Commit 90ad4035 authored by Sander Bollen's avatar Sander Bollen
Browse files

better way of finding these types of variants

parent af617116
......@@ -16,10 +16,10 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.variant.variantcontext.{GenotypeType, VariantContext}
import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
import htsjdk.variant.variantcontext.{ GenotypeType, VariantContext }
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.utils.{ToolCommand, VcfUtils}
import nl.lumc.sasc.biopet.utils.{ ToolCommand, VcfUtils }
import scala.collection.JavaConversions._
import scala.io.Source
......
......@@ -142,11 +142,11 @@ object VcfUtils {
}
/**
* Check whether genotype is of the from 0/.
* @param genotype genotype
* @return boolean
*/
* Check whether genotype is of the from 0/.
* @param genotype genotype
* @return boolean
*/
def isCompoundNoCall(genotype: Genotype): Boolean = {
!genotype.isHetNonRef && genotype.isMixed && genotype.getAlleles.last.basesMatch("")
genotype.isCalled && genotype.getAlleles.exists(_.isNoCall)
}
}
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