_gtf_io/solution1.cpp        |   39 -
 demos/tutorial/gff_and_gtf_io/solution1.cpp.stdout |   23 -
 demos/tutorial/gff_and_gtf_io/solution2.cpp        |   51 -
 demos/tutorial/gff_and_gtf_io/solution2.cpp.stdout |    2 -
 demos/tutorial/gff_and_gtf_io/solution3.cpp.stdout |    2 -
 demos/tutorial/gff_io/example1.cpp                 |   22 +
 demos/tutorial/gff_io/example2.cpp                 |   22 +
 demos/tutorial/gff_io/solution1.cpp                |   36 +
 demos/tutorial/gff_io/solution2.cpp                |   48 +
 .../{gff_and_gtf_io => gff_io}/solution3.cpp       |    0
 demos/tutorial/graph/CMakeLists.txt                |    5 +
 demos/tutorial/graph/graph_algo_scc.cpp            |    1 +
 demos/tutorial/graph/graph_algo_scc.cpp.stdout     |   35 -
 demos/tutorial/graph/graph_dijkstra.cpp.stdout     |   10 -
 demos/tutorial/graph/graph_hmm.cpp                 |    1 +
 demos/tutorial/graph/graph_hmm.cpp.stdout          |   26 -
 demos/tutorial/graph/solution_1.cpp.stdout         |   10 -
 demos/tutorial/index/CMakeLists.txt                |    5 +
 .../index_assignment1.cpp                          |    0
 .../index_assignment2.cpp                          |    0
 .../index_assignment3.cpp}                         |    0
 .../index_assignment4.cpp                          |    0
 .../{q_gram_index => index}/index_assignment5.cpp  |    0
 .../{q_gram_index => index}/index_assignment6.cpp  |    0
 .../{index_iterators => index}/index_preorder.cpp  |    0
 .../index_property_maps.cpp                        |    0
 .../{q_gram_index => index}/index_qgram.cpp        |    0
 .../{q_gram_index => index}/index_qgram_hash.cpp   |    0
 .../{index_iterators => index}/index_search.cpp    |    0
 .../{index_iterators => index}/index_search2.cpp   |    0
 .../indices_assignment_1.cpp}                      |    0
 .../indices_assignment_2.cpp}                      |    0
 .../iterator_solution1.cpp                         |    0
 .../iterator_solution2.cpp                         |    0
 .../UNUSED_index_assignment3.cpp.stdout            |   16 -
 .../index_iterators/index_assignment1.cpp.stdout   |  111 --
 .../index_iterators/index_assignment2.cpp.stdout   |    3 -
 .../index_iterators/index_assignment4.cpp.stdout   |   14 -
 .../index_iterators/index_preorder.cpp.stdout      |   12 -
 .../index_iterators/index_property_maps.cpp.stdout |   12 -
 .../index_iterators/index_search.cpp.stdout        |    5 -
 .../index_iterators/index_search2.cpp.stdout       |    2 -
 .../index_iterators/iterator_solution1.cpp.stdout  |    5 -
 .../index_iterators/iterator_solution2.cpp.stdout  |   16 -
 demos/tutorial/indices/assignment_1.cpp.stdout     |    0
 demos/tutorial/indices/assignment_2.cpp.stdout     |    2 -
 .../iterators/assignment_1_solution.cpp.stdout     |    1 -
 .../iterators/assignment_2_solution.cpp.stdout     |    1 -
 .../iterators/assignment_3_workshop_solution.cpp   |   82 -
 .../assignment_3_workshop_solution.cpp.stdout      |   34 -
 .../iterators/assignment_4_workshop_solution.cpp   |   91 --
 .../assignment_4_workshop_solution.cpp.stdout      |   48 -
 ...ion.cpp => iterators_assignment_1_solution.cpp} |    0
 ...ion.cpp => iterators_assignment_2_solution.cpp} |    0
 .../iterators_assignment_3_workshop_solution.cpp   |   82 +
 .../iterators_assignment_4_workshop_solution.cpp   |   91 ++
 .../iterators/sequence_iterator_demo.cpp.stdout    |    5 -
 .../tutorial/journaled_set/example_join.cpp.stdout |    4 -
 .../journaled_set/example_journal_string_basic.cpp |   47 -
 .../example_journal_string_basic.cpp.stdout        |   14 -
 .../journaled_set/example_online_search.cpp        |  309 ----
 .../journaled_set/example_online_search.cpp.stdout |    9 -
 .../example_online_search_assignment1_hint.cpp     |   62 -
 ...ample_online_search_assignment1_hint.cpp.stdout |    1 -
 demos/tutorial/journaled_set/sequences.fasta       |  111 --
 .../solution_online_search_assignment1.cpp         |   62 -
 .../solution_online_search_assignment1.cpp.stdout  |    1 -
 .../solution_online_search_assignment2.cpp         |  148 --
 .../solution_online_search_assignment2.cpp.stdout  |    3 -
 .../solution_online_search_assignment3.cpp         |  223 ---
 .../solution_online_search_assignment3.cpp.stdout  |    9 -
 .../solution_online_search_assignment4.cpp         |  294 ----
 .../solution_online_search_assignment4.cpp.stdout  |    9 -
 .../solution_online_search_finder.cpp              |  252 ---
 .../solution_online_search_finder.cpp.stdout       |    9 -
 demos/tutorial/metafunctions/swap.cpp.stdout       |    2 -
 demos/tutorial/mini_bowtie/mini_bowtie.cpp         |  138 ++
 demos/tutorial/mini_bowtie/nc_001454.fasta         |  491 ++++++
 demos/tutorial/mini_bowtie/reads_hamming.fasta     |   20 +
 demos/tutorial/mini_bowtie/solution1.cpp           |   65 +
 demos/tutorial/mini_bowtie/solution2.cpp           |   82 +
 demos/tutorial/mini_bowtie/solution3.cpp           |   89 ++
 demos/tutorial/mini_bowtie/solution4.cpp           |  103 ++
 demos/tutorial/mini_bowtie/solution5.cpp           |  138 ++
 .../modifiers/UNUSED_modcomplementdna.cpp.stdout   |    2 -
 demos/tutorial/modifiers/UNUSED_modview.cpp.stdout |    4 -
 demos/tutorial/modifiers/UNUSED_nested.cpp.stdout  |    5 -
 demos/tutorial/modifiers/assignment1.cpp.stdout    |    3 -
 .../modifiers/assignment1_solution.cpp.stdout      |    5 -
 ...lementdna.cpp => modifier_modcomplementdna.cpp} |    0
 .../{modreverse.cpp => modifier_modreverse.cpp}    |    0
 .../{UNUSED_modview.cpp => modifier_modview.cpp}   |    0
 .../{UNUSED_nested.cpp => modifier_nested.cpp}     |    0
 demos/tutorial/modifiers/modreverse.cpp.stdout     |    4 -
 .../alignment_banded.cpp.stdout                    |    8 -
 .../alignment_global_assignment1.cpp.stdout        |    8 -
 .../alignment_global_assignment2.cpp.stdout        |    9 -
 .../alignment_global_assignment3.cpp.stdout        |   15 -
 .../alignment_global_overlap.cpp.stdout            |    9 -
 .../alignment_global_specialised.cpp.stdout        |    8 -
 .../alignment_global_standard.cpp.stdout           |    8 -
 .../alignment_local.cpp.stdout                     |   27 -
 .../alignment_local_assignment1.cpp.stdout         |   21 -
 .../pairwise_sequence_alignment/assignment5.cpp    |  135 --
 .../assignment5.cpp.stdout                         |    8 -
 .../assignment5_step1.cpp                          |   28 -
 .../assignment5_step1.cpp.stdout                   |    0
 .../assignment5_step2.cpp                          |   51 -
 .../assignment5_step2.cpp.stdout                   |    8 -
 .../assignment5_step3.cpp                          |   67 -
 .../assignment5_step3.cpp.stdout                   |    8 -
 .../assignment5_step4.cpp                          |   88 --
 .../assignment5_step4.cpp.stdout                   |    8 -
 .../assignment5_step5.cpp                          |  100 --
 .../assignment5_step5.cpp.stdout                   |    8 -
 .../assignment5_step6.cpp                          |  123 --
 .../assignment5_step6.cpp.stdout                   |    8 -
 .../assignment2_solution.cpp                       |   43 -
 .../assignment3_solution.cpp                       |   44 -
 .../assignment4_solution.cpp                       |  114 --
 .../assignment5_solution.cpp                       |  124 --
 .../assignment6_solution.cpp                       |  106 --
 .../parsing_command_line_arguments/example1.cpp    |   39 -
 .../example1_detailed.cpp                          |   52 -
 .../example_with_modifyString.cpp                  |  103 --
 .../example_with_own_function.cpp                  |   79 -
 .../example_with_struct.cpp                        |   55 -
 .../final_solution.cpp                             |  117 --
 .../pattern_matching/assignment1.cpp.stdout        |    0
 .../assignment1_solution.cpp.stdout                |    5 -
 .../pattern_matching/assignment2.cpp.stdout        |   12 -
 .../assignment2_solution.cpp.stdout                |   12 -
 .../pattern_matching/assignment3.cpp.stdout        |    2 -
 .../assignment3_solution.cpp.stdout                |    2 -
 .../pattern_matching/find_approx.cpp.stdout        |    8 -
 .../pattern_matching/find_exact.cpp.stdout         |    3 -
 .../pattern_matching/find_index.cpp.stdout         |    4 -
 .../find_index_multiple.cpp.stdout                 |    4 -
 .../q_gram_index/index_assignment5.cpp.stdout      |    2 -
 .../q_gram_index/index_assignment6.cpp.stdout      |   20 -
 demos/tutorial/q_gram_index/index_qgram.cpp.stdout |    2 -
 .../q_gram_index/index_qgram_hash.cpp.stdout       |    1 -
 demos/tutorial/random/CMakeLists.txt               |    5 +
 demos/tutorial/random/random_examples.cpp          |   55 +
 demos/tutorial/randomness/examples.cpp             |   55 -
 demos/tutorial/randomness/examples.cpp.stdout      |    8 -
 demos/tutorial/read_mapping/CMakeLists.txt         |    5 +
 .../read_mapping}/minimapper.cpp                   |    0
 demos/tutorial/read_mapping/nc_001454.fasta        |  491 ++++++
 demos/tutorial/read_mapping/reads_edit.fasta       |   20 +
 demos/tutorial/read_mapping/reads_hamming.fasta    |   20 +
 demos/tutorial/{realignment => realign}/reads.sam  |    0
 demos/tutorial/{realignment => realign}/ref.fa     |    0
 demos/tutorial/realign/step1.cpp                   |   32 +
 .../{realignment => realign}/step1.cpp.stdout      |    0
 demos/tutorial/realign/step2.cpp                   |   36 +
 .../{realignment => realign}/step2.cpp.stdout      |    0
 demos/tutorial/realignment/step1.cpp               |   27 -
 demos/tutorial/realignment/step2.cpp               |   31 -
 demos/tutorial/rnaseq/CMakeLists.txt               |   13 +
 demos/tutorial/rnaseq/genequant_assignment1.cpp    |   73 +
 demos/tutorial/rnaseq/genequant_assignment2.cpp    |  121 ++
 demos/tutorial/rnaseq/genequant_assignment3.cpp    |  155 ++
 demos/tutorial/rnaseq/genequant_assignment4.cpp    |  172 ++
 demos/tutorial/rnaseq/genequant_assignment5.cpp    |  198 +++
 demos/tutorial/rnaseq/genequant_solution1.cpp      |   95 ++
 demos/tutorial/rnaseq/genequant_solution2.cpp      |  131 ++
 demos/tutorial/rnaseq/genequant_solution3.cpp      |  148 ++
 demos/tutorial/rnaseq/genequant_solution4.cpp      |  180 +++
 demos/tutorial/rnaseq/genequant_solution5.cpp      |  229 +++
 demos/tutorial/sam_and_bam_io/example.bam          |  Bin 365 -> 0 bytes
 demos/tutorial/sam_and_bam_io/example.bam.bai      |  Bin 104 -> 0 bytes
 demos/tutorial/sam_and_bam_io/example1.cpp         |   29 -
 demos/tutorial/sam_and_bam_io/example1.cpp.stdout  |    9 -
 demos/tutorial/sam_and_bam_io/example2.cpp         |   23 -
 demos/tutorial/sam_and_bam_io/example2.cpp.stdout  |    2 -
 demos/tutorial/sam_and_bam_io/example7.cpp         |   82 -
 demos/tutorial/sam_and_bam_io/example7.cpp.stdout  |    3 -
 demos/tutorial/sam_and_bam_io/solution1.cpp        |   41 -
 demos/tutorial/sam_and_bam_io/solution1.cpp.stdout |    9 -
 demos/tutorial/sam_and_bam_io/solution2.cpp        |   43 -
 demos/tutorial/sam_and_bam_io/solution2.cpp.stdout |    1 -
