Commit 77d657ac authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Skip empty values

parent e5e47f6c
...@@ -301,9 +301,10 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu ...@@ -301,9 +301,10 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
(for ((header, headerIndex) <- headers) yield { (for ((header, headerIndex) <- headers) yield {
val name = header.stripPrefix("[").stripSuffix("]") val name = header.stripPrefix("[").stripSuffix("]")
name.replaceAll(" ", "_") -> (contents.drop(headerIndex + 1).takeWhile(!isHeader(_)).map { line => name.replaceAll(" ", "_") -> (contents.drop(headerIndex + 1).takeWhile(!isHeader(_)).flatMap { line =>
val values = line.split("\t", 2) val values = line.split("\t", 2)
values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(values.last) if (values.last.isEmpty || values.last == "-") None
else Some(values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(values.last))
}.toMap) }.toMap)
}).toMap }).toMap
} }
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