Add ShivaVariantcalling

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

+package nl.lumc.sasc.biopet.pipelines.shiva
+
+import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 2/26/15.
+ */
+class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVariantcallingTrait {
+  def this() = this(null)
+}
+
+object ShivaVariantcalling extends PipelineCommand
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

+package nl.lumc.sasc.biopet.pipelines.shiva
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{PipelineCommand, SampleLibraryTag}
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.tools.{VcfFilter, MpileupToVcf}
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.utils.commandline.Input
+
+import scala.collection.generic.Sorted
+
+/**
+ * Created by pjvan_thof on 2/26/15.
+ */
+trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
+  qscript =>
+
+  @Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
+  var inputBams: List[File] = Nil
+
+  def init: Unit = {
+
+  }
+
+  def biopetScript: Unit = {
+    addSummaryJobs
+  }
+
+  trait Variantcaller {
+    val name: String
+    def outputDir = new File(qscript.outputDir, name)
+    val defaultUse: Boolean
+    val use: Boolean = config("use_" + name, default = defaultUse)
+    val defaultPrio: Int
+    val prio: Int = config("prio_" + name, default = defaultPrio)
+    def addJobs() : File
+  }
+
+  class RawVcf extends Variantcaller {
+    val name = "raw"
+    val defaultPrio = 999
+    val defaultUse = true
+
+    def addJobs() : File = {
+      val rawFiles = inputBams.map(bamFile => {
+        val m2v = new MpileupToVcf(qscript)
+        m2v.inputBam = bamFile
+        m2v.output = new File(outputDir, bamFile.getName.stripSuffix(".bam") + ".raw.vcf")
+        add(m2v)
+
+        val vcfFilter = new VcfFilter(qscript) {
+          override def configName = "vcffilter"
+          override def defaults = ConfigUtils.mergeMaps(Map("min_sample_depth" -> 8,
+            "min_alternate_depth" -> 2,
+            "min_samples_pass" -> 1,
+            "filter_ref_calls" -> true
+          ), super.defaults)
+        }
+        vcfFilter.inputVcf = m2v.output
+        vcfFilter.outputVcf = new File(outputDir, bamFile.getName.stripSuffix(".bam") + ".raw.filter.vcf.gz")
+        add(vcfFilter)
+        vcfFilter.outputVcf
+      })
+
+      //TODO: Combine variants
+      null
+    }
+  }
+
+  def summaryFile = new File(outputDir, "ShivaVariantcalling.summary.json")
+
+  def summarySettings = Map()
+
+  def summaryFiles = Map()
+}
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