 demos/tutorial/sam_and_bam_io/solution3.cpp        |   46 -
 demos/tutorial/sam_and_bam_io/solution3.cpp.stdout |    1 -
 demos/tutorial/seed_and_extend/example1.cpp.stdout |   16 -
 demos/tutorial/seed_and_extend/example2.cpp.stdout |    6 -
 demos/tutorial/seed_and_extend/example3.cpp.stdout |    6 -
 demos/tutorial/seed_and_extend/example4.cpp        |    2 +-
 demos/tutorial/seed_and_extend/example4.cpp.stdout |    8 -
 demos/tutorial/seed_and_extend/example5.cpp.stdout |    5 -
 demos/tutorial/seed_and_extend/example6.cpp.stdout |    0
 demos/tutorial/seed_and_extend/example7.cpp.stdout |    4 -
 demos/tutorial/seed_and_extend/example8.cpp.stdout |    8 -
 .../tutorial/seed_and_extend/solution1.cpp.stdout  |    8 -
 .../tutorial/seed_and_extend/solution2.cpp.stdout  |    6 -
 .../tutorial/seed_and_extend/solution3.cpp.stdout  |    6 -
 demos/tutorial/seed_and_extend/solution4.cpp       |    3 +-
 .../tutorial/seed_and_extend/solution4.cpp.stdout  |    8 -
 .../tutorial/seed_and_extend/solution5.cpp.stdout  |    4 -
 .../tutorial/seed_and_extend/solution6.cpp.stdout  |    0
 .../tutorial/seed_and_extend/solution7.cpp.stdout  |    8 -
 demos/tutorial/seq_io/example1.cpp                 |   15 +
 demos/tutorial/seq_io/solution1.cpp                |   21 +
 demos/tutorial/seq_io/solution2.cpp                |   36 +
 demos/tutorial/seq_io/solution3.cpp                |   37 +
 demos/tutorial/seq_io/solution4.cpp                |   38 +
 .../sequence}/CMakeLists.txt                       |    0
 .../sequence}/count_characters.cpp                 |    0
 .../sequence}/count_generic_characters.cpp         |    0
 .../sequence}/replace_as.cpp                       |    0
 .../sequence}/sequence_all_strings.cpp             |    0
 .../sequence}/sequence_iterator_demo.cpp           |    0
 demos/tutorial/sequence_io/example.fa              |    6 -
 demos/tutorial/sequence_io/example.fq              |   12 -
 demos/tutorial/sequence_io/example1.cpp            |   16 -
 demos/tutorial/sequence_io/example1.cpp.stdout     |    1 -
 demos/tutorial/sequence_io/solution1.cpp           |   16 -
 demos/tutorial/sequence_io/solution1.cpp.stdout    |    1 -
 demos/tutorial/sequence_io/solution2.cpp           |   31 -
 demos/tutorial/sequence_io/solution2.cpp.stdout    |    1 -
 demos/tutorial/sequence_io/solution3.cpp           |   33 -
 demos/tutorial/sequence_io/solution3.cpp.stdout    |    3 -
 demos/tutorial/sequence_io/solution4.cpp           |   34 -
 demos/tutorial/sequence_io/solution4.cpp.stdout    |    3 -
 demos/tutorial/sequences/assignment_1_solution.cpp |   47 -
 .../sequences/assignment_1_solution.cpp.stdout     |    3 -
 demos/tutorial/sequences/assignment_2_solution.cpp |   86 -
 .../sequences/assignment_2_solution.cpp.stdout     |   20 -
 demos/tutorial/sequences/assignment_3_solution.cpp |   22 -
 .../sequences/assignment_3_solution.cpp.stdout     |    2 -
 .../sequences/assignment_4_solution.cpp.stdout     |    4 -
 demos/tutorial/sequences/assignment_5_solution.cpp |   42 -
 .../sequences/assignment_5_solution.cpp.stdout     |    3 -
 ...olution.cpp => lexical_assignment_solution.cpp} |    0
 ...tion.cpp => segments_assignment_2_solution.cpp} |    0
 .../sequences/segments_assignment_hint.cpp         |   38 +
 .../sequences/segments_assignment_solution.cpp     |   33 +
 .../sequences/string_assignment_1_solution.cpp     |   67 +
 .../assignment_exact_generous_solution.cpp         |   22 +-
 .../assignment_exact_generous_solution.cpp.stdout  |    4 -
 .../sequences_in_depth/example_overflow.cpp        |   19 -
 .../sequences_in_depth/example_overflow.cpp.stdout |    2 -
 demos/tutorial/simple_rna_seq/example.gtf          |   12 -
 demos/tutorial/simple_rna_seq/example.sam          |   22 -
 .../simple_rna_seq/genequant_assignment1.cpp       |   34 -
 .../genequant_assignment1.cpp.stdout               |    0
 .../simple_rna_seq/genequant_assignment2.cpp       |   83 -
 .../genequant_assignment2.cpp.stdout               |    0
 .../simple_rna_seq/genequant_assignment3.cpp       |  116 --
 .../genequant_assignment3.cpp.stdout               |    0
 .../simple_rna_seq/genequant_assignment4.cpp       |  136 --
 .../genequant_assignment4.cpp.stdout               |    0
 .../simple_rna_seq/genequant_assignment5.cpp       |  163 --
 .../genequant_assignment5.cpp.stdout               |    0
 .../simple_rna_seq/genequant_solution1.cpp         |   55 -
 .../simple_rna_seq/genequant_solution1.cpp.stdout  |    2 -
 .../simple_rna_seq/genequant_solution2.cpp         |   92 --
 .../simple_rna_seq/genequant_solution2.cpp.stdout  |    2 -
 .../simple_rna_seq/genequant_solution3.cpp         |  109 --
 .../simple_rna_seq/genequant_solution3.cpp.stdout  |    2 -
 .../simple_rna_seq/genequant_solution4.cpp         |  143 --
 .../simple_rna_seq/genequant_solution4.cpp.stdout  |    2 -
 .../simple_rna_seq/genequant_solution5.cpp         |  191 ---
 .../simple_rna_seq/genequant_solution5.cpp.stdout  |    3 -
 .../simple_rna_seq/interval_tree.cpp.stdout        |    4 -
 demos/tutorial/store/CMakeLists.txt                |    5 +
 .../{fragment_store/example.fa => store/ex1.fa}    |    0
 .../{fragment_store/example.sam => store/ex1.sam}  |    0
 .../tutorial/store/store_access_aligned_reads.cpp  |   61 +
 .../tutorial/store/store_access_aligned_reads2.cpp |   64 +
 .../tutorial/store/store_diplay_aligned_reads.cpp  |   28 +
 .../string_sets/assignment_1_solution.cpp.stdout   |    5 -
 .../string_sets/assignment_2_solution.cpp.stdout   |    2 -
 .../string_sets/assignment_3_workshop_solution.cpp |   24 +-
 .../assignment_3_workshop_solution.cpp.stdout      |   48 -
 .../assignment_3b_workshop_solution.cpp            |   92 ++
 .../string_sets/assignment_4_workshop_solution.cpp |    2 +-
 .../assignment_4_workshop_solution.cpp.stdout      |   54 -
 demos/tutorial/vcf_io/example.vcf                  |   24 -
 demos/tutorial/vcf_io/example1.cpp                 |    2 +-
 demos/tutorial/vcf_io/example1.cpp.stdout          |    0
 demos/tutorial/vcf_io/solution1.cpp                |    2 +-
 demos/tutorial/vcf_io/solution1.cpp.stdout         |    0
 demos/tutorial/vcf_io/solution2.cpp                |    2 +-
 demos/tutorial/vcf_io/solution2.cpp.stdout         |    0
 demos/tutorial/vcf_io/solution3.cpp.stdout         |   20 -
 demos/unassigned_or_unused/bam_library_size.cpp    |  268 ----
 demos/unassigned_or_unused/benchmark_stream.cpp    |  422 -----
 demos/unassigned_or_unused/graph_hmm_silent.cpp    |  117 --
 demos/unassigned_or_unused/sam2svg.cpp             |  222 ---
 demos/{dox => }/vcf_io/example.vcf                 |    0
 demos/vcf_io/vcf_stream_read.cpp                   |   33 +
 demos/vcf_io/vcf_stream_read.cpp.stdout            |    5 +
 dox/pages/constraint_iterator.dox                  |   12 +-
 dox/pages/index_count_children.dox                 |    2 +-
 dox/pages/maxima_unique_matches.dox                |    2 +-
 dox/pages/maximal_repeats.dox                      |    6 +-
 dox/pages/mummy.dox                                |    2 +-
 dox/pages/suffix_array.dox                         |    2 +-
 dox/pages/supermaximal_repeats.dox                 |    6 +-
 include/seqan/align/align_base.h                   |    4 +-
 include/seqan/align/alignment_operations.h         |    4 +-
 include/seqan/align/evaluate_alignment.h           |    8 +-
 include/seqan/align/gaps_anchor.h                  |   46 +-
 include/seqan/align/gaps_base.h                    |    4 +-
 include/seqan/align/global_alignment_unbanded.h    |    8 +-
 include/seqan/align_extend/align_extend.h          |    4 +-
 include/seqan/align_profile/score_profile_seq.h    |    4 +-
 include/seqan/align_split/align_split_interface.h  |    4 +-
 include/seqan/arg_parse/arg_parse_argument.h       |    8 +-
 include/seqan/arg_parse/argument_parser.h          |    2 +-
 include/seqan/arg_parse/tool_doc.h                 |   10 +-
 include/seqan/bam_io/bam_file.h                    |   32 +-
 include/seqan/bam_io/bam_index_bai.h               |   63 +-
 include/seqan/bam_io/bam_tags_dict.h               |    4 +-
 include/seqan/bam_io/cigar.h                       |    2 +-
 include/seqan/bam_io/read_bam.h                    |    1 -
 include/seqan/bam_io/write_bam.h                   |    9 +-
 include/seqan/bam_io/write_sam.h                   |    4 -
 include/seqan/basic/alphabet_residue.h             |   10 +-
 include/seqan/basic/alphabet_residue_tabs.h        |   71 +-
 include/seqan/basic/alphabet_simple_type.h         |    2 +-
 include/seqan/basic/basic_exception.h              |   13 +-
 include/seqan/basic/basic_stream.h                 |   30 +-
 include/seqan/basic/concept_checking.h             |   15 +-
 include/seqan/basic/debug_test_system.h            |   42 +-
 include/seqan/basic/fundamental_tags.h             |   28 +-
 include/seqan/basic/iterator_adapt_std.h           |   52 +-
 include/seqan/basic/iterator_adaptor.h             |   10 +-
 include/seqan/basic/iterator_counting.h            |    7 +-
 include/seqan/basic/iterator_interface.h           |   72 +-
 include/seqan/basic/iterator_range.h               |    0
 include/seqan/basic/metaprogramming_control.h      |   10 +-
 include/seqan/basic/metaprogramming_enable_if.h    |    8 +-
 include/seqan/basic/metaprogramming_logic.h        |   44 +-
 include/seqan/basic/metaprogramming_math.h         |    6 +-
 .../seqan/consensus/consensus_aligner_interface.h  |    4 +-
 include/seqan/consensus/consensus_builder.h        |    5 +-
 include/seqan/find/find_ahocorasick.h              |    2 +-
 include/seqan/find/find_base.h                     |    8 +-
 include/seqan/find/find_set_horspool.h             |    2 -
 include/seqan/gff_io/gff_io_base.h                 |    7 +-
 .../graph_algorithms/all_pairs_shortest_path.h     |    4 +-
 include/seqan/graph_algorithms/bellman_ford.h      |    4 +-
 .../seqan/graph_algorithms/breadth_first_search.h  |    4 +-
 .../seqan/graph_algorithms/depth_first_search.h    |    4 +-
 include/seqan/graph_algorithms/dijkstra.h          |    4 +-
 include/seqan/graph_algorithms/floyd_warshall.h    |    4 +-
 include/seqan/graph_algorithms/ford_fulkerson.h    |    4 +-
 .../graph_algorithms/graph_algorithm_lis_his.h     |    6 +-
 include/seqan/graph_algorithms/kruskal.h           |    4 +-
 include/seqan/graph_algorithms/prim.h              |    4 +-
 .../graph_algorithms/single_source_shortest_path.h |    4 +-
 .../strongly_connected_compnents.h                 |    4 +-
 include/seqan/graph_algorithms/topological_sort.h  |    4 +-
 .../seqan/graph_algorithms/transitive_closure.h    |    4 +-
 include/seqan/graph_align/graph_impl_align.h       |    2 +-
 include/seqan/graph_types/graph_interface.h        |    4 +-
 include/seqan/index/index_base.h                   |   34 +-
 include/seqan/index/index_esa_base.h               |    4 +-
 include/seqan/index/index_esa_stree.h              |   22 +-
 include/seqan/index/index_fm.h                     |    9 +-
 include/seqan/index/index_fm_rank_dictionary_wt.h  |    3 +-
