Merge pull request #52 from biopet/xhmm-wisecondor-countfile

Single-sample jobs for count file generation

tarmac/src/main/scala/nl/lumc/sasc/biopet/pipelines/tarmac/Tarmac.scala

@@ -4,14 +4,23 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.{ PedigreeQscript, PipelineCommand, Reference }
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.extensions.Ln
+import nl.lumc.sasc.biopet.extensions.gatk.DepthOfCoverage
+import nl.lumc.sasc.biopet.extensions.wisecondor.WisecondorCount
+import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.function.QFunction
+
+import scalaz.{ -\/, \/, \/- }
 
 /**
  * Created by Sander Bollen on 23-3-17.
  */
 class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with SummaryQScript with Reference {
   qscript =>
+
+  private val targets: File = config("targets")
   def this() = this(null)
 
   def init() = {
@@ -29,13 +38,96 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
 
   class Sample(name: String) extends AbstractSample(name) {
 
-    val inputCountFile: Option[File] = config("count_file")
+    val inputXhmmCountFile: Option[File] = config("xhmm_count_file")
+    val inputWisecondorCountFile: Option[File] = config("wisecondor_count_file")
     val bamFile: Option[File] = config("bam")
 
+    /**
+     * Create XHMM count file or create link to input count file
+     * Precedence is given to existing count files.
+     * Returns a disjunction where right is the file, and left is
+     * a potential error message
+     */
+    protected lazy val outputXhmmCountJob: String \/ QFunction = {
+      val outFile = new File(sampleDir + File.separator + s"$name.dcov")
+      (inputXhmmCountFile, bamFile) match {
+        case (Some(f), _) => {
+          if (bamFile.isDefined) {
+            logger.warn(s"Both BAM and Xhmm count files are given for sample $name. The BAM file will be ignored")
+          }
+          val ln = new Ln(root)
+          ln.input = f
+          ln.output = outFile
+          \/-(ln)
+        }
+        case (None, Some(bam)) => {
+          val dcov = DepthOfCoverage(root, List(bam), outFile, List(targets))
+          \/-(dcov)
+        }
+        case _ => -\/(s"Cannot find bam file or xhmm count file for sample" +
+          s" $name in config. At least one must be given.")
+      }
+
+    }
+
+    /* Get count file for Xhmm method */
+    lazy val outputXhmmCountFile: String \/ File = {
+      outputXhmmCountJob match {
+        case \/-(ln: Ln)               => \/-(ln.output)
+        case \/-(doc: DepthOfCoverage) => \/-(doc.out)
+        case -\/(error)                => -\/(error)
+      }
+    }
+
+    /**
+     * Create wisecondor count file or create link to input count file.
+     * Precedence is given to existing count files.
+     * Returns a disjunction where right is the file, and left is
+     * a potential error message
+     */
+    protected lazy val outputWisecondorCountJob: String \/ QFunction = {
+      val outFile = new File(sampleDir + File.separator + s"$name.wisecondor.bed")
+      (inputWisecondorCountFile, bamFile) match {
+        case (Some(f), _) => {
+          if (bamFile.isDefined) {
+            logger.warn(s"Both BAM and Wisecondor count files are given for sample $name. The BAM file will be ignored")
+          }
+          val ln = new Ln(root)
+          ln.input = f
+          ln.output = outFile
+          \/-(ln)
+        }
+        case (None, Some(bam)) => {
+          val counter = new WisecondorCount(root)
+          counter.inputBam = bam
+          counter.output = outFile
+          counter.binFile = Some(targets)
+          \/-(counter)
+        }
+        case _ => -\/(s"Cannot find bam file or wisecondor count for sample" +
+          s" $name. At least one must be given.")
+      }
+
+    }
+
+    /* Get count file for wisecondor method */
+    lazy val outputWisecondorCountFile: String \/ File = {
+      outputWisecondorCountJob match {
+        case \/-(ln: Ln)                 => \/-(ln.output)
+        case \/-(count: WisecondorCount) => \/-(count.output)
+        case -\/(error)                  => -\/(error)
+      }
+    }
+
     /** Function to add sample jobs */
-    def addJobs(): Unit = {}
+    def addJobs(): Unit = {
+      (outputWisecondorCountJob :: outputXhmmCountJob :: Nil).foreach {
+        case -\/(error)    => Logging.addError(error)
+        case \/-(function) => add(function)
+      }
+    }
 
-    /* This is necesary for compile reasons, but library does not in fact exist for this pipeline */
+    /* This is necessary for compile reasons, but library does not in fact exist for this pipeline */
     def makeLibrary(id: String) = new Library(id)
 
     class Library(id: String) extends AbstractLibrary(id) {