src Directory Reference

Directories
	algorithms
	io
	subcommand

Files
	aligner.cpp
	aligner.hpp
	alignment.cpp
	alignment.hpp
	alignment_scorer.cpp
	alignment_scorer.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
	explainer.cpp
	explainer.hpp
	feature_set.cpp
	feature_set.hpp
	flat_file_back_translation.cpp
	flat_file_back_translation.hpp
	flow_caller.cpp
	flow_caller.hpp
	flow_sort.cpp
	flow_sort.hpp
	funnel.cpp
	funnel.hpp
	gaf_output_caller.cpp
	gaf_output_caller.hpp
	gaf_sorter.cpp
	gaf_sorter.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
	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
	gref.cpp
	gref.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
	integrated_snarl_finder.cpp
	integrated_snarl_finder.hpp
	interval_union.cpp
	interval_union.hpp
	job_schedule.cpp
	job_schedule.hpp
	kff.cpp
	kff.hpp
	kmer.cpp
	kmer.hpp
	kmp.cpp
	kmp.hpp
	legacy_caller.cpp
	legacy_caller.hpp
	log.cpp
	log.hpp
	logged_gap_alignment_scorer.cpp
	logged_gap_alignment_scorer.hpp
	longest_overlap.hpp
	main.cpp
	mapper.cpp
	mapper.hpp
	mapping_quality_calculator.cpp
	mapping_quality_calculator.hpp
	masker.cpp
	masker.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_flow_caller.cpp
	nested_flow_caller.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
	primer_filter.cpp
	primer_filter.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_graph.cpp
	snarl_graph.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
	varint.cpp
	varint.hpp
	vcf_buffer.cpp
	vcf_buffer.hpp
	vcf_genotyper.cpp
	vcf_genotyper.hpp
	vcf_output_caller.cpp
	vcf_output_caller.hpp
	vectorizer.cpp
	vectorizer.hpp
	version.cpp
	version.hpp
	vg.cpp
	vg.hpp
	vg_environment_version.hpp
	vg_git_version.hpp
	vg_set.cpp
	vg_set.hpp
	viz.cpp
	viz.hpp
	wang_hash.hpp
	watchdog.cpp
	watchdog.hpp
	xdrop_aligner.cpp
	zip_code.cpp
	zip_code.hpp
	zip_code_tree.cpp
	zip_code_tree.hpp
	zstdutil.cpp
	zstdutil.hpp