Commit ffaadd57 authored by Peter van 't Hof's avatar Peter van 't Hof

Adding ref ALT

parent 238fb305
......@@ -69,6 +69,7 @@ object MpileupToVcf extends ToolCommand {
val writer = new PrintWriter(commandArgs.output)
writer.println("##fileformat=VCFv4.1")
writer.println("##ALT=<ID=REF,Description=\"Placeholder if location has no ALT alleles\">")
writer.println("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">")
writer.println("##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">")
writer.println("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">")
......@@ -190,7 +191,7 @@ object MpileupToVcf extends ToolCommand {
}
left -= ad(max)
}
writer.println(Array(chr, pos, ".", ref.toUpperCase, alt.mkString(","), ".", ".", info.mkString(";"),
writer.println(Array(chr, pos, ".", ref.toUpperCase, (if (alt.nonEmpty) alt.mkString(",") else "<REF>"), ".", ".", info.mkString(";"),
"GT:" + format.keys.mkString(":"), gt.sortWith(_ < _).mkString("/") + ":" + format.values.mkString(":")
).mkString("\t"))
}
......
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