Documentation

VcfVariantRecord
in package

The storage shape of a VcfVariant. The reference and alternates stay raw strings, as in the value object : an ALT may be a symbolic allele or a breakend, so neither is stored as a DNA sequence.

Class VcfVariantRecord

Tags
author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Attributes
#[Entity]
#[Index]
$name: "idx_vcf_variant_locus"
$columns: ["chrom", "position"]
#[Table]
$name: "vcf_variant"

Table of Contents

Properties

$alternates  : array<string|int, string>
$chrom  : string
$filter  : string|null
$id  : int|null
$info  : array<string, string|bool>
$position  : int
$quality  : float|null
$reference  : string
$variantId  : string|null

Methods

getAlternates()  : array<string|int, string>
getChrom()  : string
getFilter()  : string|null
getId()  : int|null
getInfo()  : array<string, string|bool>
getPosition()  : int
getQuality()  : float|null
getReference()  : string
getVariantId()  : string|null
setAlternates()  : $this
setChrom()  : $this
setFilter()  : $this
setInfo()  : $this
setPosition()  : $this
setQuality()  : $this
setReference()  : $this
setVariantId()  : $this

Properties

$alternates

private array<string|int, string> $alternates = []

Empty when ALT is "."

Attributes
#[Column]
$type: \Doctrine\DBAL\Types\Types::JSON

$chrom

private string $chrom = ""
Attributes
#[Column]
$type: \Doctrine\DBAL\Types\Types::STRING
$length: 255

$filter

private string|null $filter = null
Attributes
#[Column]
$type: \Doctrine\DBAL\Types\Types::STRING
$length: 255
$nullable: true

$id

private int|null $id = null
Attributes
#[Column]
$type: \Doctrine\DBAL\Types\Types::INTEGER
#[GeneratedValue]
#[Id]

$info

private array<string, string|bool> $info = []

A flag-only INFO key (no "=value") maps to true

Attributes
#[Column]
$type: \Doctrine\DBAL\Types\Types::JSON

$position

private int $position = 1

1-based, VCF's own convention ; 0 or length + 1 for a telomere. A 64-bit column : some chromosomes (lungfish, axolotl) are longer than a signed 32-bit integer allows.

Attributes
#[Column]
$type: \Doctrine\DBAL\Types\Types::BIGINT

$quality

private float|null $quality = null
Attributes
#[Column]
$type: \Doctrine\DBAL\Types\Types::FLOAT
$nullable: true

$reference

private string $reference = ""
Attributes
#[Column]
$type: \Doctrine\DBAL\Types\Types::TEXT

$variantId

private string|null $variantId = null

The VCF ID column (e.g. an rsID) ; named apart from the primary key

Attributes
#[Column]
$type: \Doctrine\DBAL\Types\Types::STRING
$length: 255
$nullable: true

Methods

getAlternates()

public getAlternates() : array<string|int, string>
Return values
array<string|int, string>

getId()

public getId() : int|null
Return values
int|null —

Null until the record has been flushed

getInfo()

public getInfo() : array<string, string|bool>
Return values
array<string, string|bool>

getVariantId()

public getVariantId() : string|null
Return values
string|null

setAlternates()

public setAlternates(array<string|int, string> $aAlternates) : $this
Parameters
$aAlternates : array<string|int, string>
Return values
$this

setChrom()

public setChrom(string $sChrom) : $this
Parameters
$sChrom : string
Return values
$this

setFilter()

public setFilter(string|null $sFilter) : $this
Parameters
$sFilter : string|null
Return values
$this

setInfo()

public setInfo(array<string, string|bool> $aInfo) : $this
Parameters
$aInfo : array<string, string|bool>
Return values
$this

setPosition()

public setPosition(int $iPosition) : $this
Parameters
$iPosition : int
Return values
$this

setQuality()

public setQuality(float|null $fQuality) : $this
Parameters
$fQuality : float|null
Return values
$this

setReference()

public setReference(string $sReference) : $this
Parameters
$sReference : string
Return values
$this

setVariantId()

public setVariantId(string|null $sVariantId) : $this
Parameters
$sVariantId : string|null
Return values
$this
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