Added samtools modules

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala

+package nl.lumc.sasc.biopet.extensions.samtools
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import java.io.File
+
+class SamtoolsMpileup(val root: Configurable) extends Samtools {
+  @Input(doc = "Bam File")
+  var input: File = _
+
+  @Output(doc = "output File")
+  var output: File = _
+
+  @Input(doc = "Reference fasta")
+  var reference: File = config("reference")
+  
+  @Input(doc = "Interval bed")
+  var intervalBed: File = config("interval_bed")
+  
+  def cmdBase = required(executable) + 
+        required("mpileup") +
+        optional("-f", reference) +
+        optional("-l", intervalBed)
+  def cmdPipeInput = cmdBase + "-"
+  def cmdPipe = cmdBase + required(input)
+  def cmdLine = cmdPipe + " > " + required(output)
+}
+
+object SamtoolsMpileup {
+  def apply(root: Configurable, input: File, output: File): SamtoolsMpileup = {
+    val mpileup = new SamtoolsMpileup(root)
+    mpileup.input = input
+    mpileup.output = output
+    return mpileup
+  }
+
+  def apply(root: Configurable, input: File, outputDir: String): SamtoolsMpileup = {
+    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): SamtoolsMpileup = {
+    return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
+  }
+
+  private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".mpileup"
+}
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala

+package nl.lumc.sasc.biopet.extensions.samtools
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import java.io.File
+
+class SamtoolsView(val root: Configurable) extends Samtools {
+  @Input(doc = "Bam File")
+  var input: File = _
+
+  @Output(doc = "output File")
+  var output: File = _
+  
+  var quality: Option[Int] = config("quality")
+  var b: Boolean = config("b")
+  var h: Boolean = config("h")
+  
+  def cmdBase = required(executable) + 
+        required("view") +
+        optional("-q", quality) +
+        conditional(b, "-b") +
+        conditional(h, "-h")
+  def cmdPipeInput = cmdBase + "-"
+  def cmdPipe = cmdBase + required(input)
+  def cmdLine = cmdPipe + " > " + required(output)
+}
+
+object SamtoolsView {
+  def apply(root: Configurable, input: File, output: File): SamtoolsView = {
+    val view = new SamtoolsView(root)
+    view.input = input
+    view.output = output
+    return view
+  }
+
+  def apply(root: Configurable, input: File, outputDir: String): SamtoolsView = {
+    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): SamtoolsView = {
+    return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
+  }
+
+  private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".mpileup"
+}
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