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 ...@@ -16,10 +16,10 @@ package nl.lumc.sasc.biopet.tools
import java.io.File import java.io.File
import htsjdk.variant.variantcontext.{GenotypeType, VariantContext} import htsjdk.variant.variantcontext.{ GenotypeType, VariantContext }
import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder} import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf.VCFFileReader 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.collection.JavaConversions._
import scala.io.Source import scala.io.Source
......
...@@ -142,11 +142,11 @@ object VcfUtils { ...@@ -142,11 +142,11 @@ object VcfUtils {
} }
/** /**
* Check whether genotype is of the from 0/. * Check whether genotype is of the from 0/.
* @param genotype genotype * @param genotype genotype
* @return boolean * @return boolean
*/ */
def isCompoundNoCall(genotype: Genotype): Boolean = { def isCompoundNoCall(genotype: Genotype): Boolean = {
!genotype.isHetNonRef && genotype.isMixed && genotype.getAlleles.last.basesMatch("") genotype.isCalled && genotype.getAlleles.exists(_.isNoCall)
} }
} }
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment