vg
tools for working with variation graphs
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This is the complete list of members for vg::VCFGenotyper, including all inherited members.
add_variant(vcflib::Variant &var) const | vg::VCFOutputCaller | |
call_snarl(const Snarl &snarl) | vg::VCFGenotyper | virtual |
call_top_level_snarls(bool recurse_on_fail=true) | vg::GraphCaller | virtual |
get_ref_positions(const vector< vcflib::Variant * > &variants) const | vg::VCFGenotyper | protected |
graph | vg::VCFGenotyper | protected |
GraphCaller(SnarlCaller &snarl_caller, SnarlManager &snarl_manager, ostream &out_stream=cout) | vg::GraphCaller | |
input_vcf | vg::VCFGenotyper | protected |
out_stream | vg::GraphCaller | protected |
output_variants | vg::VCFOutputCaller | mutableprotected |
output_vcf | vg::VCFOutputCaller | mutableprotected |
sample_name | vg::VCFOutputCaller | protected |
scan_contig_lengths() const | vg::VCFGenotyper | protectedvirtual |
snarl_caller | vg::GraphCaller | protected |
snarl_manager | vg::GraphCaller | protected |
traversal_finder | vg::VCFGenotyper | protected |
vcf_header(const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides={}) const | vg::VCFGenotyper | virtual |
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) const | vg::VCFOutputCaller | |
~GraphCaller() | vg::GraphCaller | virtual |
~VCFGenotyper() | vg::VCFGenotyper | virtual |
~VCFOutputCaller() | vg::VCFOutputCaller | virtual |