├── .gitignore ├── License.txt ├── README.md ├── benchmark ├── IntervalTree.h ├── Makefile ├── def.h ├── evaluation.cpp ├── evaluation.h ├── lostintranslation.cpp └── lostintranslation.h ├── dataset ├── ecsample-truth.txt └── selfSampleData │ ├── README │ ├── pacbio.spec │ └── reference.fasta ├── include ├── align.hpp ├── bloomfilter.hpp ├── chain.hpp ├── common │ ├── AMGGraph.h │ ├── BitMap.h │ ├── CSC.h │ ├── CSR.h │ ├── Deleter.h │ ├── GTgraph │ │ ├── Makefile │ │ ├── Makefile.var │ │ ├── R-MAT │ │ │ ├── COPYRIGHT │ │ │ ├── Makefile │ │ │ ├── config │ │ │ ├── defs.h │ │ │ ├── drive.c │ │ │ ├── globals.c │ │ │ ├── globals.h │ │ │ ├── graph.c │ │ │ ├── graph.h │ │ │ ├── init.c │ │ │ ├── init.h │ │ │ ├── utils.c │ │ │ └── utils.h │ │ ├── README │ │ ├── SSCA2 │ │ │ ├── COPYRIGHT │ │ │ ├── Makefile │ │ │ ├── config │ │ │ ├── defs.h │ │ │ ├── drive.c │ │ │ ├── globals.c │ │ │ ├── globals.h │ │ │ ├── graph.c │ │ │ ├── graph.h │ │ │ ├── init.c │ │ │ ├── init.h │ │ │ ├── utils.c │ │ │ └── utils.h │ │ ├── gen.pdf │ │ ├── random │ │ │ ├── COPYRIGHT │ │ │ ├── Makefile │ │ │ ├── config │ │ │ ├── defs.h │ │ │ ├── drive.c │ │ │ ├── globals.c │ │ │ ├── globals.h │ │ │ ├── graph.c │ │ │ ├── graph.h │ │ │ ├── init.c │ │ │ ├── init.h │ │ │ ├── utils.c │ │ │ └── utils.h │ │ └── sprng2.0-lite │ │ │ ├── Makefile │ │ │ ├── include │ │ │ ├── interface.h │ │ │ ├── sprng.h │ │ │ └── sprng_f.h │ │ │ ├── lib │ │ │ └── Makefile │ │ │ └── src │ │ │ ├── .insertlib │ │ │ ├── .template.c │ │ │ ├── Makefile │ │ │ ├── checkid.c │ │ │ ├── cmrg │ │ │ ├── Makefile │ │ │ ├── cmrg.c │ │ │ ├── cmrg.data │ │ │ └── cmrg.h │ │ │ ├── communicate.c │ │ │ ├── cputime.c │ │ │ ├── cputime.h │ │ │ ├── drand.c │ │ │ ├── fwrap.h │ │ │ ├── fwrap_.h │ │ │ ├── fwrap_mpi.c │ │ │ ├── interface.h │ │ │ ├── lcg │ │ │ ├── Makefile │ │ │ ├── READMEver2.CHANGES │ │ │ ├── lcg.c │ │ │ ├── lcg.data │ │ │ └── lcg.h │ │ │ ├── lcg64 │ │ │ ├── Makefile │ │ │ ├── lcg64.c │ │ │ ├── lcg64.data │ │ │ └── lcg64.h │ │ │ ├── lfg │ │ │ ├── Makefile │ │ │ ├── lfg.c │ │ │ ├── lfg.data │ │ │ └── lfg.h │ │ │ ├── makeseed.c │ │ │ ├── memory.c │ │ │ ├── memory.h │ │ │ ├── mlfg │ │ │ ├── Makefile │ │ │ ├── int64.h │ │ │ ├── mlfg.c │ │ │ ├── mlfg.data │ │ │ └── mlfg.h │ │ │ ├── multiply.h │ │ │ ├── primelist_32.h │ │ │ ├── primelist_64.h │ │ │ ├── primes_32.c │ │ │ ├── primes_32.h │ │ │ ├── primes_64.c │ │ │ ├── primes_64.h │ │ │ ├── simple.c │ │ │ ├── simple_.h │ │ │ ├── simple_mpi.c │ │ │ ├── sprng.h │ │ │ ├── sprng │ │ │ ├── Makefile │ │ │ ├── READMEver2.CHANGES │ │ │ └── sprng.c │ │ │ ├── sprng_f.h │ │ │ ├── store.c │ │ │ ├── store.h │ │ │ ├── timing.c │ │ │ └── timingf.f │ ├── HeapEntry.h │ ├── IO.h │ ├── MPIType.h │ ├── Triple.h │ ├── bellaio.h │ ├── common.h │ ├── makefile │ ├── overridenew.h │ ├── transpose.h │ └── utility.h ├── cxxopts.hpp ├── kmercount.hpp ├── markov.hpp ├── minimizer.hpp ├── overlap.hpp └── syncmer.hpp ├── kmercode ├── Buffer.c ├── Buffer.h ├── Kmer.cpp ├── Kmer.hpp ├── ParallelFASTQ.h ├── bound.cpp ├── bound.hpp ├── common.h ├── fq_reader.c ├── fq_reader.h ├── hash_funcs.c ├── hash_funcs.h ├── hyperloglog.hpp ├── main.cpp ├── makefile └── usage ├── libbloom ├── .gitignore ├── CMakeLists.txt ├── LICENSE ├── Makefile ├── README ├── bloom.cpp ├── bloom.h ├── bloom64.cpp ├── bloom64.h ├── murmur2 │ ├── CMakeLists.txt │ ├── MurmurHash2.c │ ├── README │ └── murmurhash2.h └── test.cpp ├── libcuckoo ├── cuckoohash_config.hh ├── cuckoohash_map.hh ├── cuckoohash_util.hh └── libcuckoo_bucket_container.hh ├── loganGPU ├── functions.cuh ├── logan.cuh ├── score.cuh └── seed.cuh ├── makefile-mac ├── makefile-nersc ├── optlist ├── optlist.c └── optlist.h ├── sanitytests ├── reversecomptest.fastq └── reversecomptest.txt ├── script ├── README.md ├── SAMparser.py ├── mafconvert.py ├── morescript │ ├── IntervalTree.h │ ├── README.md │ ├── chainedMarkov.py │ ├── checkOutput.cpp │ ├── checkOutput.py │ ├── daligner_scripts │ │ ├── example-translation-environment.sh │ │ ├── parserLAdump.py │ │ ├── run_daligner.slurm │ │ ├── run_daligner_celegans.slurm │ │ ├── tinytest.dump │ │ ├── translateDalignerOut.sh │ │ ├── valgrind_daligner.slurm │ │ └── zip_tag.py │ ├── evaluation.cpp │ ├── evaluation.h │ ├── exactMarkov.py │ ├── filterby_overlap_length.py │ ├── mafconvert.py │ └── makefile └── run-bella-pipeline.sh ├── seqan └── seqan │ ├── align.h │ ├── align │ ├── align_base.h │ ├── align_cols.h │ ├── align_config.h │ ├── align_interface_wrapper.h │ ├── align_iterator_base.h │ ├── align_metafunctions.h │ ├── align_traceback.h │ ├── alignment_algorithm_tags.h │ ├── alignment_operations.h │ ├── dp_algorithm_impl.h │ ├── dp_align_simd_helper.h │ ├── dp_band.h │ ├── dp_cell.h │ ├── dp_cell_affine.h │ ├── dp_cell_dynamic.h │ ├── dp_cell_linear.h │ ├── dp_context.h │ ├── dp_formula.h │ ├── dp_formula_affine.h │ ├── dp_formula_dynamic.h │ ├── dp_formula_linear.h │ ├── dp_matrix.h │ ├── dp_matrix_navigator.h │ ├── dp_matrix_navigator_score_matrix.h │ ├── dp_matrix_navigator_score_matrix_sparse.h │ ├── dp_matrix_navigator_trace_matrix.h │ ├── dp_matrix_sparse.h │ ├── dp_meta_info.h │ ├── dp_profile.h │ ├── dp_scout.h │ ├── dp_scout_simd.h │ ├── dp_setup.h │ ├── dp_trace_segment.h │ ├── dp_traceback_adaptor.h │ ├── dp_traceback_impl.h │ ├── evaluate_alignment.h │ ├── fragment.h │ ├── gap_anchor.h │ ├── gapped_value_type.h │ ├── gaps_anchor.h │ ├── gaps_array.h │ ├── gaps_base.h │ ├── gaps_iterator_anchor.h │ ├── gaps_iterator_array.h │ ├── gaps_iterator_base.h │ ├── global_alignment_banded.h │ ├── global_alignment_hirschberg_impl.h │ ├── global_alignment_myers_hirschberg_impl.h │ ├── global_alignment_myers_impl.h │ ├── global_alignment_specialized.h │ ├── global_alignment_unbanded.h │ ├── local_alignment_banded.h │ ├── local_alignment_banded_waterman_eggert_impl.h │ ├── local_alignment_enumeration.h │ ├── local_alignment_enumeration_banded.h │ ├── local_alignment_enumeration_unbanded.h │ ├── local_alignment_unbanded.h │ ├── local_alignment_waterman_eggert_impl.h │ └── matrix_base.h │ ├── align_extend.h │ ├── align_extend │ ├── align_extend.h │ ├── align_extend_base.h │ └── dp_scout_xdrop.h │ ├── align_profile.h │ ├── align_profile │ ├── add_to_profile.h │ └── score_profile_seq.h │ ├── align_split.h │ ├── align_split │ ├── align_split_interface.h │ └── dp_scout_split.h │ ├── alignment_free.h │ ├── alignment_free │ ├── af_d2.h │ ├── af_d2star.h │ ├── af_d2z.h │ ├── af_n2.h │ ├── alignment_free_base.h │ ├── alignment_free_comparison.h │ └── kmer_functions.h │ ├── arg_parse.h │ ├── arg_parse │ ├── arg_parse_argument.h │ ├── arg_parse_ctd_support.h │ ├── arg_parse_doc.h │ ├── arg_parse_exceptions.h │ ├── arg_parse_option.h │ ├── arg_parse_parse.h │ ├── arg_parse_type_support.h │ ├── arg_parse_version_check.h │ ├── argument_parser.h │ ├── tool_doc.h │ └── xml_support.h │ ├── bam_io.h │ ├── bam_io │ ├── bam_alignment_record.h │ ├── bam_alignment_record_util.h │ ├── bam_file.h │ ├── bam_header_record.h │ ├── bam_index_bai.h │ ├── bam_io_context.h │ ├── bam_sam_conversion.h │ ├── bam_scanner_cache.h │ ├── bam_tags_dict.h │ ├── cigar.h │ ├── read_bam.h │ ├── read_sam.h │ ├── write_bam.h │ └── write_sam.h │ ├── basic.h │ ├── basic │ ├── aggregate_concept.h │ ├── allocator_chunkpool.h │ ├── allocator_interface.h │ ├── allocator_multipool.h │ ├── allocator_simple.h │ ├── allocator_singlepool.h │ ├── allocator_to_std.h │ ├── alphabet_adapt_builtins.h │ ├── alphabet_bio.h │ ├── alphabet_concept.h │ ├── alphabet_math.h │ ├── alphabet_profile.h │ ├── alphabet_qualities.h │ ├── alphabet_residue.h │ ├── alphabet_residue_funcs.h │ ├── alphabet_residue_tabs.h │ ├── alphabet_simple_type.h │ ├── alphabet_storage.h │ ├── array_construct_destruct.h │ ├── basic_aggregate.h │ ├── basic_allocator.h │ ├── basic_alphabet.h │ ├── basic_concept.h │ ├── basic_container.h │ ├── basic_debug.h │ ├── basic_device.h │ ├── basic_exception.h │ ├── basic_functors.h │ ├── basic_fundamental.h │ ├── basic_iterator.h │ ├── basic_math.h │ ├── basic_metaprogramming.h │ ├── basic_parallelism.h │ ├── basic_proxy.h │ ├── basic_simd_vector.h │ ├── basic_smart_pointer.h │ ├── basic_stream.h │ ├── basic_tangle.h │ ├── basic_type.h │ ├── basic_view.h │ ├── boost_preprocessor_subset.h │ ├── builtin_functions.h │ ├── concept_checking.h │ ├── container_concept.h │ ├── debug_helper.h │ ├── debug_test_system.h │ ├── fundamental_chunking.h │ ├── fundamental_comparison.h │ ├── fundamental_concepts.h │ ├── fundamental_conversion.h │ ├── fundamental_metafunctions.h │ ├── fundamental_tags.h │ ├── fundamental_transport.h │ ├── holder_base.h │ ├── holder_simple.h │ ├── holder_tristate.h │ ├── hosted_type_interface.h │ ├── iterator_adapt_pointer.h │ ├── iterator_adapt_std.h │ ├── iterator_adaptor.h │ ├── iterator_base.h │ ├── iterator_concept.h │ ├── iterator_counting.h │ ├── iterator_interface.h │ ├── iterator_position.h │ ├── iterator_range.h │ ├── iterator_zip.h │ ├── macro_deprecated.h │ ├── math_functions.h │ ├── math_log_space_value.h │ ├── metaprogramming_control.h │ ├── metaprogramming_enable_if.h │ ├── metaprogramming_logic.h │ ├── metaprogramming_math.h │ ├── metaprogramming_type.h │ ├── metaprogramming_type_algebra.h │ ├── pair_base.h │ ├── pair_bit_compressed.h │ ├── pair_packed.h │ ├── profiling.h │ ├── property_map_concept.h │ ├── proxy_base.h │ ├── proxy_iterator.h │ ├── test_system.h │ ├── triple_base.h │ ├── triple_packed.h │ ├── tuple_base.h │ ├── tuple_bit_compressed.h │ └── volatile_ptr.h │ ├── bed_io.h │ ├── bed_io │ ├── bed_file.h │ ├── bed_record.h │ ├── read_bed.h │ └── write_bed.h │ ├── blast.h │ ├── blast │ ├── blast_base.h │ ├── blast_io_context.h │ ├── blast_record.h │ ├── blast_report_out.h │ ├── blast_statistics.h │ ├── blast_tabular.h │ ├── blast_tabular_in.h │ ├── blast_tabular_lowlevel.h │ └── blast_tabular_out.h │ ├── consensus.h │ ├── consensus │ ├── consensus_aligner.h │ ├── consensus_aligner_interface.h │ ├── consensus_alignment_options.h │ ├── consensus_base.h │ ├── consensus_builder.h │ ├── consensus_library.h │ ├── consensus_realign.h │ ├── consensus_score.h │ ├── overlap_info_computation.h │ └── overlapper.h │ ├── file.h │ ├── file │ ├── file_base.h │ ├── file_cstyle.h │ ├── file_forwards.h │ ├── file_interface.h │ ├── file_mapping.h │ ├── file_page.h │ ├── string_external.h │ └── string_mmap.h │ ├── find.h │ ├── find │ ├── find_abndm.h │ ├── find_ahocorasick.h │ ├── find_base.h │ ├── find_begin.h │ ├── find_bndm.h │ ├── find_bom.h │ ├── find_hamming_simple.h │ ├── find_horspool.h │ ├── find_lambda.h │ ├── find_multi.h │ ├── find_multiple_bfam.h │ ├── find_multiple_shiftand.h │ ├── find_myers_ukkonen.h │ ├── find_pattern_base.h │ ├── find_pex.h │ ├── find_score.h │ ├── find_set_horspool.h │ ├── find_shiftand.h │ ├── find_shiftor.h │ ├── find_simple.h │ ├── find_wild_shiftand.h │ └── find_wumanber.h │ ├── gff_io.h │ ├── gff_io │ ├── gff_file.h │ └── gff_io_base.h │ ├── graph_algorithms.h │ ├── graph_algorithms │ ├── all_pairs_shortest_path.h │ ├── bellman_ford.h │ ├── bipartite_matching.h │ ├── breadth_first_search.h │ ├── connected_components.h │ ├── depth_first_search.h │ ├── dijkstra.h │ ├── floyd_warshall.h │ ├── ford_fulkerson.h │ ├── graph_algorithm_heap_tree.h │ ├── graph_algorithm_hmm.h │ ├── graph_algorithm_lis_his.h │ ├── kruskal.h │ ├── path_growing.h │ ├── prim.h │ ├── single_source_shortest_path.h │ ├── strongly_connected_compnents.h │ ├── topological_sort.h │ ├── transitive_closure.h │ ├── weakly_connected_components.h │ └── weighted_bipartite_matching.h │ ├── graph_align.h │ ├── graph_align │ ├── graph_algorithm_refine_align.h │ ├── graph_algorithm_refine_aligngraph.h │ ├── graph_algorithm_refine_annotation.h │ ├── graph_algorithm_refine_exact.h │ ├── graph_algorithm_refine_exact_iterative.h │ ├── graph_algorithm_refine_fragment.h │ ├── graph_algorithm_refine_inexact.h │ ├── graph_algorithm_refine_scoring.h │ ├── graph_impl_align.h │ └── graph_impl_align_adapt.h │ ├── graph_msa.h │ ├── graph_msa │ ├── graph_align_tcoffee_base.h │ ├── graph_align_tcoffee_distance.h │ ├── graph_align_tcoffee_guidetree.h │ ├── graph_align_tcoffee_io.h │ ├── graph_align_tcoffee_kmer.h │ ├── graph_align_tcoffee_library.h │ ├── graph_align_tcoffee_msa.h │ ├── graph_align_tcoffee_progressive.h │ └── graph_align_tcoffee_refinement.h │ ├── graph_types.h │ ├── graph_types │ ├── graph_base.h │ ├── graph_drawing.h │ ├── graph_edgestump.h │ ├── graph_idmanager.h │ ├── graph_impl_automaton.h │ ├── graph_impl_directed.h │ ├── graph_impl_hmm.h │ ├── graph_impl_oracle.h │ ├── graph_impl_tree.h │ ├── graph_impl_trie.h │ ├── graph_impl_undirected.h │ ├── graph_impl_wordgraph.h │ ├── graph_interface.h │ ├── graph_iterator.h │ ├── graph_iterator_adjacency.h │ ├── graph_iterator_bfs.h │ ├── graph_iterator_dfs.h │ ├── graph_iterator_edge.h │ ├── graph_iterator_outedge.h │ ├── graph_iterator_vertex.h │ ├── graph_utility_parsing.h │ ├── property_map_generic.h │ ├── property_map_internal.h │ └── property_map_internal_pointer.h │ ├── index.h │ ├── index │ ├── find2_backtracking.h │ ├── find2_base.h │ ├── find2_functors.h │ ├── find2_index.h │ ├── find2_index_multi.h │ ├── find2_vstree_factory.h │ ├── find_backtracking.h │ ├── find_index.h │ ├── find_index_approx.h │ ├── find_index_binary.h │ ├── find_index_esa.h │ ├── find_index_lambda.h │ ├── find_index_qgram.h │ ├── find_pigeonhole.h │ ├── find_quasar.h │ ├── find_swift.h │ ├── index_base.h │ ├── index_bidirectional.h │ ├── index_bidirectional_stree.h │ ├── index_bifm.h │ ├── index_bifm_stree.h │ ├── index_bwt.h │ ├── index_childtab.h │ ├── index_device.h │ ├── index_dfi.h │ ├── index_esa_algs.h │ ├── index_esa_algs_multi.h │ ├── index_esa_base.h │ ├── index_esa_drawing.h │ ├── index_esa_stree.h │ ├── index_fm.h │ ├── index_fm_compressed_sa.h │ ├── index_fm_compressed_sa_iterator.h │ ├── index_fm_dox.h │ ├── index_fm_lf_table.h │ ├── index_fm_rank_dictionary_base.h │ ├── index_fm_rank_dictionary_levels.h │ ├── index_fm_rank_dictionary_naive.h │ ├── index_fm_rank_dictionary_wt.h │ ├── index_fm_right_array_binary_tree.h │ ├── index_fm_right_array_binary_tree_iterator.h │ ├── index_fm_sparse_string.h │ ├── index_fm_stree.h │ ├── index_forwards.h │ ├── index_lcp.h │ ├── index_lcp_tree.h │ ├── index_pizzachili.h │ ├── index_pizzachili_find.h │ ├── index_pizzachili_string.h │ ├── index_qgram.h │ ├── index_qgram_bucketrefinement.h │ ├── index_qgram_openaddressing.h │ ├── index_qgram_stree.h │ ├── index_sa_btree.h │ ├── index_sa_bwtwalk.h │ ├── index_sa_lss.h │ ├── index_sa_mm.h │ ├── index_sa_qsort.h │ ├── index_sa_stree.h │ ├── index_sa_truncated.h │ ├── index_shawarma.h │ ├── index_shims.h │ ├── index_skew3.h │ ├── index_skew7.h │ ├── index_skew7_multi.h │ ├── index_view.h │ ├── index_wotd.h │ ├── pipe_merger3.h │ ├── pipe_merger7.h │ ├── pizzachili_api.h │ ├── pump_extender3.h │ ├── pump_extender7.h │ ├── pump_lcp_core.h │ ├── pump_separator7.h │ ├── radix.h │ ├── repeat_base.h │ ├── shape_base.h │ ├── shape_gapped.h │ ├── shape_minimizer.h │ ├── shape_onegapped.h │ ├── shape_predefined.h │ └── shape_threshold.h │ ├── journaled_set.h │ ├── journaled_set │ ├── journal_alignment_interface.h │ ├── journal_alignment_traceback_adaptor.h │ ├── journaled_set_base.h │ ├── journaled_set_impl.h │ ├── journaled_set_join.h │ ├── journaled_set_join_config.h │ ├── journaled_set_join_global_align_compact.h │ ├── journaled_set_join_global_align_manhatten.h │ ├── journaled_set_journal_trace_descriptor.h │ └── score_biaffine.h │ ├── journaled_string_tree.h │ ├── journaled_string_tree │ ├── delta_map.h │ ├── delta_map_entry.h │ ├── delta_map_iterator.h │ ├── delta_store.h │ ├── journaled_string_tree_base.h │ ├── journaled_string_tree_impl.h │ ├── journaled_string_tree_sequence_buffer.h │ ├── journaled_string_tree_traverser.h │ ├── journaled_string_tree_traverser_node.h │ ├── journaled_string_tree_traverser_util.h │ ├── jst_extension_base.h │ ├── jst_extension_horspool.h │ ├── jst_extension_myers_ukkonen.h │ ├── jst_extension_shiftand.h │ ├── jst_extension_shiftor.h │ ├── observable.h │ └── stack_observer.h │ ├── map.h │ ├── map │ ├── map_adapter_stl.h │ ├── map_base.h │ ├── map_chooser.h │ ├── map_skiplist.h │ ├── map_vector.h │ ├── sumlist.h │ ├── sumlist_mini.h │ └── sumlist_skip.h │ ├── math.h │ ├── math │ ├── math_common_factor.h │ ├── math_operators.h │ └── math_rational.h │ ├── misc │ ├── accumulators.h │ ├── base.h │ ├── bit_twiddling.h │ ├── bit_twiddling_functors.h │ ├── dequeue.h │ ├── edit_environment.h │ ├── interval_tree.h │ ├── map.h │ ├── memset.h │ ├── name_store_cache.h │ ├── priority_type_base.h │ ├── priority_type_heap.h │ ├── set.h │ ├── svg.h │ ├── terminal.h │ └── union_find.h │ ├── modifier.h │ ├── modifier │ ├── cyclic_shape.h │ ├── modifier_alphabet.h │ ├── modifier_alphabet_expansion.h │ ├── modifier_cyclic_shape.h │ ├── modifier_functors.h │ ├── modifier_iterator.h │ ├── modifier_padding.h │ ├── modifier_position.h │ ├── modifier_reverse.h │ ├── modifier_shortcuts.h │ ├── modifier_string.h │ └── modifier_view.h │ ├── parallel.h │ ├── parallel │ ├── parallel_algorithms.h │ ├── parallel_atomic_misc.h │ ├── parallel_atomic_primitives.h │ ├── parallel_lock.h │ ├── parallel_macros.h │ ├── parallel_queue.h │ ├── parallel_queue_suspendable.h │ ├── parallel_resource_pool.h │ ├── parallel_sequence.h │ ├── parallel_serializer.h │ ├── parallel_splitting.h │ └── parallel_tags.h │ ├── parse_lm.h │ ├── parse_lm │ ├── local_match_store.h │ ├── parse_blastn_tabular.h │ ├── parse_lastz_general.h │ └── parse_stellar_gff.h │ ├── pipe.h │ ├── pipe │ ├── pipe_base.h │ ├── pipe_caster.h │ ├── pipe_counter.h │ ├── pipe_echoer.h │ ├── pipe_edit_environment.h │ ├── pipe_filter.h │ ├── pipe_iterator.h │ ├── pipe_joiner.h │ ├── pipe_namer.h │ ├── pipe_sampler.h │ ├── pipe_shifter.h │ ├── pipe_source.h │ ├── pipe_tupler.h │ ├── pool_base.h │ ├── pool_mapper.h │ └── pool_sorter.h │ ├── platform.h │ ├── random.h │ ├── random │ ├── random_base.h │ ├── random_beta.h │ └── random_util.h │ ├── realign.h │ ├── realign │ ├── realign_base.h │ └── realign_helper_functions.h │ ├── reduced_aminoacid.h │ ├── reduced_aminoacid │ ├── reduced_aminoacid_base.h │ ├── reduced_aminoacid_base_late.h │ ├── reduced_aminoacid_cluster_red_base.h │ ├── reduced_aminoacid_cluster_red_tables_20_to_n_b62.h │ ├── reduced_aminoacid_cluster_red_tables_22_to_n_b62.h │ ├── reduced_aminoacid_cluster_red_tables_24_to_n_b62.h │ ├── reduced_aminoacid_murphy10_base.h │ └── reduced_aminoacid_murphy10_tables.h │ ├── rna_io.h │ ├── rna_io │ ├── bpseq_read_write.h │ ├── connect_read_write.h │ ├── dot_bracket_read_write.h │ ├── ebpseq_read_write.h │ ├── rna_header.h │ ├── rna_io_context.h │ ├── rna_record.h │ ├── rna_struct_file.h │ ├── stockholm_read_write.h │ └── vienna_read_write.h │ ├── roi_io.h │ ├── roi_io │ ├── read_roi.h │ ├── roi_file.h │ ├── roi_io_context.h │ ├── roi_record.h │ └── write_roi.h │ ├── score.h │ ├── score │ ├── score_base.h │ ├── score_edit.h │ ├── score_matrix.h │ ├── score_matrix_data.h │ ├── score_matrix_dyn.h │ ├── score_matrix_io.h │ ├── score_simd_wrapper.h │ └── score_simple.h │ ├── seeds.h │ ├── seeds │ ├── banded_chain_alignment.h │ ├── banded_chain_alignment_impl.h │ ├── banded_chain_alignment_profile.h │ ├── banded_chain_alignment_scout.h │ ├── banded_chain_alignment_traceback.h │ ├── basic_iter_indirect.h │ ├── my_seed.cpp │ ├── seeds_base.h │ ├── seeds_combination.h │ ├── seeds_extension.h │ ├── seeds_global_chaining.h │ ├── seeds_global_chaining_base.h │ ├── seeds_global_chaining_gusfield.h │ ├── seeds_seed_base.h │ ├── seeds_seed_chained.h │ ├── seeds_seed_diagonal.h │ ├── seeds_seed_set_base.h │ ├── seeds_seed_set_non_scored.h │ ├── seeds_seed_set_scored.h │ ├── seeds_seed_set_unordered.h │ └── seeds_seed_simple.h │ ├── seq_io.h │ ├── seq_io │ ├── bam_sam.h │ ├── fai_index.h │ ├── fasta_fastq.h │ ├── genomic_region.h │ ├── read_embl.h │ ├── read_genbank.h │ └── sequence_file.h │ ├── sequence.h │ ├── sequence │ ├── adapt_array_pointer.h │ ├── adapt_stl_container.h │ ├── container_view.h │ ├── container_view_zip.h │ ├── iter_concat_virtual.h │ ├── segment_base.h │ ├── segment_infix.h │ ├── segment_prefix.h │ ├── segment_suffix.h │ ├── segment_utils.h │ ├── sequence_concatenator.h │ ├── sequence_forwards.h │ ├── sequence_interface.h │ ├── sequence_lexical.h │ ├── sequence_shortcuts.h │ ├── string_alloc.h │ ├── string_array.h │ ├── string_base.h │ ├── string_block.h │ ├── string_cstyle.h │ ├── string_packed.h │ ├── string_packed_old.h │ ├── string_set_base.h │ ├── string_set_concat_direct.h │ ├── string_set_dependent_generous.h │ ├── string_set_dependent_tight.h │ ├── string_set_owner.h │ ├── string_set_segment.h │ └── string_set_view.h │ ├── sequence_journaled.h │ ├── sequence_journaled │ ├── journal_entries_sorted_array.h │ ├── journal_entry.h │ ├── sequence_journaled.h │ ├── sequence_journaled_iterator.h │ └── sequence_journaled_iterator_fast.h │ ├── simple_intervals_io.h │ ├── simple_intervals_io │ ├── simple_intervals_file.h │ └── simple_intervals_io.h │ ├── statistics.h │ ├── statistics │ ├── statistics_base.h │ └── statistics_markov_model.h │ ├── store.h │ ├── store │ ├── store_align.h │ ├── store_align_intervals.h │ ├── store_all.h │ ├── store_annotation.h │ ├── store_base.h │ ├── store_contig.h │ ├── store_intervaltree.h │ ├── store_io.h │ ├── store_io_gff.h │ ├── store_io_sam.h │ ├── store_io_ucsc.h │ ├── store_library.h │ ├── store_matepair.h │ └── store_read.h │ ├── stream.h │ ├── stream │ ├── adapt_ios.h │ ├── buffered_stream.h │ ├── file_stream.h │ ├── formatted_file.h │ ├── guess_format.h │ ├── iostream_bgzf.h │ ├── iostream_bzip2.h │ ├── iostream_bzip2_impl.h │ ├── iostream_zip.h │ ├── iostream_zip_impl.h │ ├── iostream_zutil.h │ ├── iter_stream.h │ ├── lexical_cast.h │ ├── stream_base.h │ ├── stream_compressor.h │ ├── tokenization.h │ └── virtual_stream.h │ ├── system.h │ ├── system │ ├── file_async.h │ ├── file_directory.h │ ├── file_forwards.h │ ├── file_sync.h │ ├── system_base.h │ ├── system_event_win.h │ └── system_forwards.h │ ├── tabix_io.h │ ├── tabix_io │ └── tabix_index_tbi.h │ ├── translation.h │ ├── translation │ ├── translation.h │ └── translation_tables.h │ ├── ucsc_io.h │ ├── ucsc_io │ ├── ucsc_file.h │ ├── ucsc_io.h │ └── ucsc_record.h │ ├── vcf_io.h │ ├── vcf_io │ ├── read_vcf.h │ ├── vcf_file.h │ ├── vcf_header.h │ ├── vcf_header_record.h │ ├── vcf_io_context.h │ ├── vcf_record.h │ └── write_vcf.h │ └── version.h ├── src ├── CSC.cpp ├── CSR.cpp ├── main.cpp ├── main.cu └── mkl_free_main.cpp └── xavier ├── README.md ├── demo.cpp ├── makefile ├── score.h ├── simdutils.h ├── tester.py ├── utils.h └── xavier.h /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/.gitignore -------------------------------------------------------------------------------- /License.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/License.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/README.md -------------------------------------------------------------------------------- /benchmark/IntervalTree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/benchmark/IntervalTree.h -------------------------------------------------------------------------------- /benchmark/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/benchmark/Makefile -------------------------------------------------------------------------------- /benchmark/def.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/benchmark/def.h -------------------------------------------------------------------------------- /benchmark/evaluation.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/benchmark/evaluation.cpp -------------------------------------------------------------------------------- /benchmark/evaluation.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/benchmark/evaluation.h -------------------------------------------------------------------------------- /benchmark/lostintranslation.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/benchmark/lostintranslation.cpp -------------------------------------------------------------------------------- /benchmark/lostintranslation.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/benchmark/lostintranslation.h -------------------------------------------------------------------------------- /dataset/ecsample-truth.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/dataset/ecsample-truth.txt -------------------------------------------------------------------------------- /dataset/selfSampleData/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/dataset/selfSampleData/README -------------------------------------------------------------------------------- /dataset/selfSampleData/pacbio.spec: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/dataset/selfSampleData/pacbio.spec -------------------------------------------------------------------------------- /dataset/selfSampleData/reference.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/dataset/selfSampleData/reference.fasta -------------------------------------------------------------------------------- /include/align.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/align.hpp -------------------------------------------------------------------------------- /include/bloomfilter.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/bloomfilter.hpp -------------------------------------------------------------------------------- /include/chain.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/chain.hpp -------------------------------------------------------------------------------- /include/common/AMGGraph.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/AMGGraph.h -------------------------------------------------------------------------------- /include/common/BitMap.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/BitMap.h -------------------------------------------------------------------------------- /include/common/CSC.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/CSC.h -------------------------------------------------------------------------------- /include/common/CSR.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/CSR.h -------------------------------------------------------------------------------- /include/common/Deleter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/Deleter.h -------------------------------------------------------------------------------- /include/common/GTgraph/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/Makefile.var: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/Makefile.var -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/COPYRIGHT: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/COPYRIGHT -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/config -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/defs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/defs.h -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/drive.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/drive.c -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/globals.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/globals.c -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/globals.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/globals.h -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/graph.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/graph.c -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/graph.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/graph.h -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/init.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/init.c -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/init.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/init.h -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/utils.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/utils.c -------------------------------------------------------------------------------- /include/common/GTgraph/R-MAT/utils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/R-MAT/utils.h -------------------------------------------------------------------------------- /include/common/GTgraph/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/README -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/COPYRIGHT: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/COPYRIGHT -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/config -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/defs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/defs.h -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/drive.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/drive.c -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/globals.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/globals.c -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/globals.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/globals.h -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/graph.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/graph.c -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/graph.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/graph.h -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/init.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/init.c -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/init.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/init.h -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/utils.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/utils.c -------------------------------------------------------------------------------- /include/common/GTgraph/SSCA2/utils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/SSCA2/utils.h -------------------------------------------------------------------------------- /include/common/GTgraph/gen.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/gen.pdf -------------------------------------------------------------------------------- /include/common/GTgraph/random/COPYRIGHT: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/COPYRIGHT -------------------------------------------------------------------------------- /include/common/GTgraph/random/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/random/config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/config -------------------------------------------------------------------------------- /include/common/GTgraph/random/defs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/defs.h -------------------------------------------------------------------------------- /include/common/GTgraph/random/drive.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/drive.c -------------------------------------------------------------------------------- /include/common/GTgraph/random/globals.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/globals.c -------------------------------------------------------------------------------- /include/common/GTgraph/random/globals.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/globals.h -------------------------------------------------------------------------------- /include/common/GTgraph/random/graph.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/graph.c -------------------------------------------------------------------------------- /include/common/GTgraph/random/graph.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/graph.h -------------------------------------------------------------------------------- /include/common/GTgraph/random/init.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/init.c -------------------------------------------------------------------------------- /include/common/GTgraph/random/init.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/init.h -------------------------------------------------------------------------------- /include/common/GTgraph/random/utils.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/utils.c -------------------------------------------------------------------------------- /include/common/GTgraph/random/utils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/random/utils.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/include/sprng.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/include/sprng.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/include/sprng_f.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/include/sprng_f.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/lib/Makefile: -------------------------------------------------------------------------------- 1 | clean : 2 | rm -f *.o libsprng.a 3 | -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/.insertlib: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/.template.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/.template.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/checkid.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/checkid.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/cmrg/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/cmrg/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/cmrg/cmrg.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/cmrg/cmrg.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/cmrg/cmrg.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/cmrg/cmrg.data -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/cmrg/cmrg.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/cmrg/cmrg.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/communicate.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/communicate.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/cputime.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/cputime.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/cputime.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/cputime.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/drand.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/drand.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/fwrap.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/fwrap.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/fwrap_.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/fwrap_.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/fwrap_mpi.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/fwrap_mpi.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/interface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/interface.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lcg/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lcg/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lcg/lcg.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lcg/lcg.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lcg/lcg.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lcg/lcg.data -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lcg/lcg.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lcg/lcg.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lcg64/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lcg64/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lcg64/lcg64.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lcg64/lcg64.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lcg64/lcg64.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lcg64/lcg64.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lfg/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lfg/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lfg/lfg.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lfg/lfg.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lfg/lfg.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lfg/lfg.data -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/lfg/lfg.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/lfg/lfg.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/makeseed.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/makeseed.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/memory.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/memory.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/memory.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/memory.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/mlfg/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/mlfg/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/mlfg/int64.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/mlfg/int64.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/mlfg/mlfg.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/mlfg/mlfg.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/mlfg/mlfg.data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/mlfg/mlfg.data -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/mlfg/mlfg.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/mlfg/mlfg.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/multiply.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/multiply.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/primelist_32.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/primelist_32.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/primelist_64.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/primelist_64.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/primes_32.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/primes_32.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/primes_32.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/primes_32.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/primes_64.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/primes_64.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/primes_64.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/primes_64.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/simple.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/simple.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/simple_.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/simple_.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/simple_mpi.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/simple_mpi.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/sprng.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/sprng.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/sprng/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/sprng/Makefile -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/sprng_f.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/sprng_f.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/store.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/store.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/store.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/store.h -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/timing.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/timing.c -------------------------------------------------------------------------------- /include/common/GTgraph/sprng2.0-lite/src/timingf.f: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/GTgraph/sprng2.0-lite/src/timingf.f -------------------------------------------------------------------------------- /include/common/HeapEntry.