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class asmc::HapsMatrixType

A class that stores information in a #sites x #haps matrix of booleans.

Public Functions

unsigned long getNumIndividuals() const

Return

the number of individuals, determined from the .sample[s] file

unsigned long getNumHaps() const

Return

the number of haps: twice the number of individuals

unsigned long getNumSites() const

Return

the number of sites, determined from the .map file

const std::vector<unsigned long> &getPhysicalPositions() const

Return

a vector of physical positions, read in from the .map file

const std::vector<double> &getGeneticPositions() const

Return

a vector of genetic positions, in centimorgans, read in from the .map file

const mat_uint8_t &getData() const

Return

the matrix of raw uint8_t data

mat_float_t getDataAsFloat() const

Return

the matrix of raw data, cast to float

rvec_uint8_t getSite(unsigned long siteId) const

Get all haplotype data for a single site. This is a row from the data matrix and will be a boolean row vector of length 2N where N is the number of individuals.

Return

the ith row of the data matrix, where i is siteId.

Parameters

• siteId: the id of the site

cvec_uint8_t getHap(unsigned long hapId) const

Get all site data for a single haplotype. This is a column from the data matrix and will be a boolean column vector of length N where N is the number of sites.

Return

the jth row of the data matrix, where j is hapId.

Parameters

• hapId: the id of the haplotype

mat_uint8_t getIndividual(unsigned long individualId) const

Get all site data for a single individual. This is two adjacent columns from the data matrix, returned as a matrix.

Return

the jth row of the data matrix, where j is hapId.

Parameters

• individualId: the id of the individual

unsigned long getMinorAlleleCount(unsigned long siteId) const

Get the minor allele count for a given site. This is a number in [0, #haps/2].

Return

the minor allele count for the given site

Parameters

• siteId: the site ID

unsigned long getDerivedAlleleCount(unsigned long siteId) const

Get the derived allele count for a given site. This is the raw count, assuming 1 means derived.

Return

the derived allele count for the given site

Parameters

• siteId: the site ID

cvec_ul_t getMinorAlleleCounts() const

Get the raw minor allele counts for all sites. Each is a number in [0, #haps/2].

Return

a vector of minor allele counts, one for each site

cvec_ul_t getDerivedAlleleCounts() const

Get the derived allele count for all sites. These are the raw counts, assuming 1 means derived.

Return

a vector of derived allele counts, one for each site

double getMinorAlleleFrequency(unsigned long siteId) const

Get the minor allele frequency for a given site. This is a number in [0, 0.5].

Return

the minor allele frequency for the given site

Parameters

• siteId: the site ID

double getDerivedAlleleFrequency(unsigned long siteId) const

Get the derived allele frequency for a given site. This is the raw frequency, assuming 1 means derived.

Return

the derived allele frequency for the given site

Parameters

• siteId: the site ID

cvec_dbl_t getMinorAlleleFrequencies() const

Get the minor allele frequencies for all sites. These are numbers in [0, 0.5].

Return

a vector of minor allele frequencies, one for each site

cvec_dbl_t getDerivedAlleleFrequencies() const

Get the derived allele frequencies for all sites. These are the raw frequencies, assuming 1 means derived.

Return

a vector of minor allele frequencies, one for each site

double getFrequency(unsigned long siteId) const

Public Static Functions

static HapsMatrixType createFromHapsPlusSamples(std::string_view hapsFile, std::string_view samplesFile, std::string_view mapFile)

Create a HapsMatrixType from a .hap[s][.gz], a .sample[s] file, and a .map file.

Return

instance of a HapsMatrixType

Parameters

• hapsFile: path to the .hap[s][.gz] file

• samplesFile: path to the .sample[s] file

• mapFile: path to the .map file