Commit e5e47f6c authored by Peter van 't Hof's avatar Peter van 't Hof

Fix default 0

parent cdc1f3c6
......@@ -275,8 +275,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
else Map()
}
protected val removeOnConflict = Set("Output_file", "Run_time", "Start_time", "End_time", "Novel_/_existing_variants")
protected val nonNumber = Set("VEP_version_(API)", "Cache/Database", "Species", "Command_line_options", "Input_file_(format)")
protected val removeOnConflict = Set("Output_file", "Run_time", "Start_time", "End_time", "Novel_/_existing_variants", "Input_file_(format)")
protected val nonNumber = Set("VEP_version_(API)", "Cache/Database", "Species", "Command_line_options")
override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
if (removeOnConflict.contains(key)) None
......@@ -303,7 +303,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
val name = header.stripPrefix("[").stripSuffix("]")
name.replaceAll(" ", "_") -> (contents.drop(headerIndex + 1).takeWhile(!isHeader(_)).map { line =>
val values = line.split("\t", 2)
values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(0)
values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(values.last)
}.toMap)
}).toMap
}
......
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