Added samtools flagstat

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/Samtools.scala

+package nl.lumc.sasc.biopet.function.samtools
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+
+abstract class Samtools extends BiopetCommandLineFunction {
+  executeble = config("exe", "samtools", "samtools")
+  override def versionCommand = executeble
+  override val versionRegex = """Version: (.*)""".r
+  override val versionExitcode = List(0,1)
+}
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala

+package nl.lumc.sasc.biopet.function.samtools
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.sting.commandline.{Input, Output}
+import java.io.File
+
+class SamtoolsFlagstat(val root:Configurable) extends Samtools {
+  @Input(doc="Bam File")
+  var input: File = _
+  
+  @Output(doc="output File")
+  var output: File = _
+  
+  def cmdLine = required(executeble) + required("flagstat") + required(input) + " > " + required(output)
+}
+
+object SamtoolsFlagstat {
+  def apply(root:Configurable, input:File, output:File) : SamtoolsFlagstat = {
+    val flagstat = new SamtoolsFlagstat(root)
+    flagstat.input = input
+    flagstat.output = output
+    return flagstat
+  }
+  
+  def apply(root:Configurable, input:File, outputDir:String) : SamtoolsFlagstat = {
+    val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
+    val outputFile = new File(dir + swapExtension(input.getName))
+    return apply(root, input, outputFile)
+  }
+  
+  def apply(root:Configurable, input:File) : SamtoolsFlagstat = {
+    return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
+  }
+  
+  private def swapExtension(inputFile:String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".flagstat"
+}
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