Move Shiva to a trait

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala

 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.File
-
 import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
@@ -15,156 +13,8 @@ import scala.collection.JavaConversions._
 /**
  * Created by pjvan_thof on 2/24/15.
  */
-class Shiva(val root: Configurable) extends QScript with MultiSampleQScript with SummaryQScript {
-  qscript =>
+class Shiva(val root: Configurable) extends QScript with ShivaTrait {
   def this() = this(null)
-
-  def init: Unit = {
-
-  }
-
-  def biopetScript: Unit = {
-    addSamplesJobs()
-
-    addSummaryJobs
-  }
-
-  def makeSample(id: String) = new Sample(id)
-  class Sample(sampleId: String) extends AbstractSample(sampleId) {
-    def makeLibrary(id: String) = new Library(id)
-
-    class Library(libId: String) extends AbstractLibrary(libId) {
-
-      def preProcess(input: File): Option[File] = None
-
-      def makeMapping = {
-        val mapping = new Mapping(qscript)
-        mapping.sampleId = Some(sampleId)
-        mapping.libId = Some(libId)
-        mapping.outputDir = libDir
-        (Some(mapping), Some(mapping.finalBamFile), preProcess(mapping.finalBamFile))
-      }
-
-      lazy val (mapping, bamFile, preProcessBam): (Option[Mapping], Option[File], Option[File]) =
-        (config.contains("R1"), config.contains("bam")) match {
-          case (true, _) => makeMapping // Default starting from fastq files
-          case (false, true) => // Starting from bam file
-            config("bam_to_fastq", default = false).asBoolean match {
-              case true => makeMapping // bam file will be converted to fastq
-              case false => {
-                val file = new File(libDir, sampleId + "-" + libId + ".final.bam")
-                (None, Some(file), preProcess(file))
-              }
-            }
-          case _ => (None, None, None)
-        }
-
-      def addJobs(): Unit = {
-        (config.contains("R1"), config.contains("bam")) match {
-          case (true, _) => mapping.foreach(mapping => {
-            mapping.input_R1 = config("R1")
-            mapping.input_R2 = config("R2")
-          })
-          case (false, true) =>  config("bam_to_fastq", default = false).asBoolean match {
-            case true => {
-              val samToFastq = SamToFastq(qscript, config("bam"),
-                new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
-                new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
-              samToFastq.isIntermediate = true
-              qscript.add(samToFastq)
-              mapping.foreach(mapping => {
-                mapping.input_R1 = samToFastq.fastqR1
-                mapping.input_R2 = Some(samToFastq.fastqR2)
-              })
-            }
-            case false => {
-              val inputSam = SamReaderFactory.makeDefault.open(config("bam"))
-              val readGroups = inputSam.getFileHeader.getReadGroups
-
-              val readGroupOke = readGroups.forall( readGroup => {
-                if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
-                if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
-                readGroup.getSample == sampleId && readGroup.getLibrary == libId
-              })
-              inputSam.close
-
-              if (!readGroupOke) {
-                if (config("correct_readgroups", default = false).asBoolean) {
-                  logger.info("Correcting readgroups, file:" + config("bam"))
-                  val aorrg = AddOrReplaceReadGroups(qscript, config("bam"), bamFile.get)
-                  aorrg.RGID = sampleId + "-" + libId
-                  aorrg.RGLB = libId
-                  aorrg.RGSM = sampleId
-                  aorrg.isIntermediate = true
-                  qscript.add(aorrg)
-                } else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
-                  "\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
-              } else {
-                val oldBamFile: File = config("bam")
-                val oldIndex: File = new File(oldBamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
-                val newIndex: File = swapExt(libDir, bamFile.get, ".bam", ".bai")
-                val baiLn = Ln(qscript, oldIndex, newIndex)
-                add(baiLn)
-
-                val bamLn = Ln(qscript, oldBamFile, bamFile.get)
-                bamLn.deps :+= baiLn.out
-                add(bamLn)
-              }
-
-            }
-          }
-          case _ => logger.warn("Sample: " + sampleId + "  Library: " + libId + ", no reads found")
-        }
-
-        mapping.foreach(mapping => {
-          mapping.init
-          mapping.biopetScript
-          addAll(mapping.functions) // Add functions of mapping to curent function pool
-          addSummaryQScript(mapping)
-        })
-      }
-    }
-
-    def doublePreProcess(input: List[File]): Option[File] = {
-      if (input == Nil) None
-      else if (input.tail == Nil) {
-        val bamFile = new File(sampleDir, input.head.getName)
-        val oldIndex: File = new File(input.head.getAbsolutePath.stripSuffix(".bam") + ".bai")
-        val newIndex: File = swapExt(sampleDir, bamFile, ".bam", ".bai")
-        val baiLn = Ln(qscript, oldIndex, newIndex)
-        add(baiLn)
-
-        val bamLn = Ln(qscript, input.head, bamFile)
-        bamLn.deps :+= baiLn.out
-        add(bamLn)
-        Some(bamFile)
-      } else {
-        val md = new MarkDuplicates(qscript)
-        md.input = input
-        md.output = new File(sampleDir, sampleId + ".dedup.bam")
-        md.outputMetrics = new File(sampleDir, sampleId + ".dedup.bam")
-        Some(md.output)
-      }
-    }
-
-    lazy val preProcessBam: Option[File] = doublePreProcess(libraries.map(_._2.preProcessBam).filter(_.isDefined).map(_.get).toList)
-
-    def addJobs(): Unit = {
-      addPerLibJobs()
-
-      //TODO: Singlesample variantcalling
-    }
-  }
-
-  def addMultiSampleJobs(): Unit = {
-    //TODO: Mutisample variantcalling
-  }
-
-  def summaryFile = new File(outputDir, "Shiva.summary.json")
-
-  def summarySettings = Map()
-
-  def summaryFiles = Map()
 }
 
