vg
tools for working with variation graphs
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src Directory Reference

Directories

 algorithms
 
 io
 
 subcommand
 

Files

 aligner.cpp
 
 aligner.hpp
 
 alignment.cpp
 
 alignment.hpp
 
 annotation.hpp
 
 augment.cpp
 
 augment.hpp
 
 back_translating_alignment_emitter.cpp
 
 back_translating_alignment_emitter.hpp
 
 banded_global_aligner.cpp
 
 banded_global_aligner.hpp
 
 benchmark.cpp
 
 benchmark.hpp
 
 build_index.cpp
 
 build_index.hpp
 
 cactus.cpp
 
 cactus.hpp
 
 cactus_snarl_finder.cpp
 
 cactus_snarl_finder.hpp
 
 chunker.cpp
 
 chunker.hpp
 
 clip.cpp
 
 clip.hpp
 
 cluster.cpp
 
 cluster.hpp
 
 colors.hpp
 
 constructor.cpp
 
 constructor.hpp
 
 contracting_graph.cpp
 
 contracting_graph.hpp
 
 convert.hpp
 
 crash.cpp
 
 crash.hpp
 
 dagified_graph.cpp
 
 dagified_graph.hpp
 
 deconstructor.cpp
 
 deconstructor.hpp
 
 deletion_aligner.cpp
 
 deletion_aligner.hpp
 
 dinucleotide_machine.cpp
 
 dinucleotide_machine.hpp
 
 dozeu_interface.cpp
 
 dozeu_interface.hpp
 
 dozeu_pinning_overlay.cpp
 
 dozeu_pinning_overlay.hpp
 
 endianness.hpp
 
 entropy.cpp
 
 entropy.hpp
 
 explainer.cpp
 
 explainer.hpp
 
 extra_node_graph.cpp
 
 extra_node_graph.hpp
 
 feature_set.cpp
 
 feature_set.hpp
 
 filter.cpp
 
 filter.hpp
 
 flat_file_back_translation.cpp
 
 flat_file_back_translation.hpp
 
 flow_sort.cpp
 
 flow_sort.hpp
 
 funnel.cpp
 
 funnel.hpp
 
 gbwt_extender.cpp
 
 gbwt_extender.hpp
 
 gbwt_helper.cpp
 
 gbwt_helper.hpp
 
 gbwtgraph_helper.cpp
 
 gbwtgraph_helper.hpp
 
 gbzgraph.hpp
 
 gcsa_helper.cpp
 
 gcsa_helper.hpp
 
 genome_state.cpp
 
 genome_state.hpp
 
 genotypekit.cpp
 
 genotypekit.hpp
 
 genotyper.cpp
 
 genotyper.hpp
 
 gfa.cpp
 
 gfa.hpp
 
 gff_reader.cpp
 
 gff_reader.hpp
 
 graph.cpp
 
 graph.hpp
 
 graph_caller.cpp
 
 graph_caller.hpp
 
 graph_synchronizer.cpp
 
 graph_synchronizer.hpp
 
 handle.hpp
 
 haplotype_extracter.cpp
 
 haplotype_extracter.hpp
 
 haplotype_indexer.cpp
 
 haplotype_indexer.hpp
 
 haplotypes.cpp
 
 haplotypes.hpp
 
 hash_map.hpp
 
 hts_alignment_emitter.cpp
 
 hts_alignment_emitter.hpp
 
 identity_overlay.cpp
 
 identity_overlay.hpp
 
 incremental_subgraph.cpp
 
 incremental_subgraph.hpp
 
 index_registry.cpp
 
 index_registry.hpp
 
 indexed_vg.cpp
 
 indexed_vg.hpp
 
 integrated_snarl_finder.cpp
 
 integrated_snarl_finder.hpp
 
 job_schedule.cpp
 
 job_schedule.hpp
 
 kff.cpp
 
 kff.hpp
 
 kmer.cpp
 
 kmer.hpp
 
 kmp.cpp
 
 kmp.hpp
 
 main.cpp
 
 mapper.cpp
 
 mapper.hpp
 
 mcmc_caller.cpp
 
 mcmc_caller.hpp
 
 mcmc_genotyper.cpp
 
 mcmc_genotyper.hpp
 
 mem.cpp
 
 mem.hpp
 
 mem_accelerator.cpp
 
 mem_accelerator.hpp
 
 memoizing_graph.cpp
 
 memoizing_graph.hpp
 
 memusage.cpp
 
 memusage.hpp
 
 minimizer_mapper.cpp
 
 minimizer_mapper.hpp
 
