Added freebayes

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 3/3/15.
+ */
+class Freebayes(val root: Configurable) extends BiopetCommandLineFunction {
+
+  @Input(required = true)
+  var bamfiles: List[File] = Nil
+
+  @Input(required = true)
+  var reference: File = config("reference")
+
+  @Output(required = true)
+  var outputVcf: File = null
+
+  var ploidy: Option[Int] = config("ploidy")
+
+  executable = config("exe", default = "freebayes")
+  override val versionRegex = """version:  (.*)""".r
+  override def versionCommand = executable + " --version"
+
+  def cmdLine = executable +
+    required("--fasta-reference", reference) +
+    repeat("--bam", bamfiles) +
+    optional("--vcf", outputVcf) +
+    optional("--ploidy", ploidy)
+}

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

@@ -77,7 +77,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
     addSummaryJobs
   }
 
-  protected def callersList: List[Variantcaller] = List(new RawVcf, new Bcftools)
+  protected def callersList: List[Variantcaller] = List(new Freebayes, new RawVcf, new Bcftools)
 
   trait Variantcaller {
     val name: String
@@ -88,6 +88,20 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
     def outputFile: File
   }
 
+  class Freebayes extends Variantcaller {
+    val name = "freebayes"
+    protected val defaultPrio = 7
+
+    def outputFile = new File(outputDir, namePrefix + ".freebayes.vcf")
+
+    def addJobs() {
+      val fb = new nl.lumc.sasc.biopet.extensions.Freebayes(qscript)
+      fb.bamfiles = inputBams
+      fb.outputVcf = outputFile
+      add(fb)
+    }
+  }
+
   class Bcftools extends Variantcaller {
     val name = "bcftools"
     protected val defaultPrio = 8

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

@@ -4,6 +4,7 @@ import java.io.File
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.Freebayes
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.tools.{ VcfFilter, MpileupToVcf }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
@@ -31,20 +32,21 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
   @DataProvider(name = "shivaVariantcallingOptions")
   def shivaVariantcallingOptions = {
     val bool = Array(true, false)
-    (for (bams <- 0 to 3; raw <- bool; bcftools <- bool) yield Array(bams, raw, bcftools)).toArray
+    (for (bams <- 0 to 3; raw <- bool; bcftools <- bool; freebayes <- bool) yield Array(bams, raw, bcftools, freebayes)).toArray
   }
 
   @Test(dataProvider = "shivaVariantcallingOptions")
-  def testShivaVariantcalling(bams: Int, raw: Boolean, bcftools: Boolean) = {
+  def testShivaVariantcalling(bams: Int, raw: Boolean, bcftools: Boolean, freebayes: Boolean) = {
     val callers: ListBuffer[String] = ListBuffer()
     if (raw) callers.append("raw")
     if (bcftools) callers.append("bcftools")
+    if (freebayes) callers.append("freebayes")
     val map = Map("variantcallers" -> callers.toList)
     val pipeline = initPipeline(map)
 
     pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
 
-    val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools)
+    val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !freebayes)
 
     if (illegalArgumentException) intercept[IllegalArgumentException] {
       pipeline.script()
@@ -56,6 +58,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
       pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe 1 + (if (raw) 1 else 0)
       //pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
       //FIXME: Can not check for bcftools because of piping
+      pipeline.functions.count(_.isInstanceOf[Freebayes]) shouldBe (if (freebayes) 1 else 0)
       pipeline.functions.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
       pipeline.functions.count(_.isInstanceOf[VcfFilter]) shouldBe (if (raw) bams else 0)
     }
@@ -75,6 +78,7 @@ object ShivaVariantcallingTest {
     "reference" -> "test",
     "gatk_jar" -> "test",
     "samtools" -> Map("exe" -> "test"),
-    "bcftools" -> Map("exe" -> "test")
+    "bcftools" -> Map("exe" -> "test"),
+    "freebayes" -> Map("exe" -> "test")
   )
 }
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