 object Shiva extends PipelineCommand
\ No newline at end of file

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

+package nl.lumc.sasc.biopet.pipelines.shiva
+
+import java.io.File
+
+import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.core.{MultiSampleQScript, PipelineCommand}
+import nl.lumc.sasc.biopet.extensions.Ln
+import nl.lumc.sasc.biopet.extensions.picard.{AddOrReplaceReadGroups, SamToFastq, MarkDuplicates}
+import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
+import scala.collection.JavaConversions._
+
+/**
+ * Created by pjvan_thof on 2/26/15.
+ */
+trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
+  qscript =>
+
+  def init: Unit = {
+
+  }
+
+  def biopetScript: Unit = {
+    addSamplesJobs()
+
+    addSummaryJobs
+  }
+
+  def makeSample(id: String) = new Sample(id)
+  class Sample(sampleId: String) extends AbstractSample(sampleId) {
+    def makeLibrary(id: String) = new Library(id)
+
+    class Library(libId: String) extends AbstractLibrary(libId) {
+
+      def preProcess(input: File): Option[File] = None
+
+      def makeMapping = {
+        val mapping = new Mapping(qscript)
+        mapping.sampleId = Some(sampleId)
+        mapping.libId = Some(libId)
+        mapping.outputDir = libDir
+        (Some(mapping), Some(mapping.finalBamFile), preProcess(mapping.finalBamFile))
+      }
+
+      lazy val (mapping, bamFile, preProcessBam): (Option[Mapping], Option[File], Option[File]) =
+        (config.contains("R1"), config.contains("bam")) match {
+          case (true, _) => makeMapping // Default starting from fastq files
+          case (false, true) => // Starting from bam file
+            config("bam_to_fastq", default = false).asBoolean match {
+              case true => makeMapping // bam file will be converted to fastq
+              case false => {
+                val file = new File(libDir, sampleId + "-" + libId + ".final.bam")
+                (None, Some(file), preProcess(file))
+              }
+            }
+          case _ => (None, None, None)
+        }
+
+      def addJobs(): Unit = {
+        (config.contains("R1"), config.contains("bam")) match {
+          case (true, _) => mapping.foreach(mapping => {
+            mapping.input_R1 = config("R1")
+            mapping.input_R2 = config("R2")
+          })
+          case (false, true) =>  config("bam_to_fastq", default = false).asBoolean match {
+            case true => {
+              val samToFastq = SamToFastq(qscript, config("bam"),
+                new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
+                new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
+              samToFastq.isIntermediate = true
+              qscript.add(samToFastq)
+              mapping.foreach(mapping => {
+                mapping.input_R1 = samToFastq.fastqR1
+                mapping.input_R2 = Some(samToFastq.fastqR2)
+              })
+            }
+            case false => {
+              val inputSam = SamReaderFactory.makeDefault.open(config("bam"))
+              val readGroups = inputSam.getFileHeader.getReadGroups
+
+              val readGroupOke = readGroups.forall( readGroup => {
+                if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
