vg
tools for working with variation graphs
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src
src Directory Reference
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algorithms
io
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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
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