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/HeapEntry.h -------------------------------------------------------------------------------- /include/common/IO.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/IO.h -------------------------------------------------------------------------------- /include/common/MPIType.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/MPIType.h -------------------------------------------------------------------------------- /include/common/Triple.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/Triple.h -------------------------------------------------------------------------------- /include/common/bellaio.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/bellaio.h -------------------------------------------------------------------------------- /include/common/common.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/common.h -------------------------------------------------------------------------------- /include/common/makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/makefile -------------------------------------------------------------------------------- /include/common/overridenew.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/overridenew.h -------------------------------------------------------------------------------- /include/common/transpose.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/transpose.h -------------------------------------------------------------------------------- /include/common/utility.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/common/utility.h -------------------------------------------------------------------------------- /include/cxxopts.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/cxxopts.hpp -------------------------------------------------------------------------------- /include/kmercount.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/kmercount.hpp -------------------------------------------------------------------------------- /include/markov.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/markov.hpp -------------------------------------------------------------------------------- /include/minimizer.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/minimizer.hpp -------------------------------------------------------------------------------- /include/overlap.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/overlap.hpp -------------------------------------------------------------------------------- /include/syncmer.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/include/syncmer.hpp -------------------------------------------------------------------------------- /kmercode/Buffer.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/Buffer.c -------------------------------------------------------------------------------- /kmercode/Buffer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/Buffer.h -------------------------------------------------------------------------------- /kmercode/Kmer.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/Kmer.cpp -------------------------------------------------------------------------------- /kmercode/Kmer.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/Kmer.hpp -------------------------------------------------------------------------------- /kmercode/ParallelFASTQ.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/ParallelFASTQ.h -------------------------------------------------------------------------------- /kmercode/bound.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/bound.cpp -------------------------------------------------------------------------------- /kmercode/bound.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/bound.hpp -------------------------------------------------------------------------------- /kmercode/common.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/common.h -------------------------------------------------------------------------------- /kmercode/fq_reader.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/fq_reader.c -------------------------------------------------------------------------------- /kmercode/fq_reader.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/fq_reader.h -------------------------------------------------------------------------------- /kmercode/hash_funcs.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/hash_funcs.c -------------------------------------------------------------------------------- /kmercode/hash_funcs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/hash_funcs.h -------------------------------------------------------------------------------- /kmercode/hyperloglog.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/hyperloglog.hpp -------------------------------------------------------------------------------- /kmercode/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/main.cpp -------------------------------------------------------------------------------- /kmercode/makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/makefile -------------------------------------------------------------------------------- /kmercode/usage: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/kmercode/usage -------------------------------------------------------------------------------- /libbloom/.gitignore: -------------------------------------------------------------------------------- 1 | build 2 | -------------------------------------------------------------------------------- /libbloom/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/CMakeLists.txt -------------------------------------------------------------------------------- /libbloom/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/LICENSE -------------------------------------------------------------------------------- /libbloom/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/Makefile -------------------------------------------------------------------------------- /libbloom/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/README -------------------------------------------------------------------------------- /libbloom/bloom.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/bloom.cpp -------------------------------------------------------------------------------- /libbloom/bloom.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/bloom.h -------------------------------------------------------------------------------- /libbloom/bloom64.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/bloom64.cpp -------------------------------------------------------------------------------- /libbloom/bloom64.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/bloom64.h -------------------------------------------------------------------------------- /libbloom/murmur2/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | add_library(MURMURHASH OBJECT MurmurHash2.c) 3 | 4 | -------------------------------------------------------------------------------- /libbloom/murmur2/MurmurHash2.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/murmur2/MurmurHash2.c -------------------------------------------------------------------------------- /libbloom/murmur2/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/murmur2/README -------------------------------------------------------------------------------- /libbloom/murmur2/murmurhash2.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/murmur2/murmurhash2.h -------------------------------------------------------------------------------- /libbloom/test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libbloom/test.cpp -------------------------------------------------------------------------------- /libcuckoo/cuckoohash_config.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libcuckoo/cuckoohash_config.hh -------------------------------------------------------------------------------- /libcuckoo/cuckoohash_map.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libcuckoo/cuckoohash_map.hh -------------------------------------------------------------------------------- /libcuckoo/cuckoohash_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libcuckoo/cuckoohash_util.hh -------------------------------------------------------------------------------- /libcuckoo/libcuckoo_bucket_container.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/libcuckoo/libcuckoo_bucket_container.hh -------------------------------------------------------------------------------- /loganGPU/functions.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/loganGPU/functions.cuh -------------------------------------------------------------------------------- /loganGPU/logan.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/loganGPU/logan.cuh -------------------------------------------------------------------------------- /loganGPU/score.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/loganGPU/score.cuh -------------------------------------------------------------------------------- /loganGPU/seed.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/loganGPU/seed.cuh -------------------------------------------------------------------------------- /makefile-mac: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/makefile-mac -------------------------------------------------------------------------------- /makefile-nersc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/makefile-nersc -------------------------------------------------------------------------------- /optlist/optlist.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/optlist/optlist.c -------------------------------------------------------------------------------- /optlist/optlist.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/optlist/optlist.h -------------------------------------------------------------------------------- /sanitytests/reversecomptest.fastq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/sanitytests/reversecomptest.fastq -------------------------------------------------------------------------------- /sanitytests/reversecomptest.txt: -------------------------------------------------------------------------------- 1 | sanitytests/reversecomptest.fastq 2 | -------------------------------------------------------------------------------- /script/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/README.md -------------------------------------------------------------------------------- /script/SAMparser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/SAMparser.py -------------------------------------------------------------------------------- /script/mafconvert.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/mafconvert.py -------------------------------------------------------------------------------- /script/morescript/IntervalTree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/IntervalTree.h -------------------------------------------------------------------------------- /script/morescript/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/README.md -------------------------------------------------------------------------------- /script/morescript/chainedMarkov.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/chainedMarkov.py -------------------------------------------------------------------------------- /script/morescript/checkOutput.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/checkOutput.cpp -------------------------------------------------------------------------------- /script/morescript/checkOutput.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/checkOutput.py -------------------------------------------------------------------------------- /script/morescript/daligner_scripts/parserLAdump.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/daligner_scripts/parserLAdump.py -------------------------------------------------------------------------------- /script/morescript/daligner_scripts/run_daligner.slurm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/daligner_scripts/run_daligner.slurm -------------------------------------------------------------------------------- /script/morescript/daligner_scripts/tinytest.dump: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/daligner_scripts/tinytest.dump -------------------------------------------------------------------------------- /script/morescript/daligner_scripts/zip_tag.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/daligner_scripts/zip_tag.py -------------------------------------------------------------------------------- /script/morescript/evaluation.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/evaluation.cpp -------------------------------------------------------------------------------- /script/morescript/evaluation.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/evaluation.h -------------------------------------------------------------------------------- /script/morescript/exactMarkov.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/exactMarkov.py -------------------------------------------------------------------------------- /script/morescript/filterby_overlap_length.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/filterby_overlap_length.py -------------------------------------------------------------------------------- /script/morescript/mafconvert.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/mafconvert.py -------------------------------------------------------------------------------- /script/morescript/makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/morescript/makefile -------------------------------------------------------------------------------- /script/run-bella-pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/script/run-bella-pipeline.sh -------------------------------------------------------------------------------- /seqan/seqan/align.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align.h -------------------------------------------------------------------------------- /seqan/seqan/align/align_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/align_base.h -------------------------------------------------------------------------------- /seqan/seqan/align/align_cols.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/align_cols.h -------------------------------------------------------------------------------- /seqan/seqan/align/align_config.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/align_config.h -------------------------------------------------------------------------------- /seqan/seqan/align/align_interface_wrapper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/align_interface_wrapper.h -------------------------------------------------------------------------------- /seqan/seqan/align/align_iterator_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/align_iterator_base.h -------------------------------------------------------------------------------- /seqan/seqan/align/align_metafunctions.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/align_metafunctions.h -------------------------------------------------------------------------------- /seqan/seqan/align/align_traceback.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/align_traceback.h -------------------------------------------------------------------------------- /seqan/seqan/align/alignment_algorithm_tags.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/alignment_algorithm_tags.h -------------------------------------------------------------------------------- /seqan/seqan/align/alignment_operations.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/alignment_operations.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_algorithm_impl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_algorithm_impl.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_align_simd_helper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_align_simd_helper.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_band.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_band.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_cell.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_cell.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_cell_affine.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_cell_affine.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_cell_dynamic.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_cell_dynamic.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_cell_linear.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_cell_linear.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_context.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_context.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_formula.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_formula.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_formula_affine.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_formula_affine.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_formula_dynamic.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_formula_dynamic.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_formula_linear.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_formula_linear.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_matrix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_matrix.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_matrix_navigator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_matrix_navigator.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_matrix_navigator_score_matrix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_matrix_navigator_score_matrix.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_matrix_navigator_trace_matrix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_matrix_navigator_trace_matrix.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_matrix_sparse.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_matrix_sparse.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_meta_info.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_meta_info.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_profile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_profile.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_scout.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_scout.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_scout_simd.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_scout_simd.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_setup.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_setup.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_trace_segment.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_trace_segment.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_traceback_adaptor.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_traceback_adaptor.h -------------------------------------------------------------------------------- /seqan/seqan/align/dp_traceback_impl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/dp_traceback_impl.h -------------------------------------------------------------------------------- /seqan/seqan/align/evaluate_alignment.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/evaluate_alignment.h -------------------------------------------------------------------------------- /seqan/seqan/align/fragment.