Here is a list of all files with brief descriptions:

[detail level 123456]

► deps
► libhandlegraph
► src
► include
► handlegraph
buildable_snarl_decomposition.hpp
deletable_handle_graph.hpp
expanding_overlay_graph.hpp
handle_graph.hpp
iteratee.hpp
mutable_handle_graph.hpp
mutable_path_deletable_handle_graph.hpp
mutable_path_handle_graph.hpp
mutable_path_mutable_handle_graph.hpp
path_handle_graph.hpp
path_position_handle_graph.hpp
serializable.hpp
serializable_handle_graph.hpp
snarl_decomposition.hpp
trivially_serializable.hpp
types.hpp
util.hpp
append_graph.cpp
apply_orientations.cpp
are_equivalent.cpp
copy_graph.cpp
count_walks.cpp
dagify.cpp
deletable_handle_graph.cpp
dijkstra.cpp
eades_algorithm.cpp
extend.cpp
find_shortest_paths.cpp
find_tips.cpp
handle_graph.cpp
is_acyclic.cpp
is_single_stranded.cpp
mutable_handle_graph.cpp
path_handle_graph.cpp
path_position_handle_graph.cpp
ranked_handle_graph.cpp
reverse_complement.cpp
serializable.cpp
snarl_decomposition.cpp
split_strands.cpp
strongly_connected_components.cpp
topological_sort.cpp
trivially_serializable.cpp
types.cpp
unchop.cpp
weakly_connected_components.cpp
► libvgio
► deps
vg.proto
► include
► vg
► io
alignment_emitter.hpp
alignment_io.hpp
basic_stream.hpp
blocked_gzip_input_stream.hpp
blocked_gzip_output_stream.hpp
edit.hpp
fdstream.hpp
gafkluge.hpp
hfile_cppstream.hpp
hfile_internal.hpp
json2pb.h
loader.hpp
message_emitter.hpp
message_iterator.hpp
protobuf_emitter.hpp
protobuf_iterator.hpp
registry.hpp
stream.hpp
stream_multiplexer.hpp
vpkg.hpp
► src
alignment_emitter.cpp
alignment_io.cpp
basic_stream.cpp
bin2ascii.h
blocked_gzip_input_stream.cpp
blocked_gzip_output_stream.cpp
edit.cpp
hfile_cppstream.cpp
json2pb.cpp
message_emitter.cpp
message_iterator.cpp
registry.cpp
stream.cpp
stream_multiplexer.cpp
vpkg.cpp
► xg
► src
xg.cpp
xg.hpp
► src
► algorithms
a_star.hpp
alignment_path_offsets.cpp
alignment_path_offsets.hpp
approx_path_distance.cpp
approx_path_distance.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
gfa_to_handle.cpp
gfa_to_handle.hpp
id_sort.cpp
id_sort.hpp
jump_along_path.cpp
jump_along_path.hpp
k_widest_paths.cpp
k_widest_paths.hpp
kmer.cpp
kmer.hpp
merge.cpp
merge.hpp
nearest_offsets_in_paths.cpp
nearest_offsets_in_paths.hpp
next_pos_chars.cpp
next_pos_chars.hpp
normalize.cpp
normalize.hpp
path_string.cpp
path_string.hpp
prune.cpp
prune.hpp
ref_path_distance.cpp
ref_path_distance.hpp
shortest_cycle.cpp
shortest_cycle.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
to_gfa.cpp
to_gfa.hpp
walk.cpp
walk.hpp
► io
converted_hash_graph.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_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_gcsa.cpp
register_loader_saver_gcsa.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_odgi.cpp
register_loader_saver_odgi.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
save_handle_graph.hpp
► subcommand
add_main.cpp
align_main.cpp
annotate_main.cpp
augment_main.cpp
autoindex_main.cpp
benchmark_main.cpp
call_main.cpp
chunk_main.cpp
circularize_main.cpp
cluster_main.cpp
combine_main.cpp
concat_main.cpp
construct_main.cpp
convert_main.cpp
deconstruct_main.cpp
depth_main.cpp
dotplot_main.cpp
explode_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
help_main.cpp
ids_main.cpp
index_main.cpp
inject_main.cpp
join_main.cpp
kmers_main.cpp
map_main.cpp
mcmc_main.cpp
minimizer_main.cpp
mod_main.cpp
mpmap_main.cpp
msga_main.cpp
pack_main.cpp
paths_main.cpp
prune_main.cpp
recalibrate_main.cpp
rna_main.cpp
sift_main.cpp
sim_main.cpp
simplify_main.cpp
snarls_main.cpp
sort_main.cpp
srpe_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
► unittest
driver.cpp
driver.hpp
aligner.cpp
aligner.hpp
alignment.cpp
alignment.hpp
annotation.hpp
augment.cpp
augment.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
cluster.cpp
cluster.hpp
colors.hpp
constructor.cpp
constructor.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
extra_node_graph.cpp
extra_node_graph.hpp
feature_set.cpp
feature_set.hpp
filter.cpp
filter.hpp
flow_sort.cpp
flow_sort.hpp
funnel.cpp
funnel.hpp
gapless_extender.cpp
gapless_extender.hpp
gbwt_helper.cpp
gbwt_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
homogenizer.cpp
homogenizer.hpp
hts_alignment_emitter.cpp
hts_alignment_emitter.hpp
identity_overlay.cpp
identity_overlay.hpp
incremental_subgraph.cpp
incremental_subgraph.hpp
index_manager.cpp
index_manager.hpp
index_registry.cpp
index_registry.hpp
indexed_vg.cpp
indexed_vg.hpp
integrated_snarl_finder.cpp
integrated_snarl_finder.hpp
kmer.cpp
kmer.hpp
main.cpp
mapper.cpp
mapper.hpp
mcmc_caller.cpp
mcmc_caller.hpp
mcmc_genotyper.cpp
mcmc_genotyper.hpp
mem.cpp
mem.hpp
memoizing_graph.cpp
memoizing_graph.hpp
memusage.cpp
memusage.hpp
min_distance.cpp
min_distance.hpp
minimizer_mapper.cpp
minimizer_mapper.hpp
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
region.cpp
region.hpp
region_expander.cpp
region_expander.hpp
reverse_graph.cpp
reverse_graph.hpp
sampler.cpp
sampler.hpp
scanner.cpp
scanner.hpp
seed_clusterer.cpp
seed_clusterer.hpp
sequence_complexity.hpp
small_bitset.hpp
small_snarl_simplifier.cpp
small_snarl_simplifier.hpp
snarl_caller.cpp
snarl_caller.hpp
snarls.cpp
snarls.hpp
source_sink_overlay.cpp
source_sink_overlay.hpp
splicing.cpp
splicing.hpp
split_strand_graph.cpp
split_strand_graph.hpp
srpe.cpp
srpe.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
surjecting_alignment_emitter.cpp
surjecting_alignment_emitter.hpp
surjector.cpp
surjector.hpp
swap_remove.hpp
transcriptome.cpp
transcriptome.hpp
translator.cpp
translator.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