Commit b6da3e88 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix REF column

parent 2554a70e
......@@ -106,7 +106,22 @@ object CleverFixVCF extends ToolCommand {
writer.write(extraHeader + "\n")
writer.write(vcfColReplacementHeader + "\n")
}
case _ => writer.write(line + "\n")
case _ => {
// We have to deal with matching records
// these don't start with #
line.startsWith("#") match {
case true =>
writer.write(line + "\n")
case _ => {
// this should be a record
// Ensure the REF field is at least an N
val cols = line.split("\t")
cols(3) = "N"
writer.write(cols.mkString("\t") + "\n")
}
}
}
}
}
writer.close()
......
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