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/fragment.h -------------------------------------------------------------------------------- /seqan/seqan/align/gap_anchor.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/gap_anchor.h -------------------------------------------------------------------------------- /seqan/seqan/align/gapped_value_type.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/gapped_value_type.h -------------------------------------------------------------------------------- /seqan/seqan/align/gaps_anchor.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/gaps_anchor.h -------------------------------------------------------------------------------- /seqan/seqan/align/gaps_array.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/gaps_array.h -------------------------------------------------------------------------------- /seqan/seqan/align/gaps_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/gaps_base.h -------------------------------------------------------------------------------- /seqan/seqan/align/gaps_iterator_anchor.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/gaps_iterator_anchor.h -------------------------------------------------------------------------------- /seqan/seqan/align/gaps_iterator_array.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/gaps_iterator_array.h -------------------------------------------------------------------------------- /seqan/seqan/align/gaps_iterator_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/gaps_iterator_base.h -------------------------------------------------------------------------------- /seqan/seqan/align/global_alignment_banded.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/global_alignment_banded.h -------------------------------------------------------------------------------- /seqan/seqan/align/global_alignment_hirschberg_impl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/global_alignment_hirschberg_impl.h -------------------------------------------------------------------------------- /seqan/seqan/align/global_alignment_myers_impl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/global_alignment_myers_impl.h -------------------------------------------------------------------------------- /seqan/seqan/align/global_alignment_specialized.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/global_alignment_specialized.h -------------------------------------------------------------------------------- /seqan/seqan/align/global_alignment_unbanded.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/global_alignment_unbanded.h -------------------------------------------------------------------------------- /seqan/seqan/align/local_alignment_banded.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/local_alignment_banded.h -------------------------------------------------------------------------------- /seqan/seqan/align/local_alignment_enumeration.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/local_alignment_enumeration.h -------------------------------------------------------------------------------- /seqan/seqan/align/local_alignment_unbanded.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/local_alignment_unbanded.h -------------------------------------------------------------------------------- /seqan/seqan/align/matrix_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align/matrix_base.h -------------------------------------------------------------------------------- /seqan/seqan/align_extend.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align_extend.h -------------------------------------------------------------------------------- /seqan/seqan/align_extend/align_extend.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align_extend/align_extend.h -------------------------------------------------------------------------------- /seqan/seqan/align_extend/align_extend_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align_extend/align_extend_base.h -------------------------------------------------------------------------------- /seqan/seqan/align_extend/dp_scout_xdrop.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align_extend/dp_scout_xdrop.h -------------------------------------------------------------------------------- /seqan/seqan/align_profile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align_profile.h -------------------------------------------------------------------------------- /seqan/seqan/align_profile/add_to_profile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align_profile/add_to_profile.h -------------------------------------------------------------------------------- /seqan/seqan/align_profile/score_profile_seq.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align_profile/score_profile_seq.h -------------------------------------------------------------------------------- /seqan/seqan/align_split.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align_split.h -------------------------------------------------------------------------------- /seqan/seqan/align_split/align_split_interface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align_split/align_split_interface.h -------------------------------------------------------------------------------- /seqan/seqan/align_split/dp_scout_split.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/align_split/dp_scout_split.h -------------------------------------------------------------------------------- /seqan/seqan/alignment_free.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/alignment_free.h -------------------------------------------------------------------------------- /seqan/seqan/alignment_free/af_d2.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/alignment_free/af_d2.h -------------------------------------------------------------------------------- /seqan/seqan/alignment_free/af_d2star.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/alignment_free/af_d2star.h -------------------------------------------------------------------------------- /seqan/seqan/alignment_free/af_d2z.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/alignment_free/af_d2z.h -------------------------------------------------------------------------------- /seqan/seqan/alignment_free/af_n2.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/alignment_free/af_n2.h -------------------------------------------------------------------------------- /seqan/seqan/alignment_free/alignment_free_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/alignment_free/alignment_free_base.h -------------------------------------------------------------------------------- /seqan/seqan/alignment_free/kmer_functions.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/alignment_free/kmer_functions.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/arg_parse_argument.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/arg_parse_argument.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/arg_parse_ctd_support.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/arg_parse_ctd_support.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/arg_parse_doc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/arg_parse_doc.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/arg_parse_exceptions.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/arg_parse_exceptions.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/arg_parse_option.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/arg_parse_option.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/arg_parse_parse.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/arg_parse_parse.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/arg_parse_type_support.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/arg_parse_type_support.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/arg_parse_version_check.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/arg_parse_version_check.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/argument_parser.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/argument_parser.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/tool_doc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/tool_doc.h -------------------------------------------------------------------------------- /seqan/seqan/arg_parse/xml_support.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/arg_parse/xml_support.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/bam_alignment_record.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/bam_alignment_record.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/bam_alignment_record_util.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/bam_alignment_record_util.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/bam_file.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/bam_file.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/bam_header_record.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/bam_header_record.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/bam_index_bai.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/bam_index_bai.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/bam_io_context.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/bam_io_context.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/bam_sam_conversion.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/bam_sam_conversion.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/bam_scanner_cache.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/bam_scanner_cache.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/bam_tags_dict.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/bam_tags_dict.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/cigar.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/cigar.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/read_bam.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/read_bam.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/read_sam.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/read_sam.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/write_bam.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/write_bam.h -------------------------------------------------------------------------------- /seqan/seqan/bam_io/write_sam.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bam_io/write_sam.h -------------------------------------------------------------------------------- /seqan/seqan/basic.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic.h -------------------------------------------------------------------------------- /seqan/seqan/basic/aggregate_concept.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/aggregate_concept.h -------------------------------------------------------------------------------- /seqan/seqan/basic/allocator_chunkpool.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/allocator_chunkpool.h -------------------------------------------------------------------------------- /seqan/seqan/basic/allocator_interface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/allocator_interface.h -------------------------------------------------------------------------------- /seqan/seqan/basic/allocator_multipool.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/allocator_multipool.h -------------------------------------------------------------------------------- /seqan/seqan/basic/allocator_simple.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/allocator_simple.h -------------------------------------------------------------------------------- /seqan/seqan/basic/allocator_singlepool.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/allocator_singlepool.h -------------------------------------------------------------------------------- /seqan/seqan/basic/allocator_to_std.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/allocator_to_std.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_adapt_builtins.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_adapt_builtins.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_bio.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_bio.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_concept.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_concept.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_math.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_math.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_profile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_profile.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_qualities.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_qualities.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_residue.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_residue.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_residue_funcs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_residue_funcs.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_residue_tabs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_residue_tabs.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_simple_type.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_simple_type.h -------------------------------------------------------------------------------- /seqan/seqan/basic/alphabet_storage.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/alphabet_storage.h -------------------------------------------------------------------------------- /seqan/seqan/basic/array_construct_destruct.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/array_construct_destruct.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_aggregate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_aggregate.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_allocator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_allocator.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_alphabet.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_alphabet.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_concept.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_concept.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_container.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_container.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_debug.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_debug.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_device.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_device.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_exception.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_exception.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_functors.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_functors.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_fundamental.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_fundamental.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_iterator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_iterator.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_math.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_math.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_metaprogramming.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_metaprogramming.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_parallelism.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_parallelism.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_proxy.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_proxy.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_simd_vector.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_simd_vector.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_smart_pointer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_smart_pointer.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_stream.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_stream.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_tangle.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_tangle.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_type.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_type.h -------------------------------------------------------------------------------- /seqan/seqan/basic/basic_view.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/basic_view.h -------------------------------------------------------------------------------- /seqan/seqan/basic/boost_preprocessor_subset.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/boost_preprocessor_subset.h -------------------------------------------------------------------------------- /seqan/seqan/basic/builtin_functions.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/builtin_functions.h -------------------------------------------------------------------------------- /seqan/seqan/basic/concept_checking.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/concept_checking.h -------------------------------------------------------------------------------- /seqan/seqan/basic/container_concept.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/container_concept.h -------------------------------------------------------------------------------- /seqan/seqan/basic/debug_helper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/debug_helper.h -------------------------------------------------------------------------------- /seqan/seqan/basic/debug_test_system.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/debug_test_system.h -------------------------------------------------------------------------------- /seqan/seqan/basic/fundamental_chunking.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/fundamental_chunking.h -------------------------------------------------------------------------------- /seqan/seqan/basic/fundamental_comparison.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/fundamental_comparison.h -------------------------------------------------------------------------------- /seqan/seqan/basic/fundamental_concepts.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/fundamental_concepts.h -------------------------------------------------------------------------------- /seqan/seqan/basic/fundamental_conversion.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/fundamental_conversion.h -------------------------------------------------------------------------------- /seqan/seqan/basic/fundamental_metafunctions.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/fundamental_metafunctions.h -------------------------------------------------------------------------------- /seqan/seqan/basic/fundamental_tags.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/fundamental_tags.h -------------------------------------------------------------------------------- /seqan/seqan/basic/fundamental_transport.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/fundamental_transport.h -------------------------------------------------------------------------------- /seqan/seqan/basic/holder_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/holder_base.h -------------------------------------------------------------------------------- /seqan/seqan/basic/holder_simple.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/holder_simple.h -------------------------------------------------------------------------------- /seqan/seqan/basic/holder_tristate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/holder_tristate.h -------------------------------------------------------------------------------- /seqan/seqan/basic/hosted_type_interface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/hosted_type_interface.h -------------------------------------------------------------------------------- /seqan/seqan/basic/iterator_adapt_pointer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/iterator_adapt_pointer.h -------------------------------------------------------------------------------- /seqan/seqan/basic/iterator_adapt_std.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/iterator_adapt_std.h -------------------------------------------------------------------------------- /seqan/seqan/basic/iterator_adaptor.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/iterator_adaptor.h -------------------------------------------------------------------------------- /seqan/seqan/basic/iterator_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/iterator_base.h -------------------------------------------------------------------------------- /seqan/seqan/basic/iterator_concept.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/iterator_concept.h -------------------------------------------------------------------------------- /seqan/seqan/basic/iterator_counting.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/iterator_counting.h -------------------------------------------------------------------------------- /seqan/seqan/basic/iterator_interface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/iterator_interface.h -------------------------------------------------------------------------------- /seqan/seqan/basic/iterator_position.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/iterator_position.h -------------------------------------------------------------------------------- /seqan/seqan/basic/iterator_range.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/iterator_range.h -------------------------------------------------------------------------------- /seqan/seqan/basic/iterator_zip.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/iterator_zip.h -------------------------------------------------------------------------------- /seqan/seqan/basic/macro_deprecated.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/macro_deprecated.h -------------------------------------------------------------------------------- /seqan/seqan/basic/math_functions.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/math_functions.h -------------------------------------------------------------------------------- /seqan/seqan/basic/math_log_space_value.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/math_log_space_value.h -------------------------------------------------------------------------------- /seqan/seqan/basic/metaprogramming_control.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/metaprogramming_control.h -------------------------------------------------------------------------------- /seqan/seqan/basic/metaprogramming_enable_if.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/metaprogramming_enable_if.h -------------------------------------------------------------------------------- /seqan/seqan/basic/metaprogramming_logic.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/metaprogramming_logic.h -------------------------------------------------------------------------------- /seqan/seqan/basic/metaprogramming_math.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/metaprogramming_math.h -------------------------------------------------------------------------------- /seqan/seqan/basic/metaprogramming_type.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/metaprogramming_type.h -------------------------------------------------------------------------------- /seqan/seqan/basic/metaprogramming_type_algebra.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/metaprogramming_type_algebra.h -------------------------------------------------------------------------------- /seqan/seqan/basic/pair_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/pair_base.h -------------------------------------------------------------------------------- /seqan/seqan/basic/pair_bit_compressed.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/pair_bit_compressed.h -------------------------------------------------------------------------------- /seqan/seqan/basic/pair_packed.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/pair_packed.h -------------------------------------------------------------------------------- /seqan/seqan/basic/profiling.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/profiling.h -------------------------------------------------------------------------------- /seqan/seqan/basic/property_map_concept.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/property_map_concept.h -------------------------------------------------------------------------------- /seqan/seqan/basic/proxy_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/proxy_base.h -------------------------------------------------------------------------------- /seqan/seqan/basic/proxy_iterator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/proxy_iterator.h -------------------------------------------------------------------------------- /seqan/seqan/basic/test_system.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/test_system.h -------------------------------------------------------------------------------- /seqan/seqan/basic/triple_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/triple_base.h -------------------------------------------------------------------------------- /seqan/seqan/basic/triple_packed.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/triple_packed.h -------------------------------------------------------------------------------- /seqan/seqan/basic/tuple_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/tuple_base.h -------------------------------------------------------------------------------- /seqan/seqan/basic/tuple_bit_compressed.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/tuple_bit_compressed.h -------------------------------------------------------------------------------- /seqan/seqan/basic/volatile_ptr.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/basic/volatile_ptr.h -------------------------------------------------------------------------------- /seqan/seqan/bed_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bed_io.h -------------------------------------------------------------------------------- /seqan/seqan/bed_io/bed_file.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bed_io/bed_file.h -------------------------------------------------------------------------------- /seqan/seqan/bed_io/bed_record.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bed_io/bed_record.h -------------------------------------------------------------------------------- /seqan/seqan/bed_io/read_bed.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bed_io/read_bed.h -------------------------------------------------------------------------------- /seqan/seqan/bed_io/write_bed.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/bed_io/write_bed.h -------------------------------------------------------------------------------- /seqan/seqan/blast.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/blast.h -------------------------------------------------------------------------------- /seqan/seqan/blast/blast_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/blast/blast_base.h -------------------------------------------------------------------------------- /seqan/seqan/blast/blast_io_context.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/blast/blast_io_context.h -------------------------------------------------------------------------------- /seqan/seqan/blast/blast_record.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/blast/blast_record.h -------------------------------------------------------------------------------- /seqan/seqan/blast/blast_report_out.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/blast/blast_report_out.h -------------------------------------------------------------------------------- /seqan/seqan/blast/blast_statistics.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/blast/blast_statistics.h -------------------------------------------------------------------------------- /seqan/seqan/blast/blast_tabular.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/blast/blast_tabular.h -------------------------------------------------------------------------------- /seqan/seqan/blast/blast_tabular_in.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/blast/blast_tabular_in.h -------------------------------------------------------------------------------- /seqan/seqan/blast/blast_tabular_lowlevel.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/blast/blast_tabular_lowlevel.h -------------------------------------------------------------------------------- /seqan/seqan/blast/blast_tabular_out.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/blast/blast_tabular_out.h -------------------------------------------------------------------------------- /seqan/seqan/consensus.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus.h -------------------------------------------------------------------------------- /seqan/seqan/consensus/consensus_aligner.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus/consensus_aligner.h -------------------------------------------------------------------------------- /seqan/seqan/consensus/consensus_aligner_interface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus/consensus_aligner_interface.h -------------------------------------------------------------------------------- /seqan/seqan/consensus/consensus_alignment_options.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus/consensus_alignment_options.h -------------------------------------------------------------------------------- /seqan/seqan/consensus/consensus_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus/consensus_base.h -------------------------------------------------------------------------------- /seqan/seqan/consensus/consensus_builder.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus/consensus_builder.h -------------------------------------------------------------------------------- /seqan/seqan/consensus/consensus_library.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus/consensus_library.h -------------------------------------------------------------------------------- /seqan/seqan/consensus/consensus_realign.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus/consensus_realign.h -------------------------------------------------------------------------------- /seqan/seqan/consensus/consensus_score.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus/consensus_score.h -------------------------------------------------------------------------------- /seqan/seqan/consensus/overlap_info_computation.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus/overlap_info_computation.h -------------------------------------------------------------------------------- /seqan/seqan/consensus/overlapper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/consensus/overlapper.h -------------------------------------------------------------------------------- /seqan/seqan/file.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/file.h -------------------------------------------------------------------------------- /seqan/seqan/file/file_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/file/file_base.h -------------------------------------------------------------------------------- /seqan/seqan/file/file_cstyle.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/file/file_cstyle.h -------------------------------------------------------------------------------- /seqan/seqan/file/file_forwards.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/file/file_forwards.h -------------------------------------------------------------------------------- /seqan/seqan/file/file_interface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/file/file_interface.h -------------------------------------------------------------------------------- /seqan/seqan/file/file_mapping.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/file/file_mapping.h -------------------------------------------------------------------------------- /seqan/seqan/file/file_page.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/file/file_page.h -------------------------------------------------------------------------------- /seqan/seqan/file/string_external.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/file/string_external.h -------------------------------------------------------------------------------- /seqan/seqan/file/string_mmap.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/file/string_mmap.h -------------------------------------------------------------------------------- /seqan/seqan/find.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_abndm.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_abndm.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_ahocorasick.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_ahocorasick.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_base.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_begin.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_begin.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_bndm.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_bndm.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_bom.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_bom.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_hamming_simple.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_hamming_simple.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_horspool.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_horspool.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_lambda.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_lambda.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_multi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_multi.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_multiple_bfam.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_multiple_bfam.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_multiple_shiftand.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_multiple_shiftand.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_myers_ukkonen.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_myers_ukkonen.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_pattern_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_pattern_base.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_pex.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_pex.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_score.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_score.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_set_horspool.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_set_horspool.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_shiftand.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_shiftand.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_shiftor.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_shiftor.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_simple.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_simple.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_wild_shiftand.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_wild_shiftand.h -------------------------------------------------------------------------------- /seqan/seqan/find/find_wumanber.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/find/find_wumanber.h -------------------------------------------------------------------------------- /seqan/seqan/gff_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/gff_io.h -------------------------------------------------------------------------------- /seqan/seqan/gff_io/gff_file.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/gff_io/gff_file.h -------------------------------------------------------------------------------- /seqan/seqan/gff_io/gff_io_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/gff_io/gff_io_base.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/bellman_ford.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/bellman_ford.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/bipartite_matching.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/bipartite_matching.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/breadth_first_search.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/breadth_first_search.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/connected_components.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/connected_components.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/depth_first_search.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/depth_first_search.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/dijkstra.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/dijkstra.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/floyd_warshall.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/floyd_warshall.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/ford_fulkerson.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/ford_fulkerson.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/graph_algorithm_hmm.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/graph_algorithm_hmm.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/kruskal.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/kruskal.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/path_growing.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/path_growing.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/prim.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/prim.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/topological_sort.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/topological_sort.h -------------------------------------------------------------------------------- /seqan/seqan/graph_algorithms/transitive_closure.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_algorithms/transitive_closure.h -------------------------------------------------------------------------------- /seqan/seqan/graph_align.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_align.h -------------------------------------------------------------------------------- /seqan/seqan/graph_align/graph_impl_align.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_align/graph_impl_align.h -------------------------------------------------------------------------------- /seqan/seqan/graph_align/graph_impl_align_adapt.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_align/graph_impl_align_adapt.h -------------------------------------------------------------------------------- /seqan/seqan/graph_msa.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_msa.h -------------------------------------------------------------------------------- /seqan/seqan/graph_msa/graph_align_tcoffee_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_msa/graph_align_tcoffee_base.h -------------------------------------------------------------------------------- /seqan/seqan/graph_msa/graph_align_tcoffee_distance.