Add wisecondor extensions

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/Wisecondor.scala

+package nl.lumc.sasc.biopet.extensions.wisecondor
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Created by Sander Bollen on 20-3-17.
+ */
+abstract class Wisecondor extends BiopetCommandLineFunction with Version with Reference {
+  executable = config("exe", namespace = "wisecondor", default = "wisecondor")
+
+  @Input(required = false)
+  var binFile: Option[File] = config("bin_file", namespace = "wisecondor", default = None)
+
+  @Output
+  var output: File = _
+
+  // either binSize or binFile must exist
+  var binSize: Option[Int] = config("bin_size", namespace = "wisecondor", default = None)
+
+  def binCommand: String = {
+    if (binFile.isDefined && binSize.isEmpty) {
+      required("-L", binFile)
+    } else if (binSize.isDefined && binFile.isEmpty) {
+      required("-B", binSize)
+    } else {
+      throw new IllegalStateException("bin_file *or* bin_size must be defined")
+    }
+  }
+
+  def versionCommand = executable + " --version"
+  def versionRegex = """.+, version (.*)""".r
+
+}

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorCount.scala

+package nl.lumc.sasc.biopet.extensions.wisecondor
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.Input
+
+/**
+ * Created by Sander Bollen on 20-3-17.
+ */
+class WisecondorCount(val root: Configurable) extends Wisecondor {
+
+  @Input
+  var inputBam: File = _
+
+  def cmdLine = {
+    executable + required("count") +
+      required("-I", inputBam) +
+      required("-O", output) +
+      required("-R", referenceFasta()) +
+      binCommand
+  }
+}

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorGcCorrect.scala

+package nl.lumc.sasc.biopet.extensions.wisecondor
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.Input
+
+/**
+ * Created by Sander Bollen on 20-3-17.
+ */
+class WisecondorGcCorrect(val root: Configurable) extends Wisecondor {
+
+  @Input
+  var inputBed: File = _
+
+  var fracN: Option[Float] = config("frac_n", namespace = "wisecondor", default = None)
+  var fracR: Option[Float] = config("frac_r", namespace = "wisecondor", default = None)
+  var nIter: Option[Int] = config("iter", namespace = "wisecondor", default = None)
+  var fracLowess: Option[Float] = config("frac_lowess", namespace = "wisecondor", default = None)
+
+  def cmdLine = {
+    executable + required("gc-correct") +
+      required("-I", inputBed) +
+      required("-R", referenceFasta()) +
+      required("-O", output) +
+      binCommand +
+      optional("-n", fracN) +
+      optional("-r", fracR) +
+      optional("-t", nIter) +
+      optional("-l", fracLowess)
+
+  }
+}

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorZscore.scala

+package nl.lumc.sasc.biopet.extensions.wisecondor
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.Input
+
+/**
+ * Created by Sander Bollen on 20-3-17.
+ */
+class WisecondorZscore(val root: Configurable) extends Wisecondor {
+
+  @Input
+  var inputBed: File = _
+
+  @Input
+  var referenceDictionary: File = config("reference_dictionary", namespace = "wisecondor")
+
+  def cmdLine = {
+    executable + required("zscore") +
+      required("-I", inputBed) +
+      required("-O", output) +
+      required("-R", referenceFasta()) +
+      required("-D", referenceDictionary) +
+      binCommand
+  }
+}