Commit d45432ba authored by Sander Bollen's avatar Sander Bollen
Browse files

Change variables to proper camelCase

parent 4a553316
......@@ -18,7 +18,7 @@ object VCFWithVCF extends ToolCommand {
case class Args(inputFile: File = null,
outputFile: File = null,
secondaryVCF: File = null,
secondaryVcf: File = null,
fields: List[Fields] = Nil,
matchAllele: Boolean = true) extends AbstractArgs
......@@ -29,8 +29,8 @@ object VCFWithVCF extends ToolCommand {
opt[File]('O', "outputFile") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
c.copy(outputFile = x)
}
opt[File]('S', "SecondaryVCF") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
c.copy(secondaryVCF = x)
opt[File]('S', "SecondaryVcf") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
c.copy(secondaryVcf = x)
}
opt[String]('f', "field") unbounded () valueName ("<input_field:output_field>") action { (x, c) =>
val values = x.split(":")
......@@ -47,7 +47,7 @@ object VCFWithVCF extends ToolCommand {
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
val reader = new VCFFileReader(commandArgs.inputFile)
val secondaryReader = new VCFFileReader(commandArgs.secondaryVCF)
val secondaryReader = new VCFFileReader(commandArgs.secondaryVcf)
val header = reader.getFileHeader
val secondHeader = secondaryReader.getFileHeader
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment