BioKotlin/biokotlin.util/GetVCFVariants

GetVCFVariants

class GetVCFVariants(inputFiles: List<String>, debug: Boolean = false)

Get the variant lines for the given positions from the VCF files. Input files, VCF Readers, Sample lists, and variants are kept in the same order. Sorted by the first sample name in each VCF file.

Parameters

inputFiles

List of VCF files to read

debug

If true, stores the original VCF lines in the SimpleVariant objects

Constructors

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constructor(inputFiles: List<String>, debug: Boolean = false)

Properties

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Functions

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suspend fun forAll(channel: Channel<List<Pair<Int, List<SimpleVariant?>>>>): <Error class: unknown class>
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suspend fun forPosition(position: Position): Map<VCFReader, SimpleVariant?>

Get the VCF lines for the given position. Successive calls to this method should be for increasing positions.