vg
tools for working with variation graphs
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#include <graph_caller.hpp>
Public Member Functions | |
VCFOutputCaller (const string &sample_name) | |
virtual | ~VCFOutputCaller () |
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... | |
void | add_variant (vcflib::Variant &var) const |
Add a variant to our buffer. More... | |
void | write_variants (ostream &out_stream) const |
Sort then write variants in the buffer. More... | |
Protected Member Functions | |
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, bool genotype_snarls) const |
print a vcf variant More... | |
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 |
void | flatten_common_allele_ends (vcflib::Variant &variant, bool backward, size_t len_override) const |
Protected Attributes | |
vcflib::VariantCallFile | output_vcf |
output vcf More... | |
string | sample_name |
Sample name. More... | |
vector< vector< vcflib::Variant > > | output_variants |
output buffers (1/thread) (for sorting) More... | |
size_t | max_uncalled_alleles = 5 |
print up to this many uncalled alleles when doing ref-genotpes in -a mode More... | |
Helper class that vcf writers can inherit from to for some common code to output sorted VCF
vg::VCFOutputCaller::VCFOutputCaller | ( | const string & | sample_name | ) |
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virtual |
void vg::VCFOutputCaller::add_variant | ( | vcflib::Variant & | var | ) | const |
Add a variant to our buffer.
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protected |
print a vcf variant
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protected |
clean up the alleles to not share common prefixes / suffixes if len_override given, just do that many bases without thinking
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protected |
get the interval of a snarl from our reference path using the PathPositionHandleGraph interface the bool is true if the snarl's backward on the path
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virtual |
Write the vcf header (version and contigs and basic info)
Reimplemented in vg::FlowCaller, vg::LegacyCaller, and vg::VCFGenotyper.
void vg::VCFOutputCaller::write_variants | ( | ostream & | out_stream | ) | const |
Sort then write variants in the buffer.
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protected |
print up to this many uncalled alleles when doing ref-genotpes in -a mode
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mutableprotected |
output buffers (1/thread) (for sorting)
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mutableprotected |
output vcf
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protected |
Sample name.