Commit 3b3dc0f4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added catch for U to T

parent 07c86968
...@@ -154,6 +154,7 @@ object MpileupToVcf extends ToolCommand { ...@@ -154,6 +154,7 @@ object MpileupToVcf extends ToolCommand {
val ref = values(2) match { val ref = values(2) match {
case "A" | "T" | "G" | "C" => values(2) case "A" | "T" | "G" | "C" => values(2)
case "a" | "t" | "g" | "c" => values(2).toUpperCase case "a" | "t" | "g" | "c" => values(2).toUpperCase
case "U" | "u" => "T"
case _ => "N" case _ => "N"
} }
val reads = values(3).toInt val reads = values(3).toInt
......
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