Extracted IGVTools from Yamsvp

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala

+/**
+ * Created by wyleung on 5-1-15.
+ */
+
+package nl.lumc.sasc.biopet.extensions.igvtools
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+
+abstract class IGVTools extends BiopetCommandLineFunction {
+  executable = config("exe", default = "igvtools", submodule = "igvtools", freeVar = false)
+  override def versionCommand = executable + " version"
+  override val versionRegex = """IGV Version: ([\d\.]) .*""".r
+  override val versionExitcode = List(0)
+}
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala

+
+package nl.lumc.sasc.biopet.extensions.igvtools
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+import java.io.File
+
+class IGVToolsCount(val root: Configurable) extends IGVTools {
+  @Input(doc = "Bam File")
+  var input: File = _
+
+  @Argument(doc = "Genome name")
+  var genomename: String = _
+
+  @Output(doc = "output File")
+  var output: File = _
+
+  def cmdLine = required(executable) + required("count") + required(input) + required(output) + required(genomename)
+}
+
+object IGVToolsCount {
+  def apply(root: Configurable, input: File, output: File, genomename: String): IGVToolsCount = {
+    val counting = new IGVToolsCount(root)
+    counting.input = input
+    counting.output = output
+    counting.genomename = genomename
+    return counting
+  }
+
+  def apply(root: Configurable, input: File, genomename: String): IGVToolsCount = {
+    return apply(root, input, new File(swapExtension(input.getCanonicalPath)), genomename)
+  }
+
+  private def swapExtension(inputFile: String) = inputFile + ".tdf"
+}
\ No newline at end of file