Commit 35dca269 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added contig check for each record

parent 8fc17a50
......@@ -124,6 +124,7 @@ object VcfWithVcf extends ToolCommand {
var counter = 0
for (record <- reader) {
require(vcfDict.getSequence(record.getContig) != null, s"Contig ${record.getContig} does not exist on reference")
val secondaryRecords = getSecondaryRecords(secondaryReader, record, commandArgs.matchAllele)
val fieldMap = createFieldMap(commandArgs.fields, secondaryRecords)
......@@ -202,7 +203,6 @@ object VcfWithVcf extends ToolCommand {
}
case FieldMethod.unique => scalaListToJavaObjectArrayList(attribute._2.distinct)
case _ => {
print(attribute._2.getClass.toString)
scalaListToJavaObjectArrayList(attribute._2)
}
})
......
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