vg
tools for working with variation graphs
vg::LegacyCaller Member List

This is the complete list of members for vg::LegacyCaller, including all inherited members.

add_variant(vcflib::Variant &var) constvg::VCFOutputCaller
break_chain(const HandleGraph &graph, const Chain &chain, size_t max_edges, size_t max_trivial)vg::GraphCallerprotected
call_snarl(const Snarl &snarl, int ploidy)vg::LegacyCallervirtual
call_top_level_chains(const HandleGraph &graph, int ploidy, size_t max_edges, size_t max_trivial, bool recurse_on_fail=true)vg::GraphCallervirtual
call_top_level_snarls(const HandleGraph &graph, int ploidy, bool recurse_on_fail=true)vg::GraphCallervirtual
emit_variant(const PathPositionHandleGraph &graph, SnarlCaller &snarl_caller, const Snarl &snarl, const vector< SnarlTraversal > &called_traversals, const vector< int > &genotype, int ref_trav_idx, const unique_ptr< SnarlCaller::CallInfo > &call_info, const string &ref_path_name, int ref_offset, bool genotype_snarls) constvg::VCFOutputCallerprotected
find_index(const Snarl &snarl, const vector< PathIndex * > path_indexes) constvg::LegacyCallerprotected
flatten_common_allele_ends(vcflib::Variant &variant, bool backward, size_t len_override) constvg::VCFOutputCallerprotected
get_ref_interval(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) constvg::VCFOutputCallerprotected
get_reference_traversal(const Snarl &snarl, TraversalFinder &trav_finder) constvg::LegacyCallerprotected
graphvg::LegacyCallerprotected
GraphCaller(SnarlCaller &snarl_caller, SnarlManager &snarl_manager)vg::GraphCaller
is_traversable(const Snarl &snarl)vg::LegacyCallerprotected
is_vgvg::LegacyCallerprotected
LegacyCaller(const PathPositionHandleGraph &graph, SupportBasedSnarlCaller &snarl_caller, SnarlManager &snarl_manager, const string &sample_name, const vector< string > &ref_paths={}, const vector< size_t > &ref_path_offsets={})vg::LegacyCaller
max_bubble_pathsvg::LegacyCallerprotected
max_search_depthvg::LegacyCallerprotected
max_search_widthvg::LegacyCallerprotected
max_uncalled_allelesvg::VCFOutputCallerprotected
output_variantsvg::VCFOutputCallermutableprotected
output_vcfvg::VCFOutputCallermutableprotected
path_indexesvg::LegacyCallerprotected
re_genotype(const Snarl &snarl, TraversalFinder &trav_finder, const vector< SnarlTraversal > &in_traversals, const vector< int > &in_genotype, int ploidy, const string &ref_path_name, pair< size_t, size_t > ref_interval) constvg::LegacyCallerprotected
ref_offsetsvg::LegacyCallerprotected
ref_pathsvg::LegacyCallerprotected
sample_namevg::VCFOutputCallerprotected
snarl_callervg::GraphCallerprotected
snarl_managervg::GraphCallerprotected
top_down_genotype(const Snarl &snarl, TraversalFinder &trav_finder, int ploidy, const string &ref_path_name, pair< size_t, size_t > ref_interval) constvg::LegacyCallerprotected
traversal_findervg::LegacyCallerprotected
vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides={}) constvg::LegacyCallervirtual
VCFOutputCaller(const string &sample_name)vg::VCFOutputCaller
write_variants(ostream &out_stream) constvg::VCFOutputCaller
~GraphCaller()vg::GraphCallervirtual
~LegacyCaller()vg::LegacyCallervirtual
~VCFOutputCaller()vg::VCFOutputCallervirtual