Merge branch 'fix-basecounter' into 'develop'

Fix basecounter

Fixes #377 and #378 

See merge request !440

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala

@@ -57,8 +57,13 @@ object BaseCounter extends ToolCommand {
     //Sets picard logging level
     htsjdk.samtools.util.Log.setGlobalLogLevel(htsjdk.samtools.util.Log.LogLevel.valueOf(logger.getLevel.toString))
 
+    require(cmdArgs.outputDir.exists(), s"Output dir does not exist: ${cmdArgs.outputDir}")
+    require(cmdArgs.outputDir.isDirectory, s"Output dir is not a dir: ${cmdArgs.outputDir}")
+
     logger.info("Start reading RefFlat file")
+
     val bamReader = SamReaderFactory.makeDefault().open(cmdArgs.bamFile)
+    require(bamReader.hasIndex, "Bamfile require an index")
     val geneReader = GeneAnnotationReader.loadRefFlat(cmdArgs.refFlat, bamReader.getFileHeader.getSequenceDictionary)
     bamReader.close()
     logger.info("Done reading RefFlat file")