File List

Here is a list of all files with brief descriptions:

src
algorithms
alignment_path_offsets.cpp
alignment_path_offsets.hpp
approx_path_distance.cpp
approx_path_distance.hpp
back_translate.cpp
back_translate.hpp
chain_items.cpp
chain_items.hpp
component.cpp
component.hpp
count_covered.hpp
coverage_depth.cpp
coverage_depth.hpp
dfs.cpp
dfs.hpp
disjoint_components.cpp
disjoint_components.hpp
distance_to_head.cpp
distance_to_head.hpp
distance_to_tail.cpp
distance_to_tail.hpp
expand_context.cpp
expand_context.hpp
extract_connecting_graph.cpp
extract_connecting_graph.hpp
extract_containing_graph.cpp
extract_containing_graph.hpp
extract_extending_graph.cpp
extract_extending_graph.hpp
extract_subchain.cpp
extract_subchain.hpp
find_gbwt.cpp
find_gbwt.hpp
find_gbwtgraph.cpp
find_gbwtgraph.hpp
find_translation.cpp
find_translation.hpp
gfa_to_handle.cpp
gfa_to_handle.hpp
gfaz_to_handle.cpp
gfaz_to_handle.hpp
id_sort.cpp
id_sort.hpp
intersect_path_offsets.cpp
intersect_path_offsets.hpp
jump_along_path.cpp
jump_along_path.hpp
k_widest_paths.cpp
k_widest_paths.hpp
kmer.cpp
kmer.hpp
locally_expand_graph.cpp
locally_expand_graph.hpp
merge.cpp
merge.hpp
min_cut_graph.cpp
min_cut_graph.hpp
nearest_offsets_in_paths.cpp
nearest_offsets_in_paths.hpp
next_pos_chars.cpp
next_pos_chars.hpp
normalize.cpp
normalize.hpp
pad_band.cpp
pad_band.hpp
path_string.cpp
path_string.hpp
prune.cpp
prune.hpp
prune_to_connecting_graph.cpp
prune_to_connecting_graph.hpp
ref_path_distance.cpp
ref_path_distance.hpp
sample_minimal.cpp
sample_minimal.hpp
simplify_siblings.cpp
simplify_siblings.hpp
sorted_id_ranges.cpp
sorted_id_ranges.hpp
subgraph.cpp
subgraph.hpp
three_edge_connected_components.cpp
three_edge_connected_components.hpp
walk.cpp
walk.hpp
io
converted_hash_graph.hpp
json2graph.hpp
json_stream_helper.hpp
load_proto_to_graph.cpp
load_proto_to_graph.hpp
register_libvg_io.cpp
register_libvg_io.hpp
register_loader_gfaz.cpp
register_loader_gfaz.hpp
register_loader_params_json.cpp
register_loader_params_json.hpp
register_loader_saver_distance_index.cpp
register_loader_saver_distance_index.hpp
register_loader_saver_gbwt.cpp
register_loader_saver_gbwt.hpp
register_loader_saver_gbwtgraph.cpp
register_loader_saver_gbwtgraph.hpp
register_loader_saver_gbz.cpp
register_loader_saver_gbz.hpp
register_loader_saver_gbzgraph.cpp
register_loader_saver_gbzgraph.hpp
register_loader_saver_gcsa.cpp
register_loader_saver_gcsa.hpp
register_loader_saver_gfa.cpp
register_loader_saver_gfa.hpp
register_loader_saver_hash_graph.cpp
register_loader_saver_hash_graph.hpp
register_loader_saver_lcp.cpp
register_loader_saver_lcp.hpp
register_loader_saver_minimizer.cpp
register_loader_saver_minimizer.hpp
register_loader_saver_packed_graph.cpp
register_loader_saver_packed_graph.hpp
register_loader_saver_r_index.cpp
register_loader_saver_r_index.hpp
register_loader_saver_snarl_manager.cpp
register_loader_saver_snarl_manager.hpp
register_loader_saver_vg.cpp
register_loader_saver_vg.hpp
register_loader_saver_xg.cpp
register_loader_saver_xg.hpp
register_loader_saver_zip_codes.cpp
register_loader_saver_zip_codes.hpp
save_handle_graph.hpp
subcommand
add_main.cpp
align_main.cpp
annotate_main.cpp
augment_main.cpp
autoindex_main.cpp
bench_dist_query_main.cpp
benchmark_main.cpp
call_main.cpp
chains_main.cpp
chunk_main.cpp
circularize_main.cpp
clip_main.cpp
cluster_main.cpp
combine_main.cpp
concat_main.cpp
construct_main.cpp
convert_main.cpp
deconstruct_main.cpp
depth_main.cpp
describe_main.cpp
dotplot_main.cpp
filter_main.cpp
find_main.cpp
gamcompare_main.cpp
gampcompare_main.cpp
gamsort_main.cpp
gbwt_main.cpp
genotype_main.cpp
giraffe_main.cpp
haplotypes_main.cpp
help_main.cpp
ids_main.cpp
index_main.cpp
inject_main.cpp
kmers_main.cpp
map_main.cpp
mask_main.cpp
mcmc_main.cpp
minimizer_main.cpp
mod_main.cpp
mpmap_main.cpp
options.cpp
options.hpp
pack_main.cpp
paths_main.cpp
primers_main.cpp
prune_main.cpp
rna_main.cpp
sim_main.cpp
simplify_main.cpp
snarls_main.cpp
sort_main.cpp
stats_main.cpp
subcommand.cpp
subcommand.hpp
surject_main.cpp
test_main.cpp
trace_main.cpp
translate_main.cpp
validate_main.cpp
vectorize_main.cpp
version_main.cpp
view_main.cpp
viz_main.cpp
zipcode_main.cpp
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