Commit 05d2e7ea authored by Peter van 't Hof's avatar Peter van 't Hof

Added scala docs for igvtools

parent 0c1c8db6
......@@ -6,6 +6,7 @@ package nl.lumc.sasc.biopet.extensions.igvtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/** General igvtools extension */
abstract class IGVTools extends BiopetCommandLineFunction {
executable = config("exe", default = "igvtools", submodule = "igvtools", freeVar = false)
override def versionCommand = executable + " version"
......
......@@ -61,6 +61,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
throw new IllegalArgumentException("TDF file should have a .tdf file-extension"))
}
/** Returns command to execute */
def cmdLine = {
required(executable) +
required("count") +
......@@ -81,10 +82,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
required(genomeChromSizes)
}
/**
* This part should never fail, these values are set within this wrapper
*
*/
/** This part should never fail, these values are set within this wrapper */
private def outputArg: String = {
(tdf, wig) match {
case (None, None) => throw new IllegalArgumentException("Either TDF or WIG should be supplied");
......
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