 include/seqan/index/index_qgram_openaddressing.h   |   60 -
 include/seqan/index/index_sa_qsort.h               |    2 +-
 include/seqan/index/index_shims.h                  |    4 +-
 include/seqan/index/repeat_base.h                  |    2 +-
 include/seqan/index/shape_base.h                   |    2 +-
 include/seqan/index/shape_threshold.h              |    0
 include/seqan/misc/edit_environment.h              |    4 +-
 include/seqan/misc/interval_tree.h                 |    2 +-
 include/seqan/misc/name_store_cache.h              |    4 +-
 include/seqan/misc/terminal.h                      |    2 +-
 include/seqan/modifier/cyclic_shape.h              |   14 +-
 include/seqan/modifier/modifier_cyclic_shape.h     |    6 +-
 include/seqan/modifier/modifier_iterator.h         |   87 +-
 include/seqan/modifier/modifier_reverse.h          |   23 +-
 include/seqan/modifier/modifier_string.h           |   67 +-
 include/seqan/modifier/modifier_view.h             |   89 +-
 include/seqan/parallel/parallel_macros.h           |    4 +-
 include/seqan/parallel/parallel_queue.h            |    4 +-
 include/seqan/parallel/parallel_splitting.h        |    6 +-
 include/seqan/pipe/pool_sorter.h                   |    2 +-
 include/seqan/platform.h                           |    9 -
 include/seqan/platform/platform_windows.h          |    7 -
 include/seqan/random/ext_MersenneTwister.h         |    0
 include/seqan/random/random_base.h                 |    2 +-
 include/seqan/realign/realign_base.h               |    4 +-
 .../reduced_aminoacid_murphy10_base.h              |    2 +-
 .../reduced_aminoacid_murphy10_tables.h            |    8 +-
 include/seqan/score/score_base.h                   |    4 +-
 include/seqan/score/score_matrix_data.h            |  757 +++++----
 include/seqan/score/score_simple.h                 |    9 -
 include/seqan/seeds/banded_chain_alignment_impl.h  |    1 -
 .../seqan/seeds/banded_chain_alignment_traceback.h |    7 -
 include/seqan/seeds/seeds_global_chaining.h        |    6 +-
 include/seqan/seeds/seeds_seed_base.h              |    6 +-
 include/seqan/seeds/seeds_seed_set_base.h          |    2 +-
 include/seqan/seq_io/fai_index.h                   |    4 +-
 include/seqan/seq_io/fasta_fastq.h                 |   17 +-
 include/seqan/sequence/adapt_std_list.h            |    9 -
 include/seqan/sequence/adapt_std_string.h          |   15 -
 include/seqan/sequence/segment_base.h              |    6 +-
 include/seqan/sequence/segment_infix.h             |    8 -
 include/seqan/sequence/segment_prefix.h            |    9 -
 include/seqan/sequence/segment_suffix.h            |    8 -
 include/seqan/sequence/string_array.h              |   16 -
 include/seqan/sequence/string_base.h               |   10 +-
 include/seqan/sequence/string_set_base.h           |   76 +-
 include/seqan/sequence/string_set_concat_direct.h  |   67 +-
 include/seqan/sequence/string_set_owner.h          |   15 -
 .../statistics/.statistics_markov_model.h.swp      |  Bin 0 -> 40960 bytes
 include/seqan/statistics/statistics_markov_model.h |    4 +-
 include/seqan/store/store_all.h                    |    4 +-
 include/seqan/store/store_io.h                     |   43 -
 include/seqan/store/store_io_gff.h                 |   30 +-
 include/seqan/store/store_io_sam.h                 |   27 +
 include/seqan/store/store_io_ucsc.h                |    0
 include/seqan/stream.h                             |   13 -
 include/seqan/stream/buffered_stream.h             |   19 +-
 include/seqan/stream/file_stream.h                 |    5 +-
 include/seqan/stream/formatted_file.h              |   18 +-
 include/seqan/stream/iostream_bgzf.h               |  923 -----------
 include/seqan/stream/iostream_bzip2.h              |  302 ----
 include/seqan/stream/iostream_bzip2_impl.h         |  429 -----
 include/seqan/stream/iostream_zip.h                |  383 -----
 include/seqan/stream/iostream_zip_impl.h           |  386 -----
 include/seqan/stream/iostream_zutil.h              |  229 ---
 include/seqan/stream/lexical_cast.h                |    4 +-
 include/seqan/stream/stream_base.h                 |   14 +-
 include/seqan/stream/stream_compressor.h           |    2 +-
 include/seqan/stream/tokenization.h                |    2 +-
 include/seqan/stream/virtual_stream.h              |  187 +--
 include/seqan/stream/zipstream/bgzfstream.h        |  969 ++++++++++++
 include/seqan/stream/zipstream/bgzfstream_impl.h   |  203 +++
 include/seqan/stream/zipstream/bzip2stream.h       |  305 ++++
 include/seqan/stream/zipstream/bzip2stream_impl.h  |  430 +++++
 include/seqan/stream/zipstream/zipstream.h         |  665 ++++++++
 include/seqan/stream/zipstream/zipstream_impl.h    |  675 ++++++++
 include/seqan/stream/zipstream/zutil.h             |  226 +++
 include/seqan/translation/translation.h            |    9 +-
 include/seqan/ucsc_io/ucsc_file.h                  |    2 +-
 include/seqan/vcf_io/vcf_io_context.h              |   28 -
 include/seqan/version.h                            |    2 +-
 manual/requirements.txt                            |    3 +-
 .../BuildManual/UsingTheSeqAnBuildSystem.rst       |    8 +-
 manual/source/HowTo/ClipAlignments.rst             |    2 +-
 manual/source/HowTo/GenerateSeqAnKnimeNodes.rst    |    2 +-
 manual/source/HowTo/UseSeqAnNodesInKnime.rst       |    2 +-
 .../source/HowTo/WorkWithCustomScoreMatrices.rst   |  137 +-
 manual/source/HowTo/knime_node_app.zip             |  Bin 0 -> 4697 bytes
 manual/source/HowTo/workflow_plugin_dir.zip        |  Bin 808808 -> 5912 bytes
 manual/source/Infrastructure/Documentation.rst     |   10 -
 manual/source/StyleGuide/Cpp.rst                   |   32 +-
 manual/source/StyleGuide/DoxApiDocs.rst            |   24 +-
 manual/source/Tutorial.rst                         |   25 +-
 manual/source/Tutorial/AFirstExample.rst           |  563 -------
 manual/source/Tutorial/AlignmentRepresentation.rst |   30 +-
 manual/source/Tutorial/AnnotationStore.rst         |  366 +++++
 manual/source/Tutorial/BackgroundAndMotivation.rst |  149 +-
 manual/source/Tutorial/BedIO.rst                   |    8 +-
 manual/source/Tutorial/ConsensusAlignment.rst      |   14 +-
 manual/source/Tutorial/FileIOOverview.rst          |  232 ---
 manual/source/Tutorial/FirstStepsInSeqAn.rst       |  562 +++++++
 manual/source/Tutorial/FragmentStore.rst           |   98 +-
 manual/source/Tutorial/GenomeAnnotations.rst       |  315 ----
 manual/source/Tutorial/GettingStarted.rst          |    2 +-
 manual/source/Tutorial/GffAndGtfIO.rst             |  214 ---
 manual/source/Tutorial/GffGtfIO.rst                |  243 +++
 manual/source/Tutorial/IndexIterators.rst          |   38 +-
 manual/source/Tutorial/IndexQGram.rst              |  217 +++
 manual/source/Tutorial/IndexedFastaIO.rst          |   10 +-
 manual/source/Tutorial/Indices.rst                 |   12 +-
 manual/source/Tutorial/InputOutputOverview.rst     |  227 +++
 manual/source/Tutorial/Iterators.rst               |   10 +-
 manual/source/Tutorial/JournalSet.rst              |  668 ++++++++
 manual/source/Tutorial/JournaledSet.rst            |  655 --------
 manual/source/Tutorial/Metafunctions.rst           |   20 +-
 manual/source/Tutorial/MiniBowtie.rst              |  358 +++++
 manual/source/Tutorial/Modifiers.rst               |    8 +-
 .../source/Tutorial/MultipleSequenceAlignment.rst  |   20 +-
 .../source/Tutorial/PairwiseSequenceAlignment.rst  |   97 +-
 .../Tutorial/ParsingCommandLineArguments.rst       |  891 ++++++++++-
 manual/source/Tutorial/PatternMatching.rst         |   28 +-
 manual/source/Tutorial/QgramIndex.rst              |  217 ---
 manual/source/Tutorial/Randomness.rst              |   12 +-
 manual/source/Tutorial/Realignment.rst             |    8 +-
 manual/source/Tutorial/SamAndBamIO.rst             |  342 ----
 manual/source/Tutorial/SamBamIO.rst                |  332 ++++
 manual/source/Tutorial/SequenceIO.rst              |   54 +-
 manual/source/Tutorial/Sequences.rst               |  243 ++-
 manual/source/Tutorial/SequencesInDepth.rst        |   19 +-
 manual/source/Tutorial/SimpleReadMapping.rst       |  161 ++
 manual/source/Tutorial/SimpleRnaSeq.rst            |   64 +-
 manual/source/Tutorial/StringSets.rst              |    4 +-
 ...ericProgramming.rst => TemplateSubclassing.rst} |    0
 manual/source/Tutorial/VcfIO.rst                   |   27 +-
 manual/source/Tutorial/WritingTests.rst            |    1 -
 manual/source/conf.py                              |   33 +-
 tests/align/test_evaluate_alignment.h              |    6 +-
 tests/bam_io/CMakeLists.txt                        |    4 +-
 tests/bam_io/test_bam_file.h                       |    2 +-
 tests/bam_io/test_bam_index.h                      |   45 +-
 tests/bam_io/test_bam_io.cpp                       |    5 +-
 tests/basic/test_basic_alphabet_residue.h          |   31 +-
 tests/find/test_find.cpp                           |    4 +-
 tests/gff_io/example_with_comments.gff             |    6 -
 tests/gff_io/test_gff_io.cpp                       |    9 +-
 tests/gff_io/test_gff_io.h                         |   60 -
 tests/modifier/test_modifier.cpp                   |    3 +-
 tests/modifier/test_modifier_string.h              |   85 +-
 tests/modifier/test_modifier_view.h                |    2 +-
 tests/parallel/test_parallel.cpp                   |    6 +-
 tests/reduced_aminoacid/test_reduced_aminoacid.cpp |    3 +-
 tests/reduced_aminoacid/test_reduced_aminoacid.h   |  143 +-
 tests/score/BLOSUM30                               |   55 +-
 tests/score/BLOSUM45                               |   55 +-
 tests/score/BLOSUM62                               |   55 +-
 tests/score/BLOSUM80                               |   55 +-
 tests/score/PAM120                                 |   55 +-
 tests/score/PAM200                                 |   55 +-
 tests/score/PAM250                                 |   55 +-
 tests/score/PAM40                                  |   55 +-
 tests/score/VTML200I                               |   55 +-
 tests/seeds/test_align_banded_chain_impl.cpp       |   26 -
 tests/seq_io/test_sequence_file.h                  |   15 +-
 tests/sequence/CMakeLists.txt                      |    4 -
 tests/sequence/test_sequence.h                     |    6 +-
 tests/sequence/test_string_set.h                   | 1651 +++++++++-----------
 tests/sequence/test_stringset_v2.cpp               |   47 -
 tests/store/example.gff                            |    2 +-
 util/cmake/CMakeFindJavaCommon.cmake               |   40 -
 util/cmake/FindJava.cmake                          |  228 ---
 util/cmake/FindOpenMP.cmake                        |    9 +-
 util/cmake/FindSeqAn.cmake                         |   14 +-
 util/cmake/SeqAnBuildSystem.cmake                  |   27 +-
 util/cmake/package.cmake                           |    2 +-
 util/makefile_project/src/main.cpp                 |   11 +-
 util/py_lib/seqan/auto_build.py                    |    2 +-
 util/py_lib/seqan/dox/dox_parser.py                |   24 +-
