Commit 28b88048 authored by Sander Bollen's avatar Sander Bollen
Browse files

autostyle and test fix

parent 032749ae
......@@ -18,8 +18,8 @@ import java.io.File
import java.util
import htsjdk.samtools.reference.FastaSequenceFile
import htsjdk.variant.variantcontext.{VariantContext, VariantContextBuilder}
import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf
import htsjdk.variant.vcf._
import nl.lumc.sasc.biopet.utils.ToolCommand
......@@ -206,7 +206,7 @@ object VcfWithVcf extends ToolCommand {
header.getInfoHeaderLine(attribute._1).getCountType match {
case VCFHeaderLineCount.A => scalaListToJavaObjectArrayList(secondaryRecords.flatMap(x => numberA(x, record, attribute._1)))
case VCFHeaderLineCount.R => scalaListToJavaObjectArrayList(secondaryRecords.flatMap(x => numberR(x, record, attribute._1)))
case _ => scalaListToJavaObjectArrayList(attribute._2)
case _ => scalaListToJavaObjectArrayList(attribute._2)
}
}
})
......@@ -214,12 +214,12 @@ object VcfWithVcf extends ToolCommand {
}
/**
* Get the correct values from a field that has number=A
* @param referenceRecord the reference record
* @param annotateRecord the to-be-annotated record
* @param field the field to annotate
* @return
*/
* Get the correct values from a field that has number=A
* @param referenceRecord the reference record
* @param annotateRecord the to-be-annotated record
* @param field the field to annotate
* @return
*/
def numberA(referenceRecord: VariantContext, annotateRecord: VariantContext, field: String): List[Any] = {
val refValues = referenceRecord.getAttributeAsList(field).toArray
annotateRecord.
......
......@@ -190,7 +190,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
val secRec = getSecondaryRecords(vepReader, unvepRecord, false)
val fieldMap = createFieldMap(List(new Fields("CSQ", "CSQ")), secRec)
val createdRecord = createRecord(fieldMap, unvepRecord, List(new Fields("CSQ", "CSQ")), header)
val createdRecord = createRecord(fieldMap, unvepRecord, List(new Fields("CSQ", "CSQ")), header, secRec)
identicalVariantContext(createdRecord, vepRecord) shouldBe true
}
......
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