+                if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
+                readGroup.getSample == sampleId && readGroup.getLibrary == libId
+              })
+              inputSam.close
+
+              if (!readGroupOke) {
+                if (config("correct_readgroups", default = false).asBoolean) {
+                  logger.info("Correcting readgroups, file:" + config("bam"))
+                  val aorrg = AddOrReplaceReadGroups(qscript, config("bam"), bamFile.get)
+                  aorrg.RGID = sampleId + "-" + libId
+                  aorrg.RGLB = libId
+                  aorrg.RGSM = sampleId
+                  aorrg.isIntermediate = true
+                  qscript.add(aorrg)
+                } else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
+                  "\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
+              } else {
+                val oldBamFile: File = config("bam")
+                val oldIndex: File = new File(oldBamFile.getAbsolutePath.stripSuffix(".bam") + ".bai")
+                val newIndex: File = new File(libDir, oldBamFile.getName.stripSuffix(".bam") + ".bai")
+                val baiLn = Ln(qscript, oldIndex, newIndex)
+                add(baiLn)
+
+                val bamLn = Ln(qscript, oldBamFile, bamFile.get)
+                bamLn.deps :+= baiLn.out
+                add(bamLn)
+              }
+
+            }
+          }
+          case _ => logger.warn("Sample: " + sampleId + "  Library: " + libId + ", no reads found")
+        }
+
+        mapping.foreach(mapping => {
+          mapping.init
+          mapping.biopetScript
+          addAll(mapping.functions) // Add functions of mapping to curent function pool
+          addSummaryQScript(mapping)
+        })
+
+        //TODO: library variantcalling
+      }
+    }
+
+    def doublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
+      if (input == Nil) None
+      else if (input.tail == Nil) {
+        val bamFile = new File(sampleDir, input.head.getName)
+        val oldIndex: File = new File(input.head.getAbsolutePath.stripSuffix(".bam") + ".bai")
+        val newIndex: File = new File(sampleDir, input.head.getName.stripSuffix(".bam") + ".bai")
+        val baiLn = Ln(qscript, oldIndex, newIndex)
+        add(baiLn)
+
+        val bamLn = Ln(qscript, input.head, bamFile)
+        bamLn.deps :+= baiLn.out
+        add(bamLn)
+        Some(bamFile)
+      } else {
+        val md = new MarkDuplicates(qscript)
+        md.input = input
+        md.output = new File(sampleDir, sampleId + ".dedup.bam")
+        md.outputMetrics = new File(sampleDir, sampleId + ".dedup.bam")
+        md.isIntermediate = isIntermediate
+        add(md)
+        addSummarizable(md, "mark_duplicates", Some(sampleId))
+        Some(md.output)
+      }
+    }
+
+    lazy val preProcessBam: Option[File] = doublePreProcess(libraries.map(_._2.preProcessBam).filter(_.isDefined).map(_.get).toList)
+
+    def addJobs(): Unit = {
+      addPerLibJobs()
+
+      //TODO: Singlesample variantcalling
+    }
+  }
+
+  def addMultiSampleJobs(): Unit = {
+    //TODO: Mutisample variantcalling
+  }
+
+  def summaryFile = new File(outputDir, "Shiva.summary.json")
+
+  def summarySettings = Map()
+
+  def summaryFiles = Map()
+}