 util/py_lib/seqan/dox/dox_tokens.py                |    3 +-
 util/py_lib/seqan/dox/proc_doc.py                  |   38 -
 util/py_lib/seqan/dox/raw_doc.py                   |   35 -
 util/py_lib/seqan/dox/test/test_dox_parser.py      |   20 -
 util/py_lib/seqan/dox/test/test_proc_doc.py        |   25 -
 util/py_lib/seqan/dox/test/test_raw_doc.py         |   22 -
 util/py_lib/seqan/dox/tpl/function.html            |    9 +-
 .../js/bootstrap-3.0.0.min.js                      |    6 +
 .../bootstrap-multiselect/js/jquery-2.0.3.min.js   |    6 +
 .../tpl/lib/bootstrap-multiselect/js/prettify.js   |   28 +
 util/py_lib/seqan/dox/tpl/list.html                |    2 +-
 util/py_lib/seqan/dox/tpl/macro.html               |   10 +-
 util/py_lib/seqan/dox/tpl/sections.html            |   81 +-
 util/py_lib/seqan/dox/write_html.py                |    3 +-
 util/skel/test_template/test.h                     |    1 -
 util/travis/linux-cibuild.cmake                    |   18 +-
 1075 files changed, 22423 insertions(+), 20046 deletions(-)
 create mode 100644 debian/patches/skip_splazers_test.patch
 create mode 100644 debian/seqan-apps.links
 delete mode 100644 debian/seqan-apps.lintian-overrides
 create mode 100644 debian/seqan-dev.doc-base
 delete mode 100644 debian/seqan-doc.doc-base
 mode change 100755 => 100644 debian/seqan-doc.docs
 delete mode 100644 debian/source/include-binaries
 rename demos/{dox => }/align/align.cpp (100%)
 rename demos/{dox => }/align/align.cpp.stdout (100%)
 create mode 100644 demos/align/compute_alignment_stats.cpp
 create mode 100644 demos/align/compute_alignment_stats.cpp.stdout
 rename demos/{dox => }/align/gaps_example.cpp (100%)
 rename demos/{dox => }/align/gaps_example.cpp.stdout (100%)
 rename demos/{dox => }/align/global_alignment_banded.cpp (100%)
 rename demos/{dox => }/align/global_alignment_banded.cpp.stdout (100%)
 rename demos/{dox => }/align/global_alignment_unbanded.cpp (100%)
 rename demos/{dox => }/align/global_alignment_unbanded.cpp.stdout (100%)
 rename demos/{dox => }/align/integrate_align.cpp (100%)
 rename demos/{dox => }/align/integrate_align.cpp.stdout (100%)
 rename demos/{dox => }/align_extend/extend_alignment.cpp (100%)
 rename demos/{dox => }/align_extend/extend_alignment.cpp.stdout (100%)
 create mode 100644 demos/align_gaps_clipping.cpp
 rename demos/{dox => }/align_profile/profile_seq_frac_score.cpp (100%)
 rename demos/{dox => }/align_profile/profile_seq_score.cpp (100%)
 rename demos/{dox => }/align_split/split_alignment.cpp (100%)
 rename demos/{dox => }/align_split/split_alignment.cpp.stdout (100%)
 create mode 100644 demos/alignment.cpp
 create mode 100644 demos/alignment_local.cpp
 create mode 100644 demos/allocator.cpp
 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%)
 rename demos/{dox => }/arg_parse/argument_parser.cpp (100%)
 rename demos/{dox => }/bam_io/bam_file_in.cpp (100%)
 create mode 100644 demos/bam_io/bam_tags_dict.cpp
 rename demos/{dox => }/bam_io/bam_tags_dict.cpp.stdout (100%)
 create mode 100644 demos/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/basic/enable_if.cpp
 rename demos/{dox => }/basic/metaprogramming_control.cpp (100%)
 rename demos/{dox => }/basic/metaprogramming_logic.cpp (100%)
 rename demos/{dox => }/basic/metaprogramming_math.cpp (100%)
 rename demos/{dox => }/basic/metaprogramming_switch.cpp (100%)
 rename demos/{dox => }/basic/simple_type_construction.cpp (100%)
 rename demos/{dox/bed_io/UNUSED_bed_stream_read.cpp => bed_io/bed_stream_read.cpp} (100%)
 create mode 100644 demos/benchmark_stream.cpp
 rename demos/{unassigned_or_unused => }/benchmark_stream_write.cpp (100%)
 rename demos/{dox => }/consensus/consensus_alignment.cpp (100%)
 rename demos/{dox => }/consensus/consensus_alignment.cpp.stdout (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/{dox/modifier => }/cyclic_shape.cpp (100%)
 rename demos/{dox/modifier => }/cyclic_shape.cpp.stdout (100%)
 rename demos/{dox/modifier => }/cyclic_shape_snippets.cpp (100%)
 delete mode 100644 demos/dox/align/compute_alignment_stats.cpp
 delete mode 100644 demos/dox/align/compute_alignment_stats.cpp.stdout
 delete mode 100644 demos/dox/bam_io/bam_tags_dict.cpp
 delete mode 100644 demos/dox/basic/enable_if.cpp
 delete mode 100644 demos/dox/graph_algorithms/all_pairs_shortest_path.cpp
 delete mode 100644 demos/dox/graph_algorithms/bellman_ford_algorithm.cpp
 delete mode 100644 demos/dox/graph_algorithms/breadth_first_search.cpp
 delete mode 100644 demos/dox/graph_algorithms/dag_shortest_path.cpp
 delete mode 100644 demos/dox/graph_algorithms/depth_first_search.cpp
 delete mode 100644 demos/dox/graph_algorithms/dijkstra.cpp
 delete mode 100644 demos/dox/graph_algorithms/floyd_warshall_algorithm.cpp
 delete mode 100644 demos/dox/graph_algorithms/ford_fulkerson_algorithm.cpp
 delete mode 100644 demos/dox/graph_algorithms/kruskals_algorithm.cpp
 delete mode 100644 demos/dox/graph_algorithms/prims_algorithm.cpp
 delete mode 100644 demos/dox/graph_algorithms/strongly_connected_components.cpp
 delete mode 100644 demos/dox/graph_algorithms/topological_sort.cpp
 delete mode 100644 demos/dox/graph_algorithms/transitive_closure.cpp
 delete mode 100644 demos/dox/index/length_countSequences.cpp
 delete mode 100644 demos/dox/index/open_save.cpp
 delete mode 100644 demos/dox/parallel/queue_example.cpp
 delete mode 100644 demos/dox/random/random.cpp
 delete mode 100644 demos/dox/seq_io/fai_index_example.cpp
 delete mode 100644 demos/dox/sequence/segment.cpp
 delete mode 100644 demos/dox/stream/lexical_cast.cpp
 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/{dox => }/find/finder_aho_corasick.cpp (100%)
 rename demos/{dox => }/find/finder_index.cpp (100%)
 rename demos/{dox => }/find/finder_index.cpp.stdout (100%)
 rename demos/{dox => }/find/finder_online.cpp (100%)
 rename demos/{dox => }/find/finder_online.cpp.stdout (100%)
 create mode 100644 demos/find_approx.cpp
 create mode 100644 demos/find_exact.cpp
 rename demos/{unassigned_or_unused => }/find_wild.cpp (100%)
 rename demos/{unassigned_or_unused => }/gff2gtf.cpp (100%)
 rename demos/{dox/gff_io/UNUSED_gff_stream_read.cpp => gff_io/gff_stream_read.cpp} (100%)
 rename demos/{dox/graph_types => graph}/graph_algo_dijkstra.cpp (100%)
 rename demos/{dox/graph_types => graph}/graph_algo_dijkstra.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/all_pairs_shortest_path.cpp
 rename demos/{dox => }/graph_algorithms/all_pairs_shortest_path.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/bellman_ford_algorithm.cpp
 rename demos/{dox => }/graph_algorithms/bellman_ford_algorithm.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/breadth_first_search.cpp
 rename demos/{dox => }/graph_algorithms/breadth_first_search.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/dag_shortest_path.cpp
 rename demos/{dox => }/graph_algorithms/dag_shortest_path.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/depth_first_search.cpp
 rename demos/{dox => }/graph_algorithms/depth_first_search.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/dijkstra.cpp
 rename demos/{dox => }/graph_algorithms/dijkstra.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/floyd_warshall_algorithm.cpp
 rename demos/{dox => }/graph_algorithms/floyd_warshall_algorithm.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/ford_fulkerson_algorithm.cpp
 rename demos/{dox => }/graph_algorithms/ford_fulkerson_algorithm.cpp.stdout (100%)
 rename demos/{dox => }/graph_algorithms/heaviest_increasing_subsequence.cpp (100%)
 create mode 100644 demos/graph_algorithms/kruskals_algorithm.cpp
 rename demos/{dox => }/graph_algorithms/kruskals_algorithm.cpp.stdout (100%)
 rename demos/{dox => }/graph_algorithms/longest_common_subsequence.cpp (100%)
 rename demos/{dox => }/graph_algorithms/longest_increasing_subsequence.cpp (100%)
 create mode 100644 demos/graph_algorithms/prims_algorithm.cpp
 rename demos/{dox => }/graph_algorithms/prims_algorithm.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/strongly_connected_components.cpp
 rename demos/{dox => }/graph_algorithms/strongly_connected_components.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/topological_sort.cpp
 rename demos/{dox => }/graph_algorithms/topological_sort.cpp.stdout (100%)
 create mode 100644 demos/graph_algorithms/transitive_closure.cpp
 rename demos/{dox => }/graph_algorithms/transitive_closure.cpp.stdout (100%)
 rename demos/{dox => }/graph_align/graph_align.cpp (100%)
 create mode 100644 demos/graph_hmm.cpp
 create mode 100644 demos/graph_hmm_silent.cpp
 delete mode 100644 demos/howto/align_gaps_clipping.cpp
 delete mode 100644 demos/howto/scores/init_score.cpp.stdout
 delete mode 100644 demos/howto/scores/load_score.cpp.stdout
 rename demos/{dox => }/index/demo_index_index_textAt_indexText_saAt_indexRequire.cpp.stdout (100%)
 rename demos/{dox => }/index/find_repeats.cpp (100%)
 rename demos/{dox/index/begin_atEnd_representative.cpp => index/index_begin_atEnd_representative.cpp} (100%)
 rename demos/{dox/index/begin_atEnd_representative.cpp.stdout => index/index_begin_atEnd_representative.cpp.stdout} (100%)
 rename demos/{dox/index/begin_atEnd_representative_bottomUp.cpp => index/index_begin_atEnd_representative_bottomUp.cpp} (100%)
 rename demos/{dox/index/begin_range_goDown_representative_repLength.cpp => index/index_begin_range_goDown_representative_repLength.cpp} (100%)
 rename demos/{dox/index/counting.cpp => index/index_counting.cpp} (100%)
 rename demos/{dox/index/counting.cpp.stdout => index/index_counting.cpp.stdout} (100%)
 rename demos/{dox/index/finder.cpp => index/index_finder.cpp} (100%)
 rename demos/{dox/index/finder.cpp.stdout => index/index_finder.cpp.stdout} (100%)
 rename demos/{dox/index/getOccurrences_getFrequency_range_getFibre.cpp => index/index_getOccurrences_getFrequency_range_getFibre.cpp} (100%)
 rename demos/{dox/index/getOccurrences_getFrequency_range_getFibre.cpp.stdout => index/index_getOccurrences_getFrequency_range_getFibre.cpp.stdout} (100%)
 rename demos/{dox/index/iterator.cpp => index/index_iterator.cpp} (100%)
 rename demos/{dox/index/iterator.cpp.stdout => index/index_iterator.cpp.stdout} (100%)
 rename demos/{dox/index/iterator_short.cpp => index/index_iterator_short.cpp} (100%)
 rename demos/{dox/index/iterator_short.cpp.stdout => index/index_iterator_short.cpp.stdout} (100%)
 create mode 100644 demos/index/index_length_countSequences.cpp
 rename demos/{dox/index/length_countSequences.cpp.stdout => index/index_length_countSequences.cpp.stdout} (100%)
 rename demos/{dox/index/mummy.cpp => index/index_mummy.cpp} (100%)
 rename demos/{dox/index/mummy.cpp.stdout => index/index_mummy.cpp.stdout} (100%)
 rename demos/{dox/index/mums.cpp => index/index_mums.cpp} (100%)
 rename demos/{dox/index/node_predicate.cpp => index/index_node_predicate.cpp} (100%)
 create mode 100644 demos/index/index_open_save.cpp
 rename demos/{dox/index/open_save.cpp.stdout => index/index_open_save.cpp.stdout} (100%)
 create mode 100644 demos/index/index_qgram.cpp
 rename demos/{unassigned_or_unused => index}/index_sufarray.cpp (100%)
 rename demos/{dox/index/sufarray.cpp.stdout => index/index_sufarray.cpp.stdout} (100%)
 rename demos/{dox/index/supermaxrepeats.cpp => index/index_supermaxrepeats.cpp} (100%)
 rename demos/{dox/index/textAt_indexText_saAt_indexRequire.cpp => index/index_textAt_indexText_saAt_indexRequire.cpp} (100%)
 rename demos/{dox/index/textAt_indexText_saAt_indexRequire.cpp.stdout => index/index_textAt_indexText_saAt_indexRequire.cpp.stdout} (100%)
 rename demos/{dox => }/index/ref.fa (100%)
 rename demos/{dox/index/UNUSED_shape.cpp => index/shape.cpp} (100%)
 rename demos/{dox/index/UNUSED_shape_hash.cpp => index/shape_hash.cpp} (100%)
 rename demos/{dox => }/index/shape_hash_init.cpp (100%)
 rename demos/{dox/index/UNUSED_shape_hash_next.cpp => index/shape_hash_next.cpp} (100%)
 create mode 100644 demos/index_counting.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/{dox/index/maxrepeats.cpp => index_maxrepeats.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/{dox/index/sufarray.cpp => index_sufarray.cpp} (100%)
 rename demos/{unassigned_or_unused => }/index_supermaxrepeats.cpp (100%)
 create mode 100644 demos/input_output/example.fa
 create mode 100644 demos/input_output/seqfile_reader.cpp
 create mode 100644 demos/input_output/seqfile_reader.cpp.stdout
 rename demos/{tutorial/simple_rna_seq => }/interval_tree.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/{dox => }/misc/enumerate_strings.cpp (100%)
 rename demos/{dox => }/misc/enumerate_strings.cpp.stdout (100%)
 rename demos/{dox => }/misc/get_terminal_size.cpp (100%)
 rename demos/{dox => }/misc/interval_tree_example.cpp (100%)
 rename demos/{dox => }/misc/name_store_cache.cpp (100%)
 rename demos/{dox => }/misc/name_store_cache.cpp.stdout (100%)
 rename demos/{dox => }/modifier/modified_string.cpp (100%)
 rename demos/{dox => }/modifier/modified_string.cpp.stdout (100%)
 rename demos/{dox => }/modifier/modified_string_mod_view.cpp (100%)
 rename demos/{dox => }/modifier/modified_string_mod_view.cpp.stdout (100%)
 rename demos/{dox => }/modifier/modified_string_nested.cpp (100%)
 rename demos/{dox => }/modifier/modified_string_nested.cpp.stdout (100%)
 rename demos/{unassigned_or_unused => }/modifier_modreverse.cpp (100%)
 rename demos/{unassigned_or_unused => }/modifier_modview.cpp (100%)
 rename demos/{unassigned_or_unused => }/modifier_nested.cpp (100%)
 create mode 100644 demos/parallel/queue_example.cpp
 rename demos/{dox => }/parallel/queue_example.cpp.stdout (100%)
 rename demos/{dox => }/parallel/splitter_example.cpp (100%)
 rename demos/{dox => }/parallel/splitter_example.cpp.stdout (100%)
 rename demos/{unassigned_or_unused => }/parse_lm_stellar.cpp (100%)
 rename demos/{dox => }/pipe/pool_sorter.cpp (100%)
 create mode 100644 demos/random/random.cpp
 rename demos/{unassigned_or_unused => }/rooted_iterator.cpp (100%)
 create mode 100644 demos/sam2svg.cpp
 rename demos/{unassigned_or_unused => }/sample_seqs.cpp (100%)
 rename demos/{dox => }/score/score.cpp (100%)
 rename demos/{dox => }/score/score.cpp.stdout (100%)
 rename demos/{unassigned_or_unused => }/seeds.cpp (100%)
 rename demos/{dox => }/seeds/seeds_add_seed.cpp (100%)
 rename demos/{dox => }/seeds/seeds_chaining.cpp (100%)
 rename demos/{dox => }/seeds/seeds_chaining.cpp.stdout (100%)
 rename demos/{dox => }/seeds/seeds_extension.cpp (100%)
 rename demos/{dox => }/seeds/seeds_extension.cpp.stdout (100%)
 rename demos/{unassigned_or_unused => }/segmentalignment.cpp (100%)
 rename demos/{dox => }/seq_io/example.fa (100%)
 rename demos/{dox => }/seq_io/example.fa.fai (100%)
 create mode 100644 demos/seq_io/fai_index_example.cpp
 rename demos/{dox => }/seq_io/fai_index_example.cpp.stdout (100%)
 create mode 100644 demos/seq_io/sequence_stream_read.cpp
 create mode 100644 demos/seq_io/sequence_stream_read.cpp.stdout
 create mode 100644 demos/seq_io/sequence_stream_write.cpp
 rename demos/{dox/sequence/UNUSED_infix.cpp => sequence/infix.cpp} (100%)
 rename demos/{dox/sequence/UNUSED_prefix.cpp => sequence/prefix.cpp} (100%)
 create mode 100644 demos/sequence/segment.cpp
 rename demos/{dox => }/sequence/string.cpp (100%)
 rename demos/{dox => }/sequence/string2.cpp (100%)
 rename demos/{dox => }/sequence/string2.cpp.stdout (100%)
 rename demos/{dox => }/sequence/stringset.cpp (100%)
 rename demos/{dox => }/sequence/stringset.cpp.stdout (100%)
 rename demos/{dox/sequence/UNUSED_suffix.cpp => sequence/suffix.cpp} (100%)
 rename demos/{unassigned_or_unused => }/sequence_1.fa (100%)
 rename demos/{unassigned_or_unused => }/sequence_2.fa (100%)
 rename demos/{unassigned_or_unused => }/sequence_length.cpp (100%)
 rename demos/{unassigned_or_unused => }/soft_to_hard_masking.cpp (100%)
 rename demos/{dox => }/statistics/background.fa (100%)
 rename demos/{dox => }/statistics/build_markov_model.cpp (100%)
 rename demos/{dox => }/statistics/load_markov_model.cpp (100%)
 rename demos/{dox => }/statistics/zscore_example_mm.3 (100%)
 rename demos/{dox => }/statistics/zscore_human_mm.3 (100%)
 rename demos/{dox => }/store/store_example.cpp (100%)
 create mode 100644 demos/stream/lexical_cast.cpp
 rename demos/{dox => }/stream/lexical_cast.cpp.stdout (100%)
 delete mode 100644 demos/tutorial/a_first_example/basic_code.cpp.stdout
 delete mode 100644 demos/tutorial/a_first_example/basic_code_detailed.cpp.stdout
 delete mode 100644 demos/tutorial/a_first_example/code_encapsulation.cpp.stdout
 delete mode 100644 demos/tutorial/a_first_example/final_result.cpp.stdout
 delete mode 100644 demos/tutorial/a_first_example/solution_1.cpp.stdout
 delete mode 100644 demos/tutorial/a_first_example/solution_2.cpp.stdout
 delete mode 100644 demos/tutorial/a_first_example/solution_3.cpp.stdout
 delete mode 100644 demos/tutorial/a_first_example/solution_4.cpp.stdout
 delete mode 100644 demos/tutorial/a_first_example/solution_5.cpp.stdout
 delete mode 100644 demos/tutorial/a_first_example/solution_6.cpp.stdout
 delete mode 100644 demos/tutorial/alignment_representation/align.cpp.stdout
 delete mode 100644 demos/tutorial/alignment_representation/align_assignment1.cpp.stdout
 delete mode 100644 demos/tutorial/alignment_representation/graph.cpp.stdout
 delete mode 100644 demos/tutorial/alignment_representation/graph_assignment1.cpp.stdout
 create mode 100644 demos/tutorial/alignments/CMakeLists.txt
 rename demos/tutorial/{alignment_representation/align.cpp => alignments/alignment2_align.cpp} (100%)
 rename demos/tutorial/{alignment_representation/align_assignmen1.cpp => alignments/alignment_align_assignment1.cpp} (100%)
 rename demos/tutorial/{pairwise_sequence_alignment => alignments}/alignment_banded.cpp (100%)
 copy {manual/source/Tutorial => demos/tutorial/alignments}/alignment_example.png (100%)
 mode change 100644 => 100755
 create mode 100644 demos/tutorial/alignments/alignment_gaps.cpp
 rename demos/tutorial/{pairwise_sequence_alignment => alignments}/alignment_global_assignment1.cpp (100%)
 rename demos/tutorial/{pairwise_sequence_alignment => alignments}/alignment_global_assignment2.cpp (100%)
 rename demos/tutorial/{pairwise_sequence_alignment => alignments}/alignment_global_assignment3.cpp (100%)
 create mode 100644 demos/tutorial/alignments/alignment_global_assignment4_part1.cpp
 create mode 100644 demos/tutorial/alignments/alignment_global_assignment4_part2.cpp
 rename demos/tutorial/{pairwise_sequence_alignment => alignments}/alignment_global_overlap.cpp (100%)
 rename demos/tutorial/{pairwise_sequence_alignment => alignments}/alignment_global_specialised.cpp (100%)
 rename demos/tutorial/{pairwise_sequence_alignment => alignments}/alignment_global_standard.cpp (100%)
 create mode 100644 demos/tutorial/alignments/alignment_local_standard.cpp
 create mode 100644 demos/tutorial/alignments/alignment_local_waterman_eggert.cpp
 rename demos/tutorial/{multiple_sequence_alignment/msa.cpp => alignments/alignment_msa.cpp} (100%)
 rename demos/tutorial/{multiple_sequence_alignment/msa.cpp.stdout => alignments/alignment_msa.cpp.stdout} (100%)
 rename demos/tutorial/{multiple_sequence_alignment/assignment1.cpp => alignments/alignment_msa_assignment1.cpp} (100%)
 rename demos/tutorial/{multiple_sequence_alignment/assignment1.cpp.stdout => alignments/alignment_msa_assignment1.cpp.stdout} (100%)
 rename demos/tutorial/{multiple_sequence_alignment/consensus.cpp => alignments/alignment_msa_consensus.cpp} (100%)
 rename demos/tutorial/{multiple_sequence_alignment/consensus.cpp.stdout => alignments/alignment_msa_consensus.cpp.stdout} (100%)
 create mode 100644 demos/tutorial/alignments/alignment_pairwise_global.cpp
 create mode 100644 demos/tutorial/alignments/alignment_pairwise_global2.cpp
 create mode 100644 demos/tutorial/alignments/alignment_pairwise_global_assignment1.cpp
 create mode 100644 demos/tutorial/alignments/alignment_pairwise_global_assignment2.cpp
 rename demos/tutorial/{pairwise_sequence_alignment/alignment_local.cpp => alignments/alignment_pairwise_local.cpp} (100%)
 rename demos/tutorial/{pairwise_sequence_alignment/alignment_local_assignment1.cpp => alignments/alignment_pairwise_local_assignment1.cpp} (100%)
 rename demos/tutorial/{alignment_representation/graph.cpp => alignments/alignment_representation_ag.cpp} (100%)
 rename demos/tutorial/{alignment_representation/graph_assignment1.cpp => alignments/alignment_representation_ag_assignment1.cpp} (100%)
 create mode 100644 demos/tutorial/alignments/pairwise_sequence_alignment_assignment5.cpp
 create mode 100644 demos/tutorial/alignments/pairwise_sequence_alignment_assignment5_step1.cpp
 create mode 100644 demos/tutorial/alignments/pairwise_sequence_alignment_assignment5_step2.cpp
 create mode 100644 demos/tutorial/alignments/pairwise_sequence_alignment_assignment5_step3.cpp
 create mode 100644 demos/tutorial/alignments/pairwise_sequence_alignment_assignment5_step4.cpp
 create mode 100644 demos/tutorial/alignments/pairwise_sequence_alignment_assignment5_step5.cpp
 create mode 100644 demos/tutorial/alignments/pairwise_sequence_alignment_assignment5_step6.cpp
 delete mode 100644 demos/tutorial/alphabets/alphabet_assignment_1_solution.cpp.stdout
 create mode 100644 demos/tutorial/annotation_store/assignment_1_hint.cpp
 create mode 100644 demos/tutorial/annotation_store/assignment_1_solution.cpp
 create mode 100644 demos/tutorial/annotation_store/assignment_2_solution.cpp
 create mode 100644 demos/tutorial/annotation_store/assignment_3_solution.cpp
 create mode 100644 demos/tutorial/annotation_store/assignment_4_solution.cpp
 rename demos/tutorial/{genome_annotations => annotation_store}/assignment_annotations.gtf (100%)
 rename demos/tutorial/{sam_and_bam_io => bam_io}/example.sam (100%)
 create mode 100644 demos/tutorial/bam_io/example1.cpp
 create mode 100644 demos/tutorial/bam_io/example2.cpp
 create mode 100644 demos/tutorial/bam_io/example3.cpp
 create mode 100644 demos/tutorial/bam_io/example7.cpp
 create mode 100644 demos/tutorial/bam_io/solution1.cpp
 create mode 100644 demos/tutorial/bam_io/solution2.cpp
 create mode 100644 demos/tutorial/bam_io/solution3.cpp
 create mode 100644 demos/tutorial/bam_io/solution4.cpp
