Commit 61896d06 authored by Peter van 't Hof's avatar Peter van 't Hof

Convert igvtools to a java extensions

parent e5384fc2
......@@ -14,16 +14,17 @@
*/
package nl.lumc.sasc.biopet.extensions.igvtools
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Version }
/**
* General igvtools extension
*
* Created by wyleung on 5-1-15
*/
abstract class IGVTools extends BiopetCommandLineFunction with Version {
executable = config("exe", default = "igvtools", namespace = "igvtools", freeVar = false)
def versionCommand = executable + " version"
abstract class IGVTools extends BiopetJavaCommandLineFunction with Version {
jarFile = config("igvtools_jar", namespace = "igvtools")
def versionCommand = executable + s" -jar ${jarFile.getAbsolutePath} version"
def versionRegex = """IGV Version:? ([\w\.]*) .*""".r
override def versionExitcode = List(0)
}
\ No newline at end of file
......@@ -76,25 +76,23 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
}
/** Returns command to execute */
def cmdLine = {
required(executable) +
required("count") +
optional("--maxZoom", maxZoom) +
optional("--windowSize", windowSize) +
optional("--extFactor", extFactor) +
optional("--preExtFactor", preExtFactor) +
optional("--postExtFactor", postExtFactor) +
optional("--windowFunctions", windowFunctions) +
optional("--strands", strands) +
conditional(bases, "--bases") +
optional("--query", query) +
optional("--minMapQuality", minMapQuality) +
conditional(includeDuplicates, "--includeDuplicates") +
conditional(pairs, "--pairs") +
required(input) +
required(outputArg) +
required(genomeChromSizes)
}
override def cmdLine = super.cmdLine +
required("count") +
optional("--maxZoom", maxZoom) +
optional("--windowSize", windowSize) +
optional("--extFactor", extFactor) +
optional("--preExtFactor", preExtFactor) +
optional("--postExtFactor", postExtFactor) +
optional("--windowFunctions", windowFunctions) +
optional("--strands", strands) +
conditional(bases, "--bases") +
optional("--query", query) +
optional("--minMapQuality", minMapQuality) +
conditional(includeDuplicates, "--includeDuplicates") +
conditional(pairs, "--pairs") +
required(input) +
required(outputArg) +
required(genomeChromSizes)
/** This part should never fail, these values are set within this wrapper */
private def outputArg: String = {
......
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