GLnexus::Service Class Reference

Classes
struct	body

Public Member Functions
Status	discover_alleles (const std::string &sampleset, const range &pos, discovered_alleles &ans)
Status	discover_alleles (const std::string &sampleset, const std::vector< range > &ranges, std::vector< discovered_alleles > &ans)
Status	genotype_sites (const genotyper_config &cfg, const std::string &sampleset, const std::vector< unified_site > &sites, const std::string &filename, consolidated_loss &dlosses)
	Genotype a set of samples at the given sites, producing a BCF file.

Static Public Member Functions
static Status	Start (Metadata &metadata, BCFData &data, std::unique_ptr< Service > &svc)

Member Function Documentation

Status GLnexus::Service::discover_alleles	(	const std::string &	sampleset,
		const range &	pos,
		discovered_alleles &	ans
	)

Discover all the alleles contained within the given range for a sample set. Each allele has a reference range and DNA sequence. Additionally, it's marked as REF or not, and includes an estimate of the observation count in the sample set, which may be useful for making an empirical estimate of the allele frequency. The discovered alleles may be overlapping; the set is generally used as input to allele "unification"

Status GLnexus::Service::discover_alleles	(	const std::string &	sampleset,
		const std::vector< range > &	ranges,
		std::vector< discovered_alleles > &	ans
	)

Discover all the alleles contained within each of the given disjoint ranges. Uses multithreading such that this may be preferable to calling discover_alleles repeatedly for many small ranges (e.g. exome target capture regions). However, attention should be paid to the anticipated size of the results.

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The documentation for this class was generated from the following files:

• include/service.h
• src/service.cc