 create mode 100644 demos/tutorial/bam_io/solution5.cpp
 create mode 100644 demos/tutorial/bam_io/solution6.cpp
 create mode 100644 demos/tutorial/bam_io/solution7.cpp
 create mode 100644 demos/tutorial/base_io/example1.cpp
 create mode 100644 demos/tutorial/base_io/solution1.cpp
 create mode 100644 demos/tutorial/base_io/solution2.cpp
 create mode 100644 demos/tutorial/base_io/solution3.cpp
 create mode 100644 demos/tutorial/basics/CMakeLists.txt
 delete mode 100644 demos/tutorial/basics/allocator.cpp.stdout
 delete mode 100644 demos/tutorial/basics/show_alphabets.cpp.stdout
 delete mode 100644 demos/tutorial/basics/strings.cpp.stdout
 rename demos/tutorial/{metafunctions => basics}/swap.cpp (100%)
 delete mode 100644 demos/tutorial/bed_io/example.bed
 delete mode 100644 demos/tutorial/bed_io/example1.cpp.stdout
 delete mode 100644 demos/tutorial/bed_io/solution1.cpp.stdout
 delete mode 100644 demos/tutorial/bed_io/solution2.cpp.stdout
 delete mode 100644 demos/tutorial/bed_io/solution3.cpp.stdout
 delete mode 100644 demos/tutorial/blast_io/read_assignment.cpp.stdout
 delete mode 100644 demos/tutorial/blast_io/write_assignment.cpp.stdout
 rename demos/tutorial/{consensus_alignment => consensus}/with_positions.cpp (100%)
 rename demos/tutorial/{consensus_alignment => consensus}/with_positions.cpp.stdout (100%)
 rename demos/tutorial/{consensus_alignment => consensus}/without_positions.cpp (100%)
 rename demos/tutorial/{consensus_alignment => consensus}/without_positions.cpp.stdout (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/NC_001405.fasta (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/NC_001460.fasta (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/blast_example.txt (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/example1.cpp (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/gff2_example.txt (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/newick_example.txt (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/parse_blastn.cpp (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/parse_gff2.cpp (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/reader_demo.cpp (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/solution1.cpp (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/solution2.cpp (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/solution3.cpp (100%)
 rename demos/{unassigned_or_unused/tutorials_custim_io => tutorial/custom_io}/solution4.cpp (100%)
 rename demos/tutorial/{journaled_set => data_journaling}/example_join.cpp (100%)
 create mode 100644 demos/tutorial/data_journaling/example_journal_string_basic.cpp
 create mode 100644 demos/tutorial/data_journaling/example_online_search.cpp
 create mode 100644 demos/tutorial/data_journaling/example_online_search_assignment1_hint.cpp
 create mode 100644 demos/tutorial/data_journaling/example_online_search_assignment2_hint.cpp
 create mode 100644 demos/tutorial/data_journaling/example_online_search_assignment3_hint.cpp
 create mode 100644 demos/tutorial/data_journaling/example_online_search_assignment4_hint.cpp
 create mode 100644 demos/tutorial/data_journaling/solution_online_search_assignment1.cpp
 create mode 100644 demos/tutorial/data_journaling/solution_online_search_assignment2.cpp
 create mode 100644 demos/tutorial/data_journaling/solution_online_search_assignment3.cpp
 create mode 100644 demos/tutorial/data_journaling/solution_online_search_assignment4.cpp
 create mode 100644 demos/tutorial/data_journaling/solution_online_search_finder.cpp
 rename demos/{unassigned_or_unused/tutorial_file_io => tutorial/file_io}/example1.cpp (100%)
 rename demos/{unassigned_or_unused/tutorial_file_io => tutorial/file_io}/mmap_string_example.cpp (100%)
 rename demos/{unassigned_or_unused/tutorial_file_io => tutorial/file_io}/solution1.cpp (100%)
 rename demos/{unassigned_or_unused/tutorial_file_io => tutorial/file_io}/solution2.cpp (100%)
 rename demos/{unassigned_or_unused/tutorial_file_io => tutorial/file_io}/solution3.cpp (100%)
 rename demos/{unassigned_or_unused/tutorial_file_io => tutorial/file_io}/stream_compression_formats.cpp (100%)
 delete mode 100644 demos/tutorial/file_io_overview/example.bam
 delete mode 100644 demos/tutorial/file_io_overview/example.sam
 delete mode 100644 demos/tutorial/file_io_overview/example1.cpp
 delete mode 100644 demos/tutorial/file_io_overview/example1.cpp.stdout
 delete mode 100644 demos/tutorial/file_io_overview/solution1.cpp
 delete mode 100644 demos/tutorial/file_io_overview/solution1.cpp.stdout
 delete mode 100644 demos/tutorial/file_io_overview/solution2.cpp
 delete mode 100644 demos/tutorial/file_io_overview/solution2.cpp.stdout
 delete mode 100644 demos/tutorial/file_io_overview/solution3.cpp
 delete mode 100644 demos/tutorial/file_io_overview/solution3.cpp.stdout
 create mode 100644 demos/tutorial/find/CMakeLists.txt
 rename demos/tutorial/{pattern_matching => find}/find_approx.cpp (100%)
 rename demos/tutorial/{pattern_matching/assignment1.cpp => find/find_assignment1.cpp} (100%)
 rename demos/tutorial/{pattern_matching/assignment1_solution.cpp => find/find_assignment1_solution.cpp} (100%)
 rename demos/tutorial/{pattern_matching/assignment2.cpp => find/find_assignment2.cpp} (100%)
 rename demos/tutorial/{pattern_matching/assignment2_solution.cpp => find/find_assignment2_solution.cpp} (100%)
 rename demos/tutorial/{pattern_matching/assignment3.cpp => find/find_assignment3.cpp} (100%)
 rename demos/tutorial/{pattern_matching/assignment3_solution.cpp => find/find_assignment3_solution.cpp} (100%)
 rename demos/tutorial/{pattern_matching => find}/find_exact.cpp (100%)
 rename demos/tutorial/{pattern_matching => find}/find_index.cpp (100%)
 rename demos/tutorial/{pattern_matching => find}/find_index_multiple.cpp (100%)
 rename demos/tutorial/{a_first_example => first_steps}/basic_code.cpp (100%)
 rename demos/tutorial/{a_first_example => first_steps}/basic_code_detailed.cpp (100%)
 rename demos/tutorial/{a_first_example => first_steps}/code_encapsulation.cpp (100%)
 rename demos/tutorial/{a_first_example => first_steps}/final_result.cpp (100%)
 rename demos/tutorial/{a_first_example => first_steps}/solution_1.cpp (100%)
 rename demos/tutorial/{a_first_example => first_steps}/solution_2.cpp (100%)
 rename demos/tutorial/{a_first_example => first_steps}/solution_3.cpp (100%)
 rename demos/tutorial/{a_first_example => first_steps}/solution_4.cpp (100%)
 rename demos/tutorial/{a_first_example => first_steps}/solution_5.cpp (100%)
 rename demos/tutorial/{a_first_example => first_steps}/solution_6.cpp (100%)
 delete mode 100644 demos/tutorial/fragment_store/access_aligned_reads.cpp
 delete mode 100644 demos/tutorial/fragment_store/access_aligned_reads.cpp.stdout
 delete mode 100644 demos/tutorial/fragment_store/access_aligned_reads2.cpp
 delete mode 100644 demos/tutorial/fragment_store/access_aligned_reads2.cpp.stdout
 delete mode 100644 demos/tutorial/fragment_store/display_aligned_reads.cpp
 delete mode 100644 demos/tutorial/fragment_store/display_aligned_reads.cpp.stdout
 delete mode 100644 demos/tutorial/generic_programming/template_subclassing.cpp.stdout
 delete mode 100644 demos/tutorial/genome_annotations/assignment_1_hint.cpp
 delete mode 100644 demos/tutorial/genome_annotations/assignment_1_hint.cpp.stdout
 delete mode 100644 demos/tutorial/genome_annotations/assignment_1_solution.cpp
 delete mode 100644 demos/tutorial/genome_annotations/assignment_1_solution.cpp.stdout
 delete mode 100644 demos/tutorial/genome_annotations/assignment_2_solution.cpp
 delete mode 100644 demos/tutorial/genome_annotations/assignment_2_solution.cpp.stdout
 delete mode 100644 demos/tutorial/genome_annotations/assignment_3_solution.cpp
 delete mode 100644 demos/tutorial/genome_annotations/assignment_3_solution.cpp.stdout
 delete mode 100644 demos/tutorial/genome_annotations/assignment_4_solution.cpp
 delete mode 100644 demos/tutorial/genome_annotations/assignment_4_solution.cpp.stdout
 delete mode 100644 demos/tutorial/genome_annotations/base.cpp
 delete mode 100644 demos/tutorial/genome_annotations/base.cpp.stdout
 delete mode 100644 demos/tutorial/genome_annotations/example.gtf
 create mode 100644 demos/tutorial/getting_started/CMakeLists.txt
 create mode 100644 demos/tutorial/getting_started/cmd_dir_build_src.png
 create mode 100644 demos/tutorial/getting_started/eclipse_convert_to_cpp_project.png
 create mode 100644 demos/tutorial/getting_started/eclipse_hello_world.png
 create mode 100644 demos/tutorial/getting_started/eclipse_import_build_project.png
 create mode 100644 demos/tutorial/getting_started/eclipse_new_repository_location.png
 create mode 100644 demos/tutorial/getting_started/eclipse_preference_build_on_launch.png
 create mode 100644 demos/tutorial/getting_started/eclipse_required_plugins.png
 create mode 100644 demos/tutorial/getting_started/eclipse_run_configurations.png
 create mode 100644 demos/tutorial/getting_started/mingw_installation.png
 create mode 100644 demos/tutorial/getting_started/repository_overview.pptx
 create mode 100644 demos/tutorial/getting_started/repository_overview/Folie1.jpg
 create mode 100755 demos/tutorial/getting_started/win_command_arguments.jpg
 create mode 100755 demos/tutorial/getting_started/win_new_file.jpg
 create mode 100755 demos/tutorial/getting_started/win_save_file.jpg
 create mode 100755 demos/tutorial/getting_started/win_solution_explorer.png
 create mode 100755 demos/tutorial/getting_started/win_start_up_project.png
 create mode 100755 demos/tutorial/getting_started/win_tortoise.png
 create mode 100644 demos/tutorial/getting_started/xcode/base_sdk.png
 create mode 100644 demos/tutorial/getting_started/xcode/base_sdk_selection.png
 copy {manual/source/Tutorial/GettingStarted => demos/tutorial/getting_started/xcode}/download-command-line-tools.png (100%)
 create mode 100644 demos/tutorial/getting_started/xcode/first_app_new.png
 create mode 100644 demos/tutorial/getting_started/xcode/first_app_old.png
 copy {manual/source/Tutorial/GettingStarted => demos/tutorial/getting_started/xcode}/razers2_built.png (100%)
 copy {manual/source/Tutorial/GettingStarted => demos/tutorial/getting_started/xcode}/razers2_selection.png (100%)
 create mode 100644 demos/tutorial/getting_started/xcode/test_stream_selection.png
 copy {manual/source/Tutorial/GettingStarted => demos/tutorial/getting_started/xcode}/xcode_startup.png (100%)
 create mode 100644 demos/tutorial/getting_started/xcode_first_app.jpg
 create mode 100644 demos/tutorial/getting_started/xcode_start_up_view.png
 delete mode 100644 demos/tutorial/gff_and_gtf_io/example.gff
 delete mode 100644 demos/tutorial/gff_and_gtf_io/example1.cpp
 delete mode 100644 demos/tutorial/gff_and_gtf_io/example1.cpp.stdout
 delete mode 100644 demos/tutorial/gff_and_gtf_io/example2.cpp
 delete mode 100644 demos/tutorial/gff_and_gtf_io/example2.cpp.stdout
 delete mode 100644 demos/tutorial/gff_and_gtf_io/solution1.cpp
 delete mode 100644 demos/tutorial/gff_and_gtf_io/solution1.cpp.stdout
 delete mode 100644 demos/tutorial/gff_and_gtf_io/solution2.cpp
