Merge branch 'fix-hc-gvcf' into 'develop'

fix for #372

Fixes #372 

See merge request !436

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala

@@ -42,13 +42,13 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
   )
 
   def biopetScript() {
-    val gvcfFiles = for ((sample, inputBam) <- inputBams) yield {
+    gVcfFiles = for ((sample, inputBam) <- inputBams) yield {
       val hc = gatk.HaplotypeCaller(this, List(inputBam), new File(outputDir, sample + ".gvcf.vcf.gz"))
       add(hc)
       sample -> hc.out
     }
 
-    val genotypeGVCFs = gatk.GenotypeGVCFs(this, gvcfFiles.values.toList, outputFile)
+    val genotypeGVCFs = gatk.GenotypeGVCFs(this, gVcfFiles.values.toList, outputFile)
     add(genotypeGVCFs)
   }
 }

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala

+package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
+
+import java.io.File
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+  * Created by Sander Bollen on 13-7-16.
+  */
+class HaploTypeCallerGvcfTest extends TestNGSuite with Matchers {
+
+  @Test
+  def testGvcfFiles = {
+    val samples = List("sample01", "sample02", "sample03")
+    val hc = new HaplotypeCallerGvcf(null)
+    hc.inputBams = createInputMap(samples)
+    hc.biopetScript()
+
+    hc.getGvcfs.size shouldBe 3
+    hc.getGvcfs.keys.toList.sorted shouldEqual samples.sorted
+  }
+
+  def createInputMap(samples: List[String]): Map[String, File] = {
+    samples map { x =>
+      val file = File.createTempFile(x, ".bam")
+      file.deleteOnExit()
+      x -> file
+    } toMap
+  }
+
+}