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 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... | |
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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virtual |
Write the vcf header (version and contigs and basic info)
Reimplemented in 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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mutableprotected |
output buffers (1/thread) (for sorting)
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mutableprotected |
output vcf
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protected |
Sample name.