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

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

add_variant(vcflib::Variant &var) constvg::VCFOutputCaller
call_snarl(const Snarl &snarl)vg::FlowCallervirtual
call_top_level_snarls(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) constvg::VCFOutputCallerprotected
flatten_common_allele_ends(vcflib::Variant &variant, bool backward) constvg::VCFOutputCallerprotected
FlowCaller(const PathPositionHandleGraph &graph, SupportBasedSnarlCaller &snarl_caller, SnarlManager &snarl_manager, const string &sample_name, size_t max_traverals, const vector< string > &ref_paths={}, const vector< size_t > &ref_path_offsets={}, ostream &out_stream=cout)vg::FlowCaller
get_ref_interval(const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) constvg::VCFOutputCallerprotected
graphvg::FlowCallerprotected
GraphCaller(SnarlCaller &snarl_caller, SnarlManager &snarl_manager, ostream &out_stream=cout)vg::GraphCaller
out_streamvg::GraphCallerprotected
output_variantsvg::VCFOutputCallermutableprotected
output_vcfvg::VCFOutputCallermutableprotected
ref_offsetsvg::FlowCallerprotected
ref_path_setvg::FlowCallerprotected
ref_pathsvg::FlowCallerprotected
sample_namevg::VCFOutputCallerprotected
snarl_callervg::GraphCallerprotected
snarl_managervg::GraphCallerprotected
traversal_findervg::FlowCallerprotected
vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides={}) constvg::FlowCallervirtual
VCFOutputCaller(const string &sample_name)vg::VCFOutputCaller
write_variants(ostream &out_stream) constvg::VCFOutputCaller
~FlowCaller()vg::FlowCallervirtual
~GraphCaller()vg::GraphCallervirtual
~VCFOutputCaller()vg::VCFOutputCallervirtual