src Directory Reference

Directories
directory	algorithms
directory	io
directory	subcommand

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