 minimizer_mapper_from_chains.cpp
 
 msa_converter.cpp
 
 msa_converter.hpp
 
 multipath_alignment.cpp
 
 multipath_alignment.hpp
 
 multipath_alignment_emitter.cpp
 
 multipath_alignment_emitter.hpp
 
 multipath_alignment_graph.cpp
 
 multipath_alignment_graph.hpp
 
 multipath_mapper.cpp
 
 multipath_mapper.hpp
 
 name_mapper.cpp
 
 name_mapper.hpp
 
 nested_traversal_finder.cpp
 
 nested_traversal_finder.hpp
 
 nodeside.hpp
 
 nodetraversal.hpp
 
 null_masking_graph.cpp
 
 null_masking_graph.hpp
 
 option.cpp
 
 option.hpp
 
 packer.cpp
 
 packer.hpp
 
 path.cpp
 
 path.hpp
 
 path_component_index.cpp
 
 path_component_index.hpp
 
 path_index.cpp
 
 path_index.hpp
 
 path_subgraph.cpp
 
 path_subgraph.hpp
 
 phase_unfolder.cpp
 
 phase_unfolder.hpp
 
 phased_genome.cpp
 
 phased_genome.hpp
 
 pictographs.hpp
 
 position.cpp
 
 position.hpp
 
 preflight.cpp
 
 preflight.hpp
 
 progressive.cpp
 
 progressive.hpp
 
 qual_adj_xdrop_aligner.cpp
 
 rare_variant_simplifier.cpp
 
 rare_variant_simplifier.hpp
 
 readfilter.cpp
 
 readfilter.hpp
 
 recombinator.cpp
 
 recombinator.hpp
 
 region.cpp
 
 region.hpp
 
 region_expander.cpp
 
 region_expander.hpp
 
 reverse_graph.cpp
 
 reverse_graph.hpp
 
 sampler.cpp
 
 sampler.hpp
 
 scanner.cpp
 
 scanner.hpp
 
 sequence_complexity.hpp
 
 small_bitset.hpp
 
 small_snarl_simplifier.cpp
 
 small_snarl_simplifier.hpp
 
 snarl_caller.cpp
 
 snarl_caller.hpp
 
 snarl_distance_index.cpp
 
 snarl_distance_index.hpp
 
 snarl_seed_clusterer.cpp
 
 snarl_seed_clusterer.hpp
 
 snarls.cpp
 
 snarls.hpp
 
 source_sink_overlay.cpp
 
 source_sink_overlay.hpp
 
 sparse_union_find.cpp
 
 sparse_union_find.hpp
 
 splicing.cpp
 
 splicing.hpp
 
 split_strand_graph.cpp
 
 split_strand_graph.hpp
 
 ssw_aligner.cpp
 
 ssw_aligner.hpp
 
 statistics.cpp
 
 statistics.hpp
 
 stream_index.cpp
 
 stream_index.hpp
 
 stream_sorter.cpp
 
 stream_sorter.hpp
 
 subgraph.cpp
 
 subgraph.hpp
 
 subgraph_overlay.cpp
 
 subgraph_overlay.hpp
 
 subpath_overlay.cpp
 
 subpath_overlay.hpp
 
 surjecting_alignment_emitter.cpp
 
 surjecting_alignment_emitter.hpp
 
 surjector.cpp
 
 surjector.hpp
 
 swap_remove.hpp
 
 transcriptome.cpp
 
 transcriptome.hpp
 
 translator.cpp
 
 translator.hpp
 
 traversal_clusters.cpp
 
 traversal_clusters.hpp
 
 traversal_finder.cpp
 
 traversal_finder.hpp
 
 traversal_support.cpp
 
 traversal_support.hpp
 
 tree_subgraph.cpp
 
 tree_subgraph.hpp
 
 types.hpp
 
 utility.cpp
 
 utility.hpp
 
 variant_adder.cpp
 
 variant_adder.hpp
 
 variant_recall.cpp
 
 variant_recall.hpp
 
 vcf_buffer.cpp
 
 vcf_buffer.hpp
 
 vectorizer.cpp
 
 vectorizer.hpp
 
 version.cpp
 
 version.hpp
 
 vg.cpp
 
 vg.hpp
 
 vg_set.cpp
 
 vg_set.hpp
 
 viz.cpp
 
 viz.hpp
 
 wang_hash.hpp
 
 watchdog.cpp
 
 watchdog.hpp
 
 xdrop_aligner.cpp
 
 zstdutil.cpp
 
 zstdutil.hpp