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

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

add_variant(vcflib::Variant &var) constvg::VCFOutputCaller
call_snarl(const Snarl &snarl)vg::VCFGenotypervirtual
call_top_level_snarls(bool recurse_on_fail=true)vg::GraphCallervirtual
get_ref_positions(const vector< vcflib::Variant * > &variants) constvg::VCFGenotyperprotected
graphvg::VCFGenotyperprotected
GraphCaller(SnarlCaller &snarl_caller, SnarlManager &snarl_manager, ostream &out_stream=cout)vg::GraphCaller
input_vcfvg::VCFGenotyperprotected
out_streamvg::GraphCallerprotected
output_variantsvg::VCFOutputCallermutableprotected
output_vcfvg::VCFOutputCallermutableprotected
sample_namevg::VCFOutputCallerprotected
scan_contig_lengths() constvg::VCFGenotyperprotectedvirtual
snarl_callervg::GraphCallerprotected
snarl_managervg::GraphCallerprotected
traversal_findervg::VCFGenotyperprotected
vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides={}) constvg::VCFGenotypervirtual
VCFGenotyper(const PathHandleGraph &graph, SnarlCaller &snarl_caller, SnarlManager &snarl_manager, vcflib::VariantCallFile &variant_file, const string &sample_name, const vector< string > &ref_paths={}, FastaReference *ref_fasta=nullptr, FastaReference *ins_fasta=nullptr, ostream &out_stream=cout)vg::VCFGenotyper
VCFOutputCaller(const string &sample_name)vg::VCFOutputCaller
write_variants(ostream &out_stream) constvg::VCFOutputCaller
~GraphCaller()vg::GraphCallervirtual
~VCFGenotyper()vg::VCFGenotypervirtual
~VCFOutputCaller()vg::VCFOutputCallervirtual
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