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_msa/graph_align_tcoffee_distance.h -------------------------------------------------------------------------------- /seqan/seqan/graph_msa/graph_align_tcoffee_guidetree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_msa/graph_align_tcoffee_guidetree.h -------------------------------------------------------------------------------- /seqan/seqan/graph_msa/graph_align_tcoffee_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_msa/graph_align_tcoffee_io.h -------------------------------------------------------------------------------- /seqan/seqan/graph_msa/graph_align_tcoffee_kmer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_msa/graph_align_tcoffee_kmer.h -------------------------------------------------------------------------------- /seqan/seqan/graph_msa/graph_align_tcoffee_library.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_msa/graph_align_tcoffee_library.h -------------------------------------------------------------------------------- /seqan/seqan/graph_msa/graph_align_tcoffee_msa.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_msa/graph_align_tcoffee_msa.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_base.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_drawing.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_drawing.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_edgestump.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_edgestump.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_idmanager.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_idmanager.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_impl_automaton.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_impl_automaton.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_impl_directed.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_impl_directed.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_impl_hmm.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_impl_hmm.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_impl_oracle.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_impl_oracle.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_impl_tree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_impl_tree.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_impl_trie.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_impl_trie.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_impl_undirected.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_impl_undirected.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_impl_wordgraph.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_impl_wordgraph.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_interface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_interface.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_iterator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_iterator.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_iterator_adjacency.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_iterator_adjacency.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_iterator_bfs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_iterator_bfs.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_iterator_dfs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_iterator_dfs.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_iterator_edge.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_iterator_edge.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_iterator_outedge.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_iterator_outedge.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_iterator_vertex.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_iterator_vertex.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/graph_utility_parsing.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/graph_utility_parsing.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/property_map_generic.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/property_map_generic.h -------------------------------------------------------------------------------- /seqan/seqan/graph_types/property_map_internal.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/graph_types/property_map_internal.h -------------------------------------------------------------------------------- /seqan/seqan/index.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index.h -------------------------------------------------------------------------------- /seqan/seqan/index/find2_backtracking.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find2_backtracking.h -------------------------------------------------------------------------------- /seqan/seqan/index/find2_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find2_base.h -------------------------------------------------------------------------------- /seqan/seqan/index/find2_functors.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find2_functors.h -------------------------------------------------------------------------------- /seqan/seqan/index/find2_index.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find2_index.h -------------------------------------------------------------------------------- /seqan/seqan/index/find2_index_multi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find2_index_multi.h -------------------------------------------------------------------------------- /seqan/seqan/index/find2_vstree_factory.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find2_vstree_factory.h -------------------------------------------------------------------------------- /seqan/seqan/index/find_backtracking.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find_backtracking.h -------------------------------------------------------------------------------- /seqan/seqan/index/find_index.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find_index.h -------------------------------------------------------------------------------- /seqan/seqan/index/find_index_approx.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find_index_approx.h -------------------------------------------------------------------------------- /seqan/seqan/index/find_index_binary.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find_index_binary.h -------------------------------------------------------------------------------- /seqan/seqan/index/find_index_esa.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find_index_esa.h -------------------------------------------------------------------------------- /seqan/seqan/index/find_index_lambda.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find_index_lambda.h -------------------------------------------------------------------------------- /seqan/seqan/index/find_index_qgram.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find_index_qgram.h -------------------------------------------------------------------------------- /seqan/seqan/index/find_pigeonhole.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find_pigeonhole.h -------------------------------------------------------------------------------- /seqan/seqan/index/find_quasar.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find_quasar.h -------------------------------------------------------------------------------- /seqan/seqan/index/find_swift.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/find_swift.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_base.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_bidirectional.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_bidirectional.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_bidirectional_stree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_bidirectional_stree.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_bifm.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_bifm.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_bifm_stree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_bifm_stree.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_bwt.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_bwt.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_childtab.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_childtab.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_device.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_device.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_dfi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_dfi.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_esa_algs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_esa_algs.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_esa_algs_multi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_esa_algs_multi.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_esa_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_esa_base.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_esa_drawing.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_esa_drawing.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_esa_stree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_esa_stree.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_compressed_sa.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_compressed_sa.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_compressed_sa_iterator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_compressed_sa_iterator.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_dox.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_dox.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_lf_table.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_lf_table.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_rank_dictionary_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_rank_dictionary_base.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_rank_dictionary_levels.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_rank_dictionary_levels.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_rank_dictionary_naive.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_rank_dictionary_naive.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_rank_dictionary_wt.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_rank_dictionary_wt.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_right_array_binary_tree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_right_array_binary_tree.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_sparse_string.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_sparse_string.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_fm_stree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_fm_stree.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_forwards.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_forwards.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_lcp.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_lcp.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_lcp_tree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_lcp_tree.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_pizzachili.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_pizzachili.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_pizzachili_find.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_pizzachili_find.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_pizzachili_string.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_pizzachili_string.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_qgram.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_qgram.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_qgram_bucketrefinement.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_qgram_bucketrefinement.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_qgram_openaddressing.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_qgram_openaddressing.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_qgram_stree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_qgram_stree.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_sa_btree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_sa_btree.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_sa_bwtwalk.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_sa_bwtwalk.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_sa_lss.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_sa_lss.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_sa_mm.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_sa_mm.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_sa_qsort.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_sa_qsort.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_sa_stree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_sa_stree.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_sa_truncated.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_sa_truncated.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_shawarma.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_shawarma.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_shims.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_shims.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_skew3.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_skew3.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_skew7.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_skew7.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_skew7_multi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_skew7_multi.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_view.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_view.h -------------------------------------------------------------------------------- /seqan/seqan/index/index_wotd.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/index_wotd.h -------------------------------------------------------------------------------- /seqan/seqan/index/pipe_merger3.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/pipe_merger3.h -------------------------------------------------------------------------------- /seqan/seqan/index/pipe_merger7.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/pipe_merger7.h -------------------------------------------------------------------------------- /seqan/seqan/index/pizzachili_api.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/pizzachili_api.h -------------------------------------------------------------------------------- /seqan/seqan/index/pump_extender3.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/pump_extender3.h -------------------------------------------------------------------------------- /seqan/seqan/index/pump_extender7.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/pump_extender7.h -------------------------------------------------------------------------------- /seqan/seqan/index/pump_lcp_core.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/pump_lcp_core.h -------------------------------------------------------------------------------- /seqan/seqan/index/pump_separator7.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/pump_separator7.h -------------------------------------------------------------------------------- /seqan/seqan/index/radix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/radix.h -------------------------------------------------------------------------------- /seqan/seqan/index/repeat_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/repeat_base.h -------------------------------------------------------------------------------- /seqan/seqan/index/shape_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/shape_base.h -------------------------------------------------------------------------------- /seqan/seqan/index/shape_gapped.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/shape_gapped.h -------------------------------------------------------------------------------- /seqan/seqan/index/shape_minimizer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/shape_minimizer.h -------------------------------------------------------------------------------- /seqan/seqan/index/shape_onegapped.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/shape_onegapped.h -------------------------------------------------------------------------------- /seqan/seqan/index/shape_predefined.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/shape_predefined.h -------------------------------------------------------------------------------- /seqan/seqan/index/shape_threshold.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/index/shape_threshold.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_set.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_set.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_set/journaled_set_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_set/journaled_set_base.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_set/journaled_set_impl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_set/journaled_set_impl.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_set/journaled_set_join.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_set/journaled_set_join.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_set/journaled_set_join_config.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_set/journaled_set_join_config.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_set/score_biaffine.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_set/score_biaffine.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_string_tree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_string_tree.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_string_tree/delta_map.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_string_tree/delta_map.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_string_tree/delta_map_entry.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_string_tree/delta_map_entry.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_string_tree/delta_store.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_string_tree/delta_store.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_string_tree/observable.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_string_tree/observable.h -------------------------------------------------------------------------------- /seqan/seqan/journaled_string_tree/stack_observer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/journaled_string_tree/stack_observer.h -------------------------------------------------------------------------------- /seqan/seqan/map.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/map.h -------------------------------------------------------------------------------- /seqan/seqan/map/map_adapter_stl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/map/map_adapter_stl.h -------------------------------------------------------------------------------- /seqan/seqan/map/map_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/map/map_base.h -------------------------------------------------------------------------------- /seqan/seqan/map/map_chooser.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/map/map_chooser.h -------------------------------------------------------------------------------- /seqan/seqan/map/map_skiplist.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/map/map_skiplist.h -------------------------------------------------------------------------------- /seqan/seqan/map/map_vector.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/map/map_vector.h -------------------------------------------------------------------------------- /seqan/seqan/map/sumlist.