Commit d8697889 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix args

parent d399bdb3
......@@ -25,7 +25,7 @@ class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunctio
override val defaultVmem = "8G"
memoryLimit = Option(4.0)
override def commandLine = super.commandLine + required(input) + required(bamFile) + required(output)
override def commandLine = super.commandLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
}
object BedToInterval extends ToolCommand {
......@@ -45,13 +45,15 @@ object BedToInterval extends ToolCommand {
return bedToInterval
}
case class Args (inputFile:File = null, outputFile:File = null) extends AbstractArgs
case class Args (inputFile:File = null, outputFile:File = null, bamFile:File = null) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required() valueName("<file>") action { (x, c) =>
c.copy(inputFile = x) } text("out is a required file property")
c.copy(inputFile = x) }
opt[File]('o', "output") required() valueName("<file>") action { (x, c) =>
c.copy(outputFile = x) } text("out is a required file property")
c.copy(outputFile = x) }
opt[File]('b', "bam") required() valueName("<file>") action { (x, c) =>
c.copy(bamFile = x) }
}
/**
......@@ -63,7 +65,7 @@ object BedToInterval extends ToolCommand {
val writer = new PrintWriter(commandArgs.outputFile)
val inputSam = new SAMFileReader(commandArgs.inputFile)
val inputSam = new SAMFileReader(commandArgs.bamFile)
val refs = for (SQ <- inputSam.getFileHeader.getSequenceDictionary.getSequences.toArray) yield {
val record = SQ.asInstanceOf[SAMSequenceRecord]
writer.write("@SQ\tSN:" + record.getSequenceName + "\tLN:" + record.getSequenceLength + "\n")
......@@ -72,7 +74,7 @@ object BedToInterval extends ToolCommand {
inputSam.close
val refsMap = Map(refs:_*)
val bedFile = Source.fromFile(args(0))
val bedFile = Source.fromFile(commandArgs.inputFile)
for (
line <- bedFile.getLines;
val split = line.split("\t")
......
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