Encodes a genotype. More...

#include <genotype.h>

Public Member Functions
	Genotype (const std::shared_ptr< bcf1_t > &body, const bcf_fmt_t const format_ptr, const uint8_t data_ptr)
	Constructs a genotype. More...

	Genotype (const Genotype &other)=delete
	copying of the Genotype object is not allowed. More...

Genotype &	operator= (const Genotype &other)=delete
	copying of the Genotype object is not allowed. More...

	Genotype (Genotype &&other)=default
	Explicit default as recommended by many threads on stackoverflow. More...

Genotype &	operator= (Genotype &&other)=default
	Explicit default as recommended by many threads on stackoverflow. More...

	~Genotype ()=default
	Explicit default as recommended by many threads on stackoverflow. More...

bool	operator!= (const Genotype &other) const
	Checks if another genotype does not equal this genotype. More...

bool	operator== (const Genotype &other) const
	Checks if another genotype equals this genotype. More...

bool	het () const
	Checks if this genotype vector is any type of heterozygous call. More...

bool	non_ref_het () const
	Checks if this genotype vector is a heterozygous call and none of the alleles is the reference. More...

uint32_t	fast_diploid_key_generation () const
	A bit encoding for the first two alleles. More...

bool	hom_var () const
	Checks if this genotype vector is a homozygous call that is non-reference. More...

bool	hom_ref () const
	Checks if this genotype vector is a homozygous call that is reference. More...

bool	missing () const
	Checks if all alleles are missing. More...

std::vector< std::string >	allele_strings () const
	Returns a vector with all the allele strings. More...

std::vector< int32_t >	allele_keys () const
	Returns a vector with all the allele keys. More...

std::string	allele_string (const uint32_t index) const
	Returns the allele string at index. More...

int32_t	allele_key (const uint32_t index) const
	Returns the allele key within this line. More...

int32_t	operator[] (const uint32_t index) const
	Returns the allele key within this line. More...

uint32_t	size () const
	Returns the number of alleles. More...

bool	snp (const AlleleMask &mask) const
	whether or not this genotype represents a snp More...

bool	insertion (const AlleleMask &mask) const
	whether or not this genotype represents an insertion More...

bool	deletion (const AlleleMask &mask) const
	whether or not this genotype represents an deletion More...

bool	indel (const AlleleMask &mask) const
	whether or not this genotype represents an insertion or deletion More...

bool	biallelic () const
	whether or not this genotype has at most one alternate allele More...

bool	complex () const
	literally the negation of biallelic(mask) More...

bool	mixed () const
	identifies variants with two different types of alleles More...

bool	variant () const

Static Public Member Functions
static void	encode_genotype (std::vector< int32_t > &alleles)
	Converts a vector of allele indices representing a genotype into BCF-encoded format suitable for passing to htslib. No phasing is added. More...

static void	encode_genotype (std::vector< int32_t > &alleles, bool phase_all_alleles)
	Converts a vector of allele indices representing a genotype into BCF-encoded format suitable for passing to htslib, and also allows you to phase all alleles. More...

static void	encode_genotypes (std::vector< std::vector< int32_t >> &multiple_genotypes)
	Converts multiple vectors of allele indices representing genotypes into BCF-encoded format suitable for passing to htslib. No phasing is added. More...

static void	encode_genotypes (VariantBuilderMultiSampleVector< int32_t > &multiple_genotypes)
	Converts multiple genotypes stored in a VariantBuilderMultiSampleVector into BCF-encoded format suitable for passing to htslib. No phasing is added. More...

Detailed Description

Encodes a genotype.

Constructor & Destructor Documentation

gamgee::Genotype::Genotype	(	const std::shared_ptr< bcf1_t > &	body,
		const bcf_fmt_t *const	format_ptr,
		const uint8_t *	data_ptr
	)

Constructs a genotype.

Parameters

body	The shared memory variant "line" from a vcf, or bcf.
format_ptr	The GT field from the line.
data_ptr	The GT for this sample.

Note: Most of the patterns here are directly copied or adapted from htslib.

gamgee::Genotype::Genotype ( const Genotype & other )

delete

copying of the Genotype object is not allowed.

gamgee::Genotype::Genotype ( Genotype && other )

default

Explicit default as recommended by many threads on stackoverflow.

Parameters

other Other genotype.

gamgee::Genotype::~Genotype ( )

default

Explicit default as recommended by many threads on stackoverflow.

Member Function Documentation

int32_t gamgee::Genotype::allele_key ( const uint32_t index ) const

Returns the allele key within this line.

Parameters

index Zero based allele index

Returns: the allele key within this line

std::vector< int32_t > gamgee::Genotype::allele_keys ( ) const

Returns a vector with all the allele keys.

Returns: a vector with all the allele keys

std::string gamgee::Genotype::allele_string ( const uint32_t index ) const

Returns the allele string at index.

Parameters

index Zero based allele index

Returns: the allele string

std::vector< std::string > gamgee::Genotype::allele_strings ( ) const

Returns a vector with all the allele strings.

Returns: a vector with all the allele strings

bool gamgee::Genotype::biallelic ( ) const

whether or not this genotype has at most one alternate allele

This function will check whether this is a simple heterozygous or homozygous site where both alleles are either the same, or reference and one alternate allele. No two different alleles would pass.

Warning: complexity is O(n) in the number of alleles. If you are using many of these convenience functions (snp(), insertion(), deletion(), indel(), complex(),...), you will be better off implementing one loop that makes all the checks in one pass instead of calling many O(n) functions.

Returns: whether or not all alleles are either the same, or there is one alt allele mixed with reference alleles.

bool gamgee::Genotype::complex ( ) const

inline

literally the negation of biallelic(mask)

Warning: complexity is O(n) in the number of alleles. If you are using many of these convenience functions (snp(), insertion(), deletion(), indel(), complex(),...), you will be better off implementing one loop that makes all the checks in one pass instead of calling many O(n) functions.

Returns: whether or not there are more than one alt allele in this record

bool gamgee::Genotype::deletion ( const AlleleMask & mask ) const

whether or not this genotype represents an deletion

This function will check that at least one deletion exists and that no other type of allele (snp or insertion) is present. Multiple deletions will return true.

Warning: complexity is O(n) in the number of alleles. If you are using many of these convenience functions (snp(), insertion(), deletion(), indel(), complex(),...), you will be better off implementing one loop that makes all the checks in one pass instead of calling many O(n) functions.

Returns: whether or not there is at least one deletion in this genotype and nothing else but deletions and reference alleles

static void gamgee::Genotype::encode_genotype ( std::vector< int32_t > & alleles )

inlinestatic

Converts a vector of allele indices representing a genotype into BCF-encoded format suitable for passing to htslib. No phasing is added.

Example: if you want to BCF-encode the genotype 0/1, create a vector with {0, 1} and then pass it to this function

Note: Do not call this function yourself before passing genotypes into VariantBuilder – the builder will call it for you as necessary. Unless you are working with low-level BCF data you probably do not ever need to call this function.

static void gamgee::Genotype::encode_genotype	(	std::vector< int32_t > &	alleles,
		bool	phase_all_alleles
	)

inlinestatic

Converts a vector of allele indices representing a genotype into BCF-encoded format suitable for passing to htslib, and also allows you to phase all alleles.

Example: if you want to BCF-encode the genotype 0|1, create a vector with {0, 1} and then pass it to this function with phase_all_alleles set to true

Note: Do not call this function yourself before passing genotypes into VariantBuilder – the builder will call it for you as necessary. Unless you are working with low-level BCF data you probably do not ever need to call this function.

static void gamgee::Genotype::encode_genotypes ( std::vector< std::vector< int32_t >> & multiple_genotypes )

inlinestatic

Converts multiple vectors of allele indices representing genotypes into BCF-encoded format suitable for passing to htslib. No phasing is added.

Example: if you want to BCF-encode the genotypes 0/1 and 1/1, create a vector with { {0, 1}, {1, 1} } and pass it to this function

Note: Do not call this function yourself before passing genotypes into VariantBuilder – the builder will call it for you as necessary. Unless you are working with low-level BCF data you probably do not ever need to call this function.

static void gamgee::Genotype::encode_genotypes ( VariantBuilderMultiSampleVector< int32_t > & multiple_genotypes )

inlinestatic

Converts multiple genotypes stored in a VariantBuilderMultiSampleVector into BCF-encoded format suitable for passing to htslib. No phasing is added.

Note: Do not call this function yourself before passing genotypes into VariantBuilder – the builder will call it for you as necessary. Unless you are working with low-level BCF data you probably do not ever need to call this function.

uint32_t gamgee::Genotype::fast_diploid_key_generation ( ) const

A bit encoding for the first two alleles.

Returns: A bit encoding for the first two alleles.

Note: only for diploids, returns false otherwise.

bool gamgee::Genotype::het ( ) const

Checks if this genotype vector is any type of heterozygous call.

Returns: True if this GT is a het.

Note: only for diploids.

bool gamgee::Genotype::hom_ref ( ) const

Checks if this genotype vector is a homozygous call that is reference.

Returns: True if this GT is a hom ref.

bool gamgee::Genotype::hom_var ( ) const

Checks if this genotype vector is a homozygous call that is non-reference.

Returns: True if this GT is a hom var.

bool gamgee::Genotype::indel ( const AlleleMask & mask ) const

whether or not this genotype represents an insertion or deletion

This function will check that at least one insertion or deletion exists and that no other type of allele (snp or insertion) is present. Multiple deletions will return true.

Note: this is not the same as insertion(mask) || deletion(mask) because it will also tolerate sites with insertions and deletions, while both other functions would return false to such a site.

Warning: complexity is O(n) in the number of alleles. If you are using many of these convenience functions (snp(), insertion(), deletion(), indel(), complex(),...), you will be better off implementing one loop that makes all the checks in one pass instead of calling many O(n) functions.

Returns: whether or not there is at least one insertion or deletion in this genotype and nothing else but insertions, deletions and reference alleles

bool gamgee::Genotype::insertion ( const AlleleMask & mask ) const

whether or not this genotype represents an insertion

This function will check that at least one insertion exists and that no other type of allele (snp or deletion) is present. Multiple insertions will return true.

Warning: complexity is O(n) in the number of alleles. If you are using many of these convenience functions (snp(), insertion(), deletion(), indel(), complex(),...), you will be better off implementing one loop that makes all the checks in one pass instead of calling many O(n) functions.

Returns: whether or not there is at least one insertion in this genotype and nothing else but insertions and reference alleles

bool gamgee::Genotype::missing ( ) const

Checks if all alleles are missing.

Returns: True if all alleles are missing.

Warning: Missing GT fields are untested.

bool gamgee::Genotype::mixed ( ) const

identifies variants with two different types of alleles

Warning: complexity is O(n) in the number of alleles. If you are using many of these convenience functions (snp(), insertion(), deletion(), indel(), complex(),...), you will be better off implementing one loop that makes all the checks in one pass instead of calling many O(n) functions.

Returns: whether or not there are more than one types of alt allele in this record

bool gamgee::Genotype::non_ref_het ( ) const

Checks if this genotype vector is a heterozygous call and none of the alleles is the reference.

Returns: True if this GT is a het and none of the alleles is the reference.

Note: only for diploids.

bool gamgee::Genotype::operator!= ( const Genotype & other ) const

Checks if another genotype does not equal this genotype.

Parameters

other The other genotype to compare.

Returns: False if other genotype equals this genotype.

Genotype& gamgee::Genotype::operator= ( const Genotype & other )

delete

copying of the Genotype object is not allowed.

Parameters

other Other genotype.

Genotype& gamgee::Genotype::operator= ( Genotype && other )

default

Explicit default as recommended by many threads on stackoverflow.

Parameters

other Other genotype.

bool gamgee::Genotype::operator== ( const Genotype & other ) const

Checks if another genotype equals this genotype.

Parameters

other The other genotype to compare.

Returns: True if other genotype equals this genotype.

Note: No string comparison is done. This operation is supposed to be fast.

int32_t gamgee::Genotype::operator[] ( const uint32_t index ) const

Returns the allele key within this line.

Parameters

index Zero based allele index

Returns: the allele key within this line

uint32_t gamgee::Genotype::size ( ) const

Returns the number of alleles.

Returns: the number of alleles

bool gamgee::Genotype::snp ( const AlleleMask & mask ) const

whether or not this genotype represents a snp

In the true sense of the word, single nucleotide polymorphism restricts the number of loci (nucleotides) that are polymorphic, but not the number of potentially different alleles it may have (as long as they are all single nucleotide polymorphisms). This function will check that at least one of these SNPs exists and that no other type of allele (insertion or deletion) is present. Multiple SNPs will return true.

Warning: complexity is O(n) in the number of alleles. If you are using many of these convenience functions (snp(), insertion(), deletion(), indel(), complex(),...), you will be better off implementing one loop that makes all the checks in one pass instead of calling many O(n) functions.

Returns: whether or not there is at least one snp in this genotype and nothing else but snps and reference alleles

bool gamgee::Genotype::variant ( ) const

inline

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

gamgee/variant/genotype.h
gamgee/variant/genotype.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation