Added test on main method

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

@@ -56,7 +56,7 @@ object BaseCounter extends ToolCommand {
     val overlapGenes = groupGenesOnOverlap(geneReader.getAll)
 
     logger.info("Start reading bamFile")
-    val counts = (for (genes <- overlapGenes.values.flatten.par) yield bamToGeneCount(cmdArgs.bamFile, genes)).toList
+    val counts = (for (genes <- overlapGenes.values.flatten.par) yield runThread(cmdArgs.bamFile, genes)).toList
     logger.info("Done reading bamFile")
 
     writeGeneCounts(counts.flatMap(_.geneCounts), cmdArgs.outputDir, cmdArgs.prefix)
@@ -281,7 +281,7 @@ object BaseCounter extends ToolCommand {
                                          nonStrandedMetaExonCounts: List[(String, RegionCount)],
                                          strandedMetaExonCounts: List[(String, RegionCount)])
 
-  def bamToGeneCount(bamFile: File, genes: List[Gene]): ThreadOutput = {
+  private[tools] def runThread(bamFile: File, genes: List[Gene]): ThreadOutput = {
     val counts = genes.map(gene => gene -> new GeneCount(gene)).toMap
     val bamReader = SamReaderFactory.makeDefault().open(bamFile)
 
@@ -304,25 +304,27 @@ object BaseCounter extends ToolCommand {
   }
 
   def createMetaExonCounts(genes: List[Gene]): List[(String, RegionCount)] = {
-    val regions = genes.map(gene => gene.getName -> generateMergedExonRegions(gene).sorted)
-    val chr = genes.head.getContig
-    val begin = regions.map(_._2.allRecords.head.start).min
-    val end = regions.map(_._2.allRecords.last.end).max
-
-    val posibleEnds = (regions.flatMap(_._2.allRecords.map(_.end)) ++ regions.flatMap(_._2.allRecords.map(_.start))).distinct.sorted
-
-    def mergeRegions(newBegin: Int, output: List[(String, RegionCount)] = Nil): List[(String, RegionCount)] = {
-      val newEnds = posibleEnds.filter(_ > newBegin)
-      if (newBegin > end || newEnds.isEmpty) output
-      else {
-        val newEnd = newEnds.min
-        val record = BedRecord(chr, newBegin, newEnd)
-        val names = regions.filter(_._2.overlapWith(record).nonEmpty).map(_._1)
-        if (names.nonEmpty) mergeRegions(newEnd, (names.mkString(","), new RegionCount(record.start + 1, record.end)) :: output)
-        else mergeRegions(newEnd, output)
+    if (genes.nonEmpty) {
+      val regions = genes.map(gene => gene.getName -> generateMergedExonRegions(gene).sorted)
+      val chr = genes.head.getContig
+      val begin = regions.map(_._2.allRecords.head.start).min
+      val end = regions.map(_._2.allRecords.last.end).max
+
+      val posibleEnds = (regions.flatMap(_._2.allRecords.map(_.end)) ++ regions.flatMap(_._2.allRecords.map(_.start))).distinct.sorted
+
+      def mergeRegions(newBegin: Int, output: List[(String, RegionCount)] = Nil): List[(String, RegionCount)] = {
+        val newEnds = posibleEnds.filter(_ > newBegin)
+        if (newBegin > end || newEnds.isEmpty) output
+        else {
+          val newEnd = newEnds.min
+          val record = BedRecord(chr, newBegin, newEnd)
+          val names = regions.filter(_._2.overlapWith(record).nonEmpty).map(_._1)
+          if (names.nonEmpty) mergeRegions(newEnd, (names.mkString(","), new RegionCount(record.start + 1, record.end)) :: output)
+          else mergeRegions(newEnd, output)
+        }
       }
-    }
-    mergeRegions(begin)
+      mergeRegions(begin)
+    } else Nil
   }
 
   def bamRecordBasesOverlap(samRecord: SAMRecord, start: Int, end: Int): Int = {

public/biopet-tools/src/test/resources/chrQ.refflat

+geneA	t1	chrQ	+	200	500	225	475	3	200,300,400	250,350,500

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

 package nl.lumc.sasc.biopet.tools
 
+import java.io.File
+import java.nio.file.Paths
+
+import com.google.common.io.Files
 import htsjdk.samtools.{SAMReadGroupRecord, SAMSequenceRecord, SAMLineParser, SAMFileHeader}
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
@@ -164,6 +168,22 @@