GLnexus::Metadata Class Reference

#include <data.h>

Inheritance diagram for GLnexus::Metadata:

Public Member Functions
virtual Status	contigs (std::vector< std::pair< std::string, size_t > > &ans) const =0
virtual Status	sampleset_samples (const std::string &sampleset, std::shared_ptr< const std::set< std::string > > &ans) const =0
virtual Status	sample_dataset (const std::string &sample, std::string &ans) const =0
virtual Status	all_samples_sampleset (std::string &ans)=0
virtual Status	sample_count (size_t &ans) const =0
	Return the count of all samples in the database.

Detailed Description

Abstract interface to "metadata" – namely contigs and sample sets.

Definitions: Each sample (individual whose GLs are stored) has a unique string identifier. A sample set is simply a set of sample identifiers. A data set contains all the allele/genotype/likelihood data for one or more samples – just like a [V/B]CF file. All the GL data for each sample resides in exactly one data set. Sample sets and data sets are immutable.

Member Function Documentation

virtual Status GLnexus::Metadata::all_samples_sampleset ( std::string &  ans )

pure virtual

Return the name of a sample set representing all samples currently available. This may either create a new sample set if needed, or return an existing one if available. As always, the sample set is immutable: it will not include samples added to the database later (but one could call all_samples_sampleset again to get a different sample set including them).

Implemented in GLnexus::MetadataCache, and GLnexus::BCFKeyValueData.

virtual Status GLnexus::Metadata::contigs ( std::vector< std::pair< std::string, size_t > > &  ans ) const

pure virtual

Get the reference contigs.

The indices of the vector are the "rid" used in range()

Implemented in GLnexus::MetadataCache, and GLnexus::BCFKeyValueData.

virtual Status GLnexus::Metadata::sample_dataset ( const std::string &  sample, std::string &  ans  ) const

pure virtual

Find the data set containing the sample.

The data set may contain other samples.

Implemented in GLnexus::MetadataCache, and GLnexus::BCFKeyValueData.

virtual Status GLnexus::Metadata::sampleset_samples ( const std::string &  sampleset, std::shared_ptr< const std::set< std::string > > &  ans  ) const

pure virtual

List the samples in a sample set.

The resulting data structure may be shared, so the strings must not be mutated. They aren't declared const because...C++ http://stackoverflow.com/a/21365478

Implemented in GLnexus::MetadataCache, and GLnexus::BCFKeyValueData.

---

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

• include/data.h