#include <graph_caller.hpp>
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| 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) |
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virtual | ~VCFGenotyper () |
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virtual bool | call_snarl (const Snarl &snarl) |
| Call a given snarl, and print the output to out_stream. More...
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virtual string | vcf_header (const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides={}) const |
| Write the vcf header (version and contigs and basic info) More...
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| GraphCaller (SnarlCaller &snarl_caller, SnarlManager &snarl_manager, ostream &out_stream=cout) |
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virtual | ~GraphCaller () |
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virtual void | call_top_level_snarls (bool recurse_on_fail=true) |
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| VCFOutputCaller (const string &sample_name) |
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virtual | ~VCFOutputCaller () |
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void | add_variant (vcflib::Variant &var) const |
| Add a variant to our buffer. More...
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void | write_variants (ostream &out_stream) const |
| Sort then write variants in the buffer. More...
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tuple< string, size_t, size_t > | get_ref_positions (const vector< vcflib::Variant * > &variants) const |
| get path positions bounding a set of variants More...
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virtual unordered_map< string, size_t > | scan_contig_lengths () const |
| munge out the contig lengths from the VCF header More...
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void | 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) const |
| print a vcf variant More...
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tuple< size_t, size_t, bool, step_handle_t, step_handle_t > | get_ref_interval (const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) const |
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void | flatten_common_allele_ends (vcflib::Variant &variant, bool backward) const |
| clean up the alleles to not share common prefixes / suffixes More...
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VCFGenotyper : Genotype variants in a given VCF file
◆ VCFGenotyper()
vg::VCFGenotyper::VCFGenotyper |
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const PathHandleGraph & |
graph, |
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SnarlCaller & |
snarl_caller, |
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SnarlManager & |
snarl_manager, |
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vcflib::VariantCallFile & |
variant_file, |
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const string & |
sample_name, |
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const vector< string > & |
ref_paths = {} , |
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FastaReference * |
ref_fasta = nullptr , |
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FastaReference * |
ins_fasta = nullptr , |
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ostream & |
out_stream = cout |
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) |
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◆ ~VCFGenotyper()
vg::VCFGenotyper::~VCFGenotyper |
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virtual |
◆ call_snarl()
bool vg::VCFGenotyper::call_snarl |
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const Snarl & |
snarl | ) |
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virtual |
Call a given snarl, and print the output to out_stream.
Implements vg::GraphCaller.
◆ get_ref_positions()
tuple< string, size_t, size_t > vg::VCFGenotyper::get_ref_positions |
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const vector< vcflib::Variant * > & |
variants | ) |
const |
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protected |
get path positions bounding a set of variants
◆ scan_contig_lengths()
unordered_map< string, size_t > vg::VCFGenotyper::scan_contig_lengths |
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const |
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munge out the contig lengths from the VCF header
◆ vcf_header()
string vg::VCFGenotyper::vcf_header |
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const PathHandleGraph & |
graph, |
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const vector< string > & |
contigs, |
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const vector< size_t > & |
contig_length_overrides = {} |
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virtual |
Write the vcf header (version and contigs and basic info)
Reimplemented from vg::VCFOutputCaller.
◆ graph
◆ input_vcf
vcflib::VariantCallFile& vg::VCFGenotyper::input_vcf |
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protected |
input VCF to genotype, must have been loaded etc elsewhere
◆ traversal_finder
traversal finder uses alt paths to map VCF alleles from input_vcf back to traversals in the snarl
The documentation for this class was generated from the following files: