> 85% class coverage for BastyGenerateFasta

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala

@@ -172,9 +172,12 @@ object BastyGenerateFasta extends ToolCommand {
     if (cmdArgs.outputConsensus != null || cmdArgs.outputConsensusVariants != null) {
       writeConsensus()
     }
+
+    //FIXME: what to do if outputcConsensus is set, but not outputConsensusVariants (and vice versa)?
   }
 
   protected def writeConsensus() {
+    //FIXME: preferably split this up in functions, so that they can be unit tested
     val referenceFile = new IndexedFastaSequenceFile(cmdArgs.reference)
     val referenceDict = referenceFile.getSequenceDictionary
 

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala

@@ -47,6 +47,15 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
     main(arguments)
   }
 
+  @Test def testMainVcfAndBamMore = {
+    val tmp = File.createTempFile("basty_out", ".fa")
+    val tmppath = tmp.getAbsolutePath
+    tmp.deleteOnExit()
+
+    val arguments = Array("-V", chrQ_path, "--outputConsensus", tmppath, "--outputConsensusVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Child_7006504", "--reference", chrQRef_path, "--outputName", "test")
+    main(arguments)
+  }
+
   @Test def testGetMaxAllele = {
     val reader = new VCFFileReader(vepped, false)
     val record = reader.iterator().next()