GVCFReader

class GVCFReader(val gvcfFile: String, val referenceFile: String, val sizeOfQueue: Int = 5) : SequenceIterator

This reads a GVCF formatted file. The file is required to only have one sample. The file can only be read one time. Either as an iterator (hasNext(), next()), repeatedly calling read(), or using readAll().

Constructors

GVCFReader

constructor(gvcfFile: String, referenceFile: String, sizeOfQueue: Int = 5)

Properties

gvcfFile

val gvcfFile: String

referenceFile

val referenceFile: String

sizeOfQueue

val sizeOfQueue: Int = 5

Functions

forEachRemaining

open fun forEachRemaining(p0: Consumer<in SeqRecord>)

hasNext

open operator override fun hasNext(): Boolean

open operator override fun next(): SeqRecord

read

open override fun read(): SeqRecord?

Returns next SeqRecord or null if finished reading.

readAll

open override fun readAll(): Map<String, SeqRecord>

Reads a GVCF file (.gvcf) and returns a map of Chromosomes (String) to Sequence (SeqRecord)