 delete mode 100644 demos/tutorial/gff_and_gtf_io/solution2.cpp.stdout
 delete mode 100644 demos/tutorial/gff_and_gtf_io/solution3.cpp.stdout
 create mode 100644 demos/tutorial/gff_io/example1.cpp
 create mode 100644 demos/tutorial/gff_io/example2.cpp
 create mode 100644 demos/tutorial/gff_io/solution1.cpp
 create mode 100644 demos/tutorial/gff_io/solution2.cpp
 rename demos/tutorial/{gff_and_gtf_io => gff_io}/solution3.cpp (100%)
 create mode 100644 demos/tutorial/graph/CMakeLists.txt
 delete mode 100644 demos/tutorial/graph/graph_algo_scc.cpp.stdout
 delete mode 100644 demos/tutorial/graph/graph_dijkstra.cpp.stdout
 delete mode 100644 demos/tutorial/graph/graph_hmm.cpp.stdout
 delete mode 100644 demos/tutorial/graph/solution_1.cpp.stdout
 create mode 100644 demos/tutorial/index/CMakeLists.txt
 rename demos/tutorial/{index_iterators => index}/index_assignment1.cpp (100%)
 rename demos/tutorial/{index_iterators => index}/index_assignment2.cpp (100%)
 rename demos/tutorial/{index_iterators/UNUSED_index_assignment3.cpp => index/index_assignment3.cpp} (100%)
 rename demos/tutorial/{index_iterators => index}/index_assignment4.cpp (100%)
 rename demos/tutorial/{q_gram_index => index}/index_assignment5.cpp (100%)
 rename demos/tutorial/{q_gram_index => index}/index_assignment6.cpp (100%)
 rename demos/tutorial/{index_iterators => index}/index_preorder.cpp (100%)
 rename demos/tutorial/{index_iterators => index}/index_property_maps.cpp (100%)
 rename demos/tutorial/{q_gram_index => index}/index_qgram.cpp (100%)
 rename demos/tutorial/{q_gram_index => index}/index_qgram_hash.cpp (100%)
 rename demos/tutorial/{index_iterators => index}/index_search.cpp (100%)
 rename demos/tutorial/{index_iterators => index}/index_search2.cpp (100%)
 rename demos/tutorial/{indices/assignment_1.cpp => index/indices_assignment_1.cpp} (100%)
 rename demos/tutorial/{indices/assignment_2.cpp => index/indices_assignment_2.cpp} (100%)
 rename demos/tutorial/{index_iterators => index}/iterator_solution1.cpp (100%)
 rename demos/tutorial/{index_iterators => index}/iterator_solution2.cpp (100%)
 delete mode 100644 demos/tutorial/index_iterators/UNUSED_index_assignment3.cpp.stdout
 delete mode 100644 demos/tutorial/index_iterators/index_assignment1.cpp.stdout
 delete mode 100644 demos/tutorial/index_iterators/index_assignment2.cpp.stdout
 delete mode 100644 demos/tutorial/index_iterators/index_assignment4.cpp.stdout
 delete mode 100644 demos/tutorial/index_iterators/index_preorder.cpp.stdout
 delete mode 100644 demos/tutorial/index_iterators/index_property_maps.cpp.stdout
 delete mode 100644 demos/tutorial/index_iterators/index_search.cpp.stdout
 delete mode 100644 demos/tutorial/index_iterators/index_search2.cpp.stdout
 delete mode 100644 demos/tutorial/index_iterators/iterator_solution1.cpp.stdout
 delete mode 100644 demos/tutorial/index_iterators/iterator_solution2.cpp.stdout
 delete mode 100644 demos/tutorial/indices/assignment_1.cpp.stdout
 delete mode 100644 demos/tutorial/indices/assignment_2.cpp.stdout
 delete mode 100644 demos/tutorial/iterators/assignment_1_solution.cpp.stdout
 delete mode 100644 demos/tutorial/iterators/assignment_2_solution.cpp.stdout
 delete mode 100644 demos/tutorial/iterators/assignment_3_workshop_solution.cpp
 delete mode 100644 demos/tutorial/iterators/assignment_3_workshop_solution.cpp.stdout
 delete mode 100644 demos/tutorial/iterators/assignment_4_workshop_solution.cpp
 delete mode 100644 demos/tutorial/iterators/assignment_4_workshop_solution.cpp.stdout
 rename demos/tutorial/iterators/{assignment_1_solution.cpp => iterators_assignment_1_solution.cpp} (100%)
 rename demos/tutorial/iterators/{assignment_2_solution.cpp => iterators_assignment_2_solution.cpp} (100%)
 create mode 100644 demos/tutorial/iterators/iterators_assignment_3_workshop_solution.cpp
 create mode 100644 demos/tutorial/iterators/iterators_assignment_4_workshop_solution.cpp
 delete mode 100644 demos/tutorial/iterators/sequence_iterator_demo.cpp.stdout
 delete mode 100644 demos/tutorial/journaled_set/example_join.cpp.stdout
 delete mode 100644 demos/tutorial/journaled_set/example_journal_string_basic.cpp
 delete mode 100644 demos/tutorial/journaled_set/example_journal_string_basic.cpp.stdout
 delete mode 100644 demos/tutorial/journaled_set/example_online_search.cpp
 delete mode 100644 demos/tutorial/journaled_set/example_online_search.cpp.stdout
 delete mode 100644 demos/tutorial/journaled_set/example_online_search_assignment1_hint.cpp
 delete mode 100644 demos/tutorial/journaled_set/example_online_search_assignment1_hint.cpp.stdout
 delete mode 100644 demos/tutorial/journaled_set/sequences.fasta
 delete mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment1.cpp
 delete mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment1.cpp.stdout
 delete mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment2.cpp
 delete mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment2.cpp.stdout
 delete mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment3.cpp
 delete mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment3.cpp.stdout
 delete mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment4.cpp
 delete mode 100644 demos/tutorial/journaled_set/solution_online_search_assignment4.cpp.stdout
 delete mode 100644 demos/tutorial/journaled_set/solution_online_search_finder.cpp
 delete mode 100644 demos/tutorial/journaled_set/solution_online_search_finder.cpp.stdout
 delete mode 100644 demos/tutorial/metafunctions/swap.cpp.stdout
 create mode 100644 demos/tutorial/mini_bowtie/mini_bowtie.cpp
 create mode 100755 demos/tutorial/mini_bowtie/nc_001454.fasta
 create mode 100755 demos/tutorial/mini_bowtie/reads_hamming.fasta
 create mode 100644 demos/tutorial/mini_bowtie/solution1.cpp
 create mode 100644 demos/tutorial/mini_bowtie/solution2.cpp
 create mode 100644 demos/tutorial/mini_bowtie/solution3.cpp
 create mode 100644 demos/tutorial/mini_bowtie/solution4.cpp
 create mode 100644 demos/tutorial/mini_bowtie/solution5.cpp
 delete mode 100644 demos/tutorial/modifiers/UNUSED_modcomplementdna.cpp.stdout
 delete mode 100644 demos/tutorial/modifiers/UNUSED_modview.cpp.stdout
 delete mode 100644 demos/tutorial/modifiers/UNUSED_nested.cpp.stdout
 delete mode 100644 demos/tutorial/modifiers/assignment1.cpp.stdout
 delete mode 100644 demos/tutorial/modifiers/assignment1_solution.cpp.stdout
 rename demos/tutorial/modifiers/{UNUSED_modcomplementdna.cpp => modifier_modcomplementdna.cpp} (100%)
 rename demos/tutorial/modifiers/{modreverse.cpp => modifier_modreverse.cpp} (100%)
 rename demos/tutorial/modifiers/{UNUSED_modview.cpp => modifier_modview.cpp} (100%)
 rename demos/tutorial/modifiers/{UNUSED_nested.cpp => modifier_nested.cpp} (100%)
 delete mode 100644 demos/tutorial/modifiers/modreverse.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_banded.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment1.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment2.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment3.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_global_overlap.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_global_specialised.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_global_standard.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5.cpp
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp.stdout
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp
 delete mode 100644 demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp.stdout
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/assignment2_solution.cpp
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/assignment3_solution.cpp
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/assignment4_solution.cpp
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/assignment5_solution.cpp
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/assignment6_solution.cpp
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/example1.cpp
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/example1_detailed.cpp
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/example_with_modifyString.cpp
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/example_with_own_function.cpp
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/example_with_struct.cpp
 delete mode 100644 demos/tutorial/parsing_command_line_arguments/final_solution.cpp
 delete mode 100644 demos/tutorial/pattern_matching/assignment1.cpp.stdout
 delete mode 100644 demos/tutorial/pattern_matching/assignment1_solution.cpp.stdout
 delete mode 100644 demos/tutorial/pattern_matching/assignment2.cpp.stdout
 delete mode 100644 demos/tutorial/pattern_matching/assignment2_solution.cpp.stdout
 delete mode 100644 demos/tutorial/pattern_matching/assignment3.cpp.stdout
 delete mode 100644 demos/tutorial/pattern_matching/assignment3_solution.cpp.stdout
 delete mode 100644 demos/tutorial/pattern_matching/find_approx.cpp.stdout
 delete mode 100644 demos/tutorial/pattern_matching/find_exact.cpp.stdout
 delete mode 100644 demos/tutorial/pattern_matching/find_index.cpp.stdout
 delete mode 100644 demos/tutorial/pattern_matching/find_index_multiple.cpp.stdout
 delete mode 100644 demos/tutorial/q_gram_index/index_assignment5.cpp.stdout
 delete mode 100644 demos/tutorial/q_gram_index/index_assignment6.cpp.stdout
 delete mode 100644 demos/tutorial/q_gram_index/index_qgram.cpp.stdout
 delete mode 100644 demos/tutorial/q_gram_index/index_qgram_hash.cpp.stdout
 create mode 100644 demos/tutorial/random/CMakeLists.txt
 create mode 100644 demos/tutorial/random/random_examples.cpp
 delete mode 100644 demos/tutorial/randomness/examples.cpp
 delete mode 100644 demos/tutorial/randomness/examples.cpp.stdout
 create mode 100644 demos/tutorial/read_mapping/CMakeLists.txt
 rename demos/{unassigned_or_unused => tutorial/read_mapping}/minimapper.cpp (100%)
 create mode 100644 demos/tutorial/read_mapping/nc_001454.fasta
 create mode 100644 demos/tutorial/read_mapping/reads_edit.fasta
 create mode 100644 demos/tutorial/read_mapping/reads_hamming.fasta
 rename demos/tutorial/{realignment => realign}/reads.sam (100%)
 rename demos/tutorial/{realignment => realign}/ref.fa (100%)
 create mode 100644 demos/tutorial/realign/step1.cpp
 rename demos/tutorial/{realignment => realign}/step1.cpp.stdout (100%)
 create mode 100644 demos/tutorial/realign/step2.cpp
 rename demos/tutorial/{realignment => realign}/step2.cpp.stdout (100%)
 delete mode 100644 demos/tutorial/realignment/step1.cpp
 delete mode 100644 demos/tutorial/realignment/step2.cpp
 create mode 100644 demos/tutorial/rnaseq/CMakeLists.txt
 create mode 100644 demos/tutorial/rnaseq/genequant_assignment1.cpp
 create mode 100644 demos/tutorial/rnaseq/genequant_assignment2.cpp
 create mode 100644 demos/tutorial/rnaseq/genequant_assignment3.cpp
 create mode 100644 demos/tutorial/rnaseq/genequant_assignment4.cpp
 create mode 100644 demos/tutorial/rnaseq/genequant_assignment5.cpp
 create mode 100644 demos/tutorial/rnaseq/genequant_solution1.cpp
 create mode 100644 demos/tutorial/rnaseq/genequant_solution2.cpp
 create mode 100644 demos/tutorial/rnaseq/genequant_solution3.cpp