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/map/sumlist.h -------------------------------------------------------------------------------- /seqan/seqan/map/sumlist_mini.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/map/sumlist_mini.h -------------------------------------------------------------------------------- /seqan/seqan/map/sumlist_skip.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/map/sumlist_skip.h -------------------------------------------------------------------------------- /seqan/seqan/math.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/math.h -------------------------------------------------------------------------------- /seqan/seqan/math/math_common_factor.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/math/math_common_factor.h -------------------------------------------------------------------------------- /seqan/seqan/math/math_operators.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/math/math_operators.h -------------------------------------------------------------------------------- /seqan/seqan/math/math_rational.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/math/math_rational.h -------------------------------------------------------------------------------- /seqan/seqan/misc/accumulators.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/accumulators.h -------------------------------------------------------------------------------- /seqan/seqan/misc/base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/base.h -------------------------------------------------------------------------------- /seqan/seqan/misc/bit_twiddling.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/bit_twiddling.h -------------------------------------------------------------------------------- /seqan/seqan/misc/bit_twiddling_functors.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/bit_twiddling_functors.h -------------------------------------------------------------------------------- /seqan/seqan/misc/dequeue.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/dequeue.h -------------------------------------------------------------------------------- /seqan/seqan/misc/edit_environment.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/edit_environment.h -------------------------------------------------------------------------------- /seqan/seqan/misc/interval_tree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/interval_tree.h -------------------------------------------------------------------------------- /seqan/seqan/misc/map.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/map.h -------------------------------------------------------------------------------- /seqan/seqan/misc/memset.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/memset.h -------------------------------------------------------------------------------- /seqan/seqan/misc/name_store_cache.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/name_store_cache.h -------------------------------------------------------------------------------- /seqan/seqan/misc/priority_type_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/priority_type_base.h -------------------------------------------------------------------------------- /seqan/seqan/misc/priority_type_heap.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/priority_type_heap.h -------------------------------------------------------------------------------- /seqan/seqan/misc/set.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/set.h -------------------------------------------------------------------------------- /seqan/seqan/misc/svg.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/svg.h -------------------------------------------------------------------------------- /seqan/seqan/misc/terminal.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/terminal.h -------------------------------------------------------------------------------- /seqan/seqan/misc/union_find.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/misc/union_find.h -------------------------------------------------------------------------------- /seqan/seqan/modifier.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/cyclic_shape.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/cyclic_shape.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_alphabet.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_alphabet.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_alphabet_expansion.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_alphabet_expansion.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_cyclic_shape.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_cyclic_shape.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_functors.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_functors.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_iterator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_iterator.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_padding.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_padding.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_position.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_position.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_reverse.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_reverse.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_shortcuts.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_shortcuts.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_string.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_string.h -------------------------------------------------------------------------------- /seqan/seqan/modifier/modifier_view.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/modifier/modifier_view.h -------------------------------------------------------------------------------- /seqan/seqan/parallel.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_algorithms.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_algorithms.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_atomic_misc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_atomic_misc.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_atomic_primitives.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_atomic_primitives.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_lock.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_lock.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_macros.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_macros.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_queue.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_queue.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_queue_suspendable.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_queue_suspendable.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_resource_pool.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_resource_pool.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_sequence.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_sequence.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_serializer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_serializer.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_splitting.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_splitting.h -------------------------------------------------------------------------------- /seqan/seqan/parallel/parallel_tags.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parallel/parallel_tags.h -------------------------------------------------------------------------------- /seqan/seqan/parse_lm.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parse_lm.h -------------------------------------------------------------------------------- /seqan/seqan/parse_lm/local_match_store.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parse_lm/local_match_store.h -------------------------------------------------------------------------------- /seqan/seqan/parse_lm/parse_blastn_tabular.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parse_lm/parse_blastn_tabular.h -------------------------------------------------------------------------------- /seqan/seqan/parse_lm/parse_lastz_general.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parse_lm/parse_lastz_general.h -------------------------------------------------------------------------------- /seqan/seqan/parse_lm/parse_stellar_gff.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/parse_lm/parse_stellar_gff.h -------------------------------------------------------------------------------- /seqan/seqan/pipe.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_base.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_caster.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_caster.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_counter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_counter.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_echoer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_echoer.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_edit_environment.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_edit_environment.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_filter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_filter.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_iterator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_iterator.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_joiner.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_joiner.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_namer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_namer.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_sampler.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_sampler.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_shifter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_shifter.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_source.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_source.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pipe_tupler.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pipe_tupler.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pool_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pool_base.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pool_mapper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pool_mapper.h -------------------------------------------------------------------------------- /seqan/seqan/pipe/pool_sorter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/pipe/pool_sorter.h -------------------------------------------------------------------------------- /seqan/seqan/platform.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/platform.h -------------------------------------------------------------------------------- /seqan/seqan/random.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/random.h -------------------------------------------------------------------------------- /seqan/seqan/random/random_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/random/random_base.h -------------------------------------------------------------------------------- /seqan/seqan/random/random_beta.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/random/random_beta.h -------------------------------------------------------------------------------- /seqan/seqan/random/random_util.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/random/random_util.h -------------------------------------------------------------------------------- /seqan/seqan/realign.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/realign.h -------------------------------------------------------------------------------- /seqan/seqan/realign/realign_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/realign/realign_base.h -------------------------------------------------------------------------------- /seqan/seqan/realign/realign_helper_functions.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/realign/realign_helper_functions.h -------------------------------------------------------------------------------- /seqan/seqan/reduced_aminoacid.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/reduced_aminoacid.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io/bpseq_read_write.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io/bpseq_read_write.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io/connect_read_write.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io/connect_read_write.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io/dot_bracket_read_write.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io/dot_bracket_read_write.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io/ebpseq_read_write.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io/ebpseq_read_write.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io/rna_header.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io/rna_header.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io/rna_io_context.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io/rna_io_context.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io/rna_record.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io/rna_record.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io/rna_struct_file.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io/rna_struct_file.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io/stockholm_read_write.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io/stockholm_read_write.h -------------------------------------------------------------------------------- /seqan/seqan/rna_io/vienna_read_write.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/rna_io/vienna_read_write.h -------------------------------------------------------------------------------- /seqan/seqan/roi_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/roi_io.h -------------------------------------------------------------------------------- /seqan/seqan/roi_io/read_roi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/roi_io/read_roi.h -------------------------------------------------------------------------------- /seqan/seqan/roi_io/roi_file.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/roi_io/roi_file.h -------------------------------------------------------------------------------- /seqan/seqan/roi_io/roi_io_context.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/roi_io/roi_io_context.h -------------------------------------------------------------------------------- /seqan/seqan/roi_io/roi_record.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/roi_io/roi_record.h -------------------------------------------------------------------------------- /seqan/seqan/roi_io/write_roi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/roi_io/write_roi.h -------------------------------------------------------------------------------- /seqan/seqan/score.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/score.h -------------------------------------------------------------------------------- /seqan/seqan/score/score_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/score/score_base.h -------------------------------------------------------------------------------- /seqan/seqan/score/score_edit.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/score/score_edit.h -------------------------------------------------------------------------------- /seqan/seqan/score/score_matrix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/score/score_matrix.h -------------------------------------------------------------------------------- /seqan/seqan/score/score_matrix_data.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/score/score_matrix_data.h -------------------------------------------------------------------------------- /seqan/seqan/score/score_matrix_dyn.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/score/score_matrix_dyn.h -------------------------------------------------------------------------------- /seqan/seqan/score/score_matrix_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/score/score_matrix_io.h -------------------------------------------------------------------------------- /seqan/seqan/score/score_simd_wrapper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/score/score_simd_wrapper.h -------------------------------------------------------------------------------- /seqan/seqan/score/score_simple.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/score/score_simple.h -------------------------------------------------------------------------------- /seqan/seqan/seeds.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/banded_chain_alignment.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/banded_chain_alignment.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/banded_chain_alignment_impl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/banded_chain_alignment_impl.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/banded_chain_alignment_profile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/banded_chain_alignment_profile.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/banded_chain_alignment_scout.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/banded_chain_alignment_scout.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/banded_chain_alignment_traceback.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/banded_chain_alignment_traceback.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/basic_iter_indirect.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/basic_iter_indirect.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/my_seed.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/my_seed.cpp -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_base.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_combination.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_combination.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_extension.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_extension.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_global_chaining.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_global_chaining.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_global_chaining_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_global_chaining_base.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_global_chaining_gusfield.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_global_chaining_gusfield.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_seed_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_seed_base.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_seed_chained.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_seed_chained.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_seed_diagonal.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_seed_diagonal.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_seed_set_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_seed_set_base.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_seed_set_non_scored.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_seed_set_non_scored.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_seed_set_scored.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_seed_set_scored.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_seed_set_unordered.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_seed_set_unordered.h -------------------------------------------------------------------------------- /seqan/seqan/seeds/seeds_seed_simple.