Commit 9e1bc3d0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix args

parent 1d3bd651
...@@ -38,15 +38,15 @@ object CheckAllelesVcfInBam extends ToolCommand { ...@@ -38,15 +38,15 @@ object CheckAllelesVcfInBam extends ToolCommand {
case class Args (inputFile:File = null, outputFile:File = null, samples:List[String] = Nil, bamFiles:List[File] = Nil, minMapQual:Int = 1) extends AbstractArgs case class Args (inputFile:File = null, outputFile:File = null, samples:List[String] = Nil, bamFiles:List[File] = Nil, minMapQual:Int = 1) extends AbstractArgs
class OptParser extends AbstractOptParser { class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") unbounded() required() maxOccurs(1) valueName("<file>") action { (x, c) => opt[File]('I', "inputFile") required() maxOccurs(1) valueName("<file>") action { (x, c) =>
c.copy(inputFile = x) } c.copy(inputFile = x) }
opt[File]('o', "outputFile") unbounded() required() maxOccurs(1) valueName("<file>") action { (x, c) => opt[File]('o', "outputFile") required() maxOccurs(1) valueName("<file>") action { (x, c) =>
c.copy(outputFile = x) } c.copy(outputFile = x) }
opt[String]('s', "sample") unbounded() action { (x, c) => opt[String]('s', "sample") unbounded() minOccurs(1) action { (x, c) =>
c.copy(samples = x :: c.samples) } c.copy(samples = x :: c.samples) }
opt[File]('b', "bam") unbounded() action { (x, c) => opt[File]('b', "bam") unbounded() minOccurs(1) action { (x, c) =>
c.copy(bamFiles = x :: c.bamFiles) } c.copy(bamFiles = x :: c.bamFiles) }
opt[Int]('m', "min_mapping_quality") unbounded() maxOccurs(1) action { (x, c) => opt[Int]('m', "min_mapping_quality") maxOccurs(1) action { (x, c) =>
c.copy(minMapQual = c.minMapQual) } c.copy(minMapQual = c.minMapQual) }
} }
......
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