Commit 7d9fcf6b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added last star arguments

parent 3009ebc0
......@@ -147,11 +147,11 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
var outFilterIntronMotifs: Option[String] = config("outfilterintronmotifs")
var outSJfilterReads: Option[String] = config("outsjfilterreads")
// var outSJfilterOverhangMin: List[String] = config("outsjfilteroverhandmin",default = List.empty[String])
// var outSJfilterCountUniqueMin: List[String] = config("outsjfiltercountuniquemin",default = List.empty[String])
// var outSJfilterCountTotalMin: List[String] = config("outsjfiltercounttotalmin",default = List.empty[String])
// var outSJfilterDistToOtherSJmin: List[String] = config("outsjfilterdisttoothersjmin",default = List.empty[String])
// var outSJfilterIntronMaxVsReadN: List[String] = config("outsjfilterintronmaxvsreadn",default = List.empty[String])
var outSJfilterOverhangMin: List[String] = config("outsjfilteroverhandmin", default = Nil)
var outSJfilterCountUniqueMin: List[String] = config("outsjfiltercountuniquemin", default = Nil)
var outSJfilterCountTotalMin: List[String] = config("outsjfiltercounttotalmin", default = Nil)
var outSJfilterDistToOtherSJmin: List[String] = config("outsjfilterdisttoothersjmin", default = Nil)
var outSJfilterIntronMaxVsReadN: List[String] = config("outsjfilterintronmaxvsreadn", default = Nil)
var scoreGap: Option[Int] = config("scoregap")
var scoreGapNoncan: Option[Int] = config("scoregapnoncan")
......@@ -272,7 +272,12 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
optional("--limitBAMsortRAM", limitBAMsortRAM) +
optional("--limitSjdbInsertNsj", limitSjdbInsertNsj) +
optional("--outTmpDir", outTmpDir) +
optional("--outStd", outStd)
optional("--outStd", outStd) +
multiArg("--outSJfilterOverhangMin", outSJfilterOverhangMin, groupSize = 4, maxGroups = 1) +
multiArg("--outSJfilterCountUniqueMin", outSJfilterCountUniqueMin, groupSize = 4, maxGroups = 1) +
multiArg("--outSJfilterCountTotalMin", outSJfilterCountTotalMin, groupSize = 4, maxGroups = 1) +
multiArg("--outSJfilterDistToOtherSJmin", outSJfilterDistToOtherSJmin, groupSize = 4, maxGroups = 1) +
multiArg("--outSJfilterIntronMaxVsReadN", outSJfilterIntronMaxVsReadN, groupSize = 3, maxGroups = 1)
// Break as workaround for a stackoverflow error for the compiler
cmd += optional("--outReadsUnmapped", outReadsUnmapped) +
......
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