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seeds/seeds_seed_simple.h -------------------------------------------------------------------------------- /seqan/seqan/seq_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seq_io.h -------------------------------------------------------------------------------- /seqan/seqan/seq_io/bam_sam.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seq_io/bam_sam.h -------------------------------------------------------------------------------- /seqan/seqan/seq_io/fai_index.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seq_io/fai_index.h -------------------------------------------------------------------------------- /seqan/seqan/seq_io/fasta_fastq.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seq_io/fasta_fastq.h -------------------------------------------------------------------------------- /seqan/seqan/seq_io/genomic_region.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seq_io/genomic_region.h -------------------------------------------------------------------------------- /seqan/seqan/seq_io/read_embl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seq_io/read_embl.h -------------------------------------------------------------------------------- /seqan/seqan/seq_io/read_genbank.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seq_io/read_genbank.h -------------------------------------------------------------------------------- /seqan/seqan/seq_io/sequence_file.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/seq_io/sequence_file.h -------------------------------------------------------------------------------- /seqan/seqan/sequence.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/adapt_array_pointer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/adapt_array_pointer.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/adapt_stl_container.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/adapt_stl_container.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/container_view.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/container_view.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/container_view_zip.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/container_view_zip.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/iter_concat_virtual.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/iter_concat_virtual.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/segment_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/segment_base.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/segment_infix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/segment_infix.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/segment_prefix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/segment_prefix.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/segment_suffix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/segment_suffix.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/segment_utils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/segment_utils.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/sequence_concatenator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/sequence_concatenator.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/sequence_forwards.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/sequence_forwards.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/sequence_interface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/sequence_interface.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/sequence_lexical.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/sequence_lexical.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/sequence_shortcuts.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/sequence_shortcuts.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_alloc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_alloc.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_array.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_array.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_base.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_block.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_block.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_cstyle.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_cstyle.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_packed.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_packed.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_packed_old.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_packed_old.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_set_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_set_base.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_set_concat_direct.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_set_concat_direct.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_set_dependent_generous.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_set_dependent_generous.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_set_dependent_tight.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_set_dependent_tight.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_set_owner.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_set_owner.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_set_segment.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_set_segment.h -------------------------------------------------------------------------------- /seqan/seqan/sequence/string_set_view.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence/string_set_view.h -------------------------------------------------------------------------------- /seqan/seqan/sequence_journaled.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence_journaled.h -------------------------------------------------------------------------------- /seqan/seqan/sequence_journaled/journal_entry.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence_journaled/journal_entry.h -------------------------------------------------------------------------------- /seqan/seqan/sequence_journaled/sequence_journaled.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/sequence_journaled/sequence_journaled.h -------------------------------------------------------------------------------- /seqan/seqan/simple_intervals_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/simple_intervals_io.h -------------------------------------------------------------------------------- /seqan/seqan/simple_intervals_io/simple_intervals_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/simple_intervals_io/simple_intervals_io.h -------------------------------------------------------------------------------- /seqan/seqan/statistics.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/statistics.h -------------------------------------------------------------------------------- /seqan/seqan/statistics/statistics_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/statistics/statistics_base.h -------------------------------------------------------------------------------- /seqan/seqan/statistics/statistics_markov_model.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/statistics/statistics_markov_model.h -------------------------------------------------------------------------------- /seqan/seqan/store.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_align.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_align.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_align_intervals.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_align_intervals.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_all.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_all.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_annotation.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_annotation.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_base.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_contig.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_contig.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_intervaltree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_intervaltree.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_io.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_io_gff.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_io_gff.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_io_sam.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_io_sam.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_io_ucsc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_io_ucsc.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_library.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_library.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_matepair.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_matepair.h -------------------------------------------------------------------------------- /seqan/seqan/store/store_read.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/store/store_read.h -------------------------------------------------------------------------------- /seqan/seqan/stream.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream.h -------------------------------------------------------------------------------- /seqan/seqan/stream/adapt_ios.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/adapt_ios.h -------------------------------------------------------------------------------- /seqan/seqan/stream/buffered_stream.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/buffered_stream.h -------------------------------------------------------------------------------- /seqan/seqan/stream/file_stream.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/file_stream.h -------------------------------------------------------------------------------- /seqan/seqan/stream/formatted_file.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/formatted_file.h -------------------------------------------------------------------------------- /seqan/seqan/stream/guess_format.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/guess_format.h -------------------------------------------------------------------------------- /seqan/seqan/stream/iostream_bgzf.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/iostream_bgzf.h -------------------------------------------------------------------------------- /seqan/seqan/stream/iostream_bzip2.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/iostream_bzip2.h -------------------------------------------------------------------------------- /seqan/seqan/stream/iostream_bzip2_impl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/iostream_bzip2_impl.h -------------------------------------------------------------------------------- /seqan/seqan/stream/iostream_zip.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/iostream_zip.h -------------------------------------------------------------------------------- /seqan/seqan/stream/iostream_zip_impl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/iostream_zip_impl.h -------------------------------------------------------------------------------- /seqan/seqan/stream/iostream_zutil.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/iostream_zutil.h -------------------------------------------------------------------------------- /seqan/seqan/stream/iter_stream.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/iter_stream.h -------------------------------------------------------------------------------- /seqan/seqan/stream/lexical_cast.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/lexical_cast.h -------------------------------------------------------------------------------- /seqan/seqan/stream/stream_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/stream_base.h -------------------------------------------------------------------------------- /seqan/seqan/stream/stream_compressor.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/stream_compressor.h -------------------------------------------------------------------------------- /seqan/seqan/stream/tokenization.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/tokenization.h -------------------------------------------------------------------------------- /seqan/seqan/stream/virtual_stream.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/stream/virtual_stream.h -------------------------------------------------------------------------------- /seqan/seqan/system.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/system.h -------------------------------------------------------------------------------- /seqan/seqan/system/file_async.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/system/file_async.h -------------------------------------------------------------------------------- /seqan/seqan/system/file_directory.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/system/file_directory.h -------------------------------------------------------------------------------- /seqan/seqan/system/file_forwards.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/system/file_forwards.h -------------------------------------------------------------------------------- /seqan/seqan/system/file_sync.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/system/file_sync.h -------------------------------------------------------------------------------- /seqan/seqan/system/system_base.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/system/system_base.h -------------------------------------------------------------------------------- /seqan/seqan/system/system_event_win.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/system/system_event_win.h -------------------------------------------------------------------------------- /seqan/seqan/system/system_forwards.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/system/system_forwards.h -------------------------------------------------------------------------------- /seqan/seqan/tabix_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/tabix_io.h -------------------------------------------------------------------------------- /seqan/seqan/tabix_io/tabix_index_tbi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/tabix_io/tabix_index_tbi.h -------------------------------------------------------------------------------- /seqan/seqan/translation.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/translation.h -------------------------------------------------------------------------------- /seqan/seqan/translation/translation.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/translation/translation.h -------------------------------------------------------------------------------- /seqan/seqan/translation/translation_tables.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/translation/translation_tables.h -------------------------------------------------------------------------------- /seqan/seqan/ucsc_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/ucsc_io.h -------------------------------------------------------------------------------- /seqan/seqan/ucsc_io/ucsc_file.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/ucsc_io/ucsc_file.h -------------------------------------------------------------------------------- /seqan/seqan/ucsc_io/ucsc_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/ucsc_io/ucsc_io.h -------------------------------------------------------------------------------- /seqan/seqan/ucsc_io/ucsc_record.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/ucsc_io/ucsc_record.h -------------------------------------------------------------------------------- /seqan/seqan/vcf_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/vcf_io.h -------------------------------------------------------------------------------- /seqan/seqan/vcf_io/read_vcf.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/vcf_io/read_vcf.h -------------------------------------------------------------------------------- /seqan/seqan/vcf_io/vcf_file.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/vcf_io/vcf_file.h -------------------------------------------------------------------------------- /seqan/seqan/vcf_io/vcf_header.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/vcf_io/vcf_header.h -------------------------------------------------------------------------------- /seqan/seqan/vcf_io/vcf_header_record.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/vcf_io/vcf_header_record.h -------------------------------------------------------------------------------- /seqan/seqan/vcf_io/vcf_io_context.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/vcf_io/vcf_io_context.h -------------------------------------------------------------------------------- /seqan/seqan/vcf_io/vcf_record.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/vcf_io/vcf_record.h -------------------------------------------------------------------------------- /seqan/seqan/vcf_io/write_vcf.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/vcf_io/write_vcf.h -------------------------------------------------------------------------------- /seqan/seqan/version.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/seqan/seqan/version.h -------------------------------------------------------------------------------- /src/CSC.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/src/CSC.cpp -------------------------------------------------------------------------------- /src/CSR.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/src/CSR.cpp -------------------------------------------------------------------------------- /src/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/src/main.cpp -------------------------------------------------------------------------------- /src/main.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/src/main.cu -------------------------------------------------------------------------------- /src/mkl_free_main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/src/mkl_free_main.cpp -------------------------------------------------------------------------------- /xavier/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/xavier/README.md -------------------------------------------------------------------------------- /xavier/demo.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/xavier/demo.cpp -------------------------------------------------------------------------------- /xavier/makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/xavier/makefile -------------------------------------------------------------------------------- /xavier/score.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/xavier/score.h -------------------------------------------------------------------------------- /xavier/simdutils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/xavier/simdutils.h -------------------------------------------------------------------------------- /xavier/tester.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/xavier/tester.py -------------------------------------------------------------------------------- /xavier/utils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/xavier/utils.h -------------------------------------------------------------------------------- /xavier/xavier.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PASSIONLab/BELLA/HEAD/xavier/xavier.h --------------------------------------------------------------------------------