 create mode 100644 demos/tutorial/rnaseq/genequant_solution4.cpp
 create mode 100644 demos/tutorial/rnaseq/genequant_solution5.cpp
 delete mode 100644 demos/tutorial/sam_and_bam_io/example.bam
 delete mode 100644 demos/tutorial/sam_and_bam_io/example.bam.bai
 delete mode 100644 demos/tutorial/sam_and_bam_io/example1.cpp
 delete mode 100644 demos/tutorial/sam_and_bam_io/example1.cpp.stdout
 delete mode 100644 demos/tutorial/sam_and_bam_io/example2.cpp
 delete mode 100644 demos/tutorial/sam_and_bam_io/example2.cpp.stdout
 delete mode 100644 demos/tutorial/sam_and_bam_io/example7.cpp
 delete mode 100644 demos/tutorial/sam_and_bam_io/example7.cpp.stdout
 delete mode 100644 demos/tutorial/sam_and_bam_io/solution1.cpp
 delete mode 100644 demos/tutorial/sam_and_bam_io/solution1.cpp.stdout
 delete mode 100644 demos/tutorial/sam_and_bam_io/solution2.cpp
 delete mode 100644 demos/tutorial/sam_and_bam_io/solution2.cpp.stdout
 delete mode 100644 demos/tutorial/sam_and_bam_io/solution3.cpp
 delete mode 100644 demos/tutorial/sam_and_bam_io/solution3.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/example1.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/example2.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/example3.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/example4.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/example5.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/example6.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/example7.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/example8.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/solution1.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/solution2.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/solution3.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/solution4.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/solution5.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/solution6.cpp.stdout
 delete mode 100644 demos/tutorial/seed_and_extend/solution7.cpp.stdout
 create mode 100644 demos/tutorial/seq_io/example1.cpp
 create mode 100644 demos/tutorial/seq_io/solution1.cpp
 create mode 100644 demos/tutorial/seq_io/solution2.cpp
 create mode 100644 demos/tutorial/seq_io/solution3.cpp
 create mode 100644 demos/tutorial/seq_io/solution4.cpp
 rename demos/{unassigned_or_unused/tutorial_sequence => tutorial/sequence}/CMakeLists.txt (100%)
 rename demos/{unassigned_or_unused/tutorial_sequence => tutorial/sequence}/count_characters.cpp (100%)
 rename demos/{unassigned_or_unused/tutorial_sequence => tutorial/sequence}/count_generic_characters.cpp (100%)
 rename demos/{unassigned_or_unused/tutorial_sequence => tutorial/sequence}/replace_as.cpp (100%)
 rename demos/{unassigned_or_unused/tutorial_sequence => tutorial/sequence}/sequence_all_strings.cpp (100%)
 rename demos/{unassigned_or_unused/tutorial_sequence => tutorial/sequence}/sequence_iterator_demo.cpp (100%)
 delete mode 100644 demos/tutorial/sequence_io/example.fa
 delete mode 100644 demos/tutorial/sequence_io/example.fq
 delete mode 100644 demos/tutorial/sequence_io/example1.cpp
 delete mode 100644 demos/tutorial/sequence_io/example1.cpp.stdout
 delete mode 100644 demos/tutorial/sequence_io/solution1.cpp
 delete mode 100644 demos/tutorial/sequence_io/solution1.cpp.stdout
 delete mode 100644 demos/tutorial/sequence_io/solution2.cpp
 delete mode 100644 demos/tutorial/sequence_io/solution2.cpp.stdout
 delete mode 100644 demos/tutorial/sequence_io/solution3.cpp
 delete mode 100644 demos/tutorial/sequence_io/solution3.cpp.stdout
 delete mode 100644 demos/tutorial/sequence_io/solution4.cpp
 delete mode 100644 demos/tutorial/sequence_io/solution4.cpp.stdout
 delete mode 100644 demos/tutorial/sequences/assignment_1_solution.cpp
 delete mode 100644 demos/tutorial/sequences/assignment_1_solution.cpp.stdout
 delete mode 100644 demos/tutorial/sequences/assignment_2_solution.cpp
 delete mode 100644 demos/tutorial/sequences/assignment_2_solution.cpp.stdout
 delete mode 100644 demos/tutorial/sequences/assignment_3_solution.cpp
 delete mode 100644 demos/tutorial/sequences/assignment_3_solution.cpp.stdout
 delete mode 100644 demos/tutorial/sequences/assignment_4_solution.cpp.stdout
 delete mode 100644 demos/tutorial/sequences/assignment_5_solution.cpp
 delete mode 100644 demos/tutorial/sequences/assignment_5_solution.cpp.stdout
 rename demos/tutorial/sequences/{assignment_4_solution.cpp => lexical_assignment_solution.cpp} (100%)
 rename demos/tutorial/sequences/{assignment_6_solution.cpp => segments_assignment_2_solution.cpp} (100%)
 create mode 100644 demos/tutorial/sequences/segments_assignment_hint.cpp
 create mode 100644 demos/tutorial/sequences/segments_assignment_solution.cpp
 create mode 100644 demos/tutorial/sequences/string_assignment_1_solution.cpp
 delete mode 100644 demos/tutorial/sequences_in_depth/assignment_exact_generous_solution.cpp.stdout
 delete mode 100644 demos/tutorial/sequences_in_depth/example_overflow.cpp
 delete mode 100644 demos/tutorial/sequences_in_depth/example_overflow.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/example.gtf
 delete mode 100644 demos/tutorial/simple_rna_seq/example.sam
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment1.cpp
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment1.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment2.cpp
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment2.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment3.cpp
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment3.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment4.cpp
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment4.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment5.cpp
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_assignment5.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_solution1.cpp
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_solution1.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_solution2.cpp
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_solution2.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_solution3.cpp
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_solution3.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_solution4.cpp
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_solution4.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_solution5.cpp
 delete mode 100644 demos/tutorial/simple_rna_seq/genequant_solution5.cpp.stdout
 delete mode 100644 demos/tutorial/simple_rna_seq/interval_tree.cpp.stdout
 create mode 100644 demos/tutorial/store/CMakeLists.txt
 rename demos/tutorial/{fragment_store/example.fa => store/ex1.fa} (100%)
 rename demos/tutorial/{fragment_store/example.sam => store/ex1.sam} (100%)
 create mode 100644 demos/tutorial/store/store_access_aligned_reads.cpp
 create mode 100644 demos/tutorial/store/store_access_aligned_reads2.cpp
 create mode 100644 demos/tutorial/store/store_diplay_aligned_reads.cpp
 delete mode 100644 demos/tutorial/string_sets/assignment_1_solution.cpp.stdout
 delete mode 100644 demos/tutorial/string_sets/assignment_2_solution.cpp.stdout
 delete mode 100644 demos/tutorial/string_sets/assignment_3_workshop_solution.cpp.stdout
 create mode 100644 demos/tutorial/string_sets/assignment_3b_workshop_solution.cpp
 delete mode 100644 demos/tutorial/string_sets/assignment_4_workshop_solution.cpp.stdout
 delete mode 100644 demos/tutorial/vcf_io/example.vcf
 delete mode 100644 demos/tutorial/vcf_io/example1.cpp.stdout
 delete mode 100644 demos/tutorial/vcf_io/solution1.cpp.stdout
 delete mode 100644 demos/tutorial/vcf_io/solution2.cpp.stdout
 delete mode 100644 demos/tutorial/vcf_io/solution3.cpp.stdout
 delete mode 100644 demos/unassigned_or_unused/bam_library_size.cpp
 delete mode 100644 demos/unassigned_or_unused/benchmark_stream.cpp
 delete mode 100644 demos/unassigned_or_unused/graph_hmm_silent.cpp
 delete mode 100644 demos/unassigned_or_unused/sam2svg.cpp
 rename demos/{dox => }/vcf_io/example.vcf (100%)
 create mode 100644 demos/vcf_io/vcf_stream_read.cpp
 create mode 100644 demos/vcf_io/vcf_stream_read.cpp.stdout
 mode change 100644 => 100755 include/seqan/basic/iterator_range.h
 mode change 100644 => 100755 include/seqan/index/shape_threshold.h
 mode change 100644 => 100755 include/seqan/misc/name_store_cache.h
 mode change 100644 => 100755 include/seqan/random/ext_MersenneTwister.h
 create mode 100644 include/seqan/statistics/.statistics_markov_model.h.swp
 mode change 100644 => 100755 include/seqan/store/store_io_ucsc.h
 delete mode 100644 include/seqan/stream/iostream_bgzf.h
 delete mode 100644 include/seqan/stream/iostream_bzip2.h
 delete mode 100644 include/seqan/stream/iostream_bzip2_impl.h
 delete mode 100644 include/seqan/stream/iostream_zip.h
 delete mode 100644 include/seqan/stream/iostream_zip_impl.h
 delete mode 100644 include/seqan/stream/iostream_zutil.h
 create mode 100644 include/seqan/stream/zipstream/bgzfstream.h
 create mode 100644 include/seqan/stream/zipstream/bgzfstream_impl.h
 create mode 100644 include/seqan/stream/zipstream/bzip2stream.h
 create mode 100644 include/seqan/stream/zipstream/bzip2stream_impl.h
 create mode 100644 include/seqan/stream/zipstream/zipstream.h
 create mode 100644 include/seqan/stream/zipstream/zipstream_impl.h
 create mode 100644 include/seqan/stream/zipstream/zutil.h
 create mode 100644 manual/source/HowTo/knime_node_app.zip
 delete mode 100644 manual/source/Tutorial/AFirstExample.rst
 create mode 100644 manual/source/Tutorial/AnnotationStore.rst
 delete mode 100644 manual/source/Tutorial/FileIOOverview.rst
 create mode 100644 manual/source/Tutorial/FirstStepsInSeqAn.rst
 delete mode 100644 manual/source/Tutorial/GenomeAnnotations.rst
 delete mode 100644 manual/source/Tutorial/GffAndGtfIO.rst
 create mode 100644 manual/source/Tutorial/GffGtfIO.rst
 create mode 100644 manual/source/Tutorial/IndexQGram.rst
 create mode 100644 manual/source/Tutorial/InputOutputOverview.rst
 create mode 100644 manual/source/Tutorial/JournalSet.rst
 delete mode 100644 manual/source/Tutorial/JournaledSet.rst
 create mode 100644 manual/source/Tutorial/MiniBowtie.rst
 delete mode 100644 manual/source/Tutorial/QgramIndex.rst
 delete mode 100644 manual/source/Tutorial/SamAndBamIO.rst
 create mode 100644 manual/source/Tutorial/SamBamIO.rst
 create mode 100644 manual/source/Tutorial/SimpleReadMapping.rst
 rename manual/source/Tutorial/{GenericProgramming.rst => TemplateSubclassing.rst} (100%)
 delete mode 100644 tests/gff_io/example_with_comments.gff
 delete mode 100644 tests/sequence/test_stringset_v2.cpp
 delete mode 100644 util/cmake/CMakeFindJavaCommon.cmake
 delete mode 100644 util/cmake/FindJava.cmake
 create mode 100755 util/py_lib/seqan/dox/tpl/lib/bootstrap-multiselect/js/bootstrap-3.0.0.min.js
 create mode 100644 util/py_lib/seqan/dox/tpl/lib/bootstrap-multiselect/js/jquery-2.0.3.min.js
 create mode 100644 util/py_lib/seqan/dox/tpl/lib/bootstrap-multiselect/js/prettify.js

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqan.git



More information about the debian-med-commit mailing list