BioKotlin/biokotlin.util/SimpleVariant

SimpleVariant

data class SimpleVariant(val contig: String, val start: Int, val end: Int, val refAllele: String, val altAlleles: List<String>, val samples: List<String>, val genotypes: List<String>, val originalText: String? = null) : Comparable<SimpleVariant>

Data class to represent a simple VCF variant

Constructors

SimpleVariant

constructor(contig: String, start: Int, end: Int, refAllele: String, altAlleles: List<String>, samples: List<String>, genotypes: List<String>, originalText: String? = null)

Properties

altAlleles

val altAlleles: List<String>

contig

val contig: String

end

val end: Int

endPosition

val endPosition: <Error class: unknown class>

genotypes

val genotypes: List<String>

isDEL

val isDEL: Boolean

Function to check if this is a deletion. A deletion is a variant where the length of one or more variants is less than the reference allele.

isIndel

val isIndel: Boolean

Function to check if this is an indel. An indel is a variant where the length of one or more variants is not the same as the reference allele.

isINS

val isINS: Boolean

Function to check if this is an insertion. An insertion is a variant where the length of one or more variants is greater than the reference allele.

isRefBlock

val isRefBlock: Boolean

isSNP

val isSNP: Boolean

An SNP is a variant where the length of the reference allele and all alternate alleles length is 1.

isVariant

val isVariant: Boolean

Function to check if this is a variant. A variant is a site where the genotype is not 0/0 for all samples.

length

val length: Int

The length is the number of base pairs of the reference allele associated with this. The start and end positions are inclusive. The reference allele recorded may only be a single base pair, which is the first base pair of the reference sequence.

numSamples

val numSamples: Int

originalText

val originalText: String? = null

positionRange

val positionRange: <Error class: unknown class>

refAllele

val refAllele: String

samples

val samples: List<String>

start

val start: Int

startPosition

val startPosition: <Error class: unknown class>

Functions

allele

fun allele(index: Int): String

Function to get the allele given the allele index from the genotype. The allele index 0 is the reference allele, and the rest are the alternate alleles. If the allele index is -1, then the allele is missing (.).

compareTo

open operator override fun compareTo(other: SimpleVariant): Int

contains

fun contains(position: Position): Boolean

Returns whether position is within the range of this variant.

fun contains(position: Int): Boolean

genotype

fun genotype(sampleIndex: Int): List<Int>

fun genotype(sample: String): List<Int>

Function to get the genotype of a sample. The returned list of integers are the allele indices for each ploidy. Allele index 0 is the reference allele, and the rest are the alternate alleles. If the genotype is missing, the value will be -1.

genotypeStrs

fun genotypeStrs(sampleIndex: Int): List<String>

fun genotypeStrs(sample: String): List<String>

isDEL

fun isDEL(sampleIndex: Int): Boolean

fun isDEL(sample: String): Boolean

isINS

fun isINS(sampleIndex: Int): Boolean

fun isINS(sample: String): Boolean

isPhased

fun isPhased(sampleIndex: Int): Boolean

fun isPhased(sample: String): Boolean

Function to check if a sample is phased. A sample is phased if it contains '|' between the genotype. This checks for '/' as a haploid sample will be considered phased.

sample

fun sample(index: Int): String

Function to get the sample name with given index.

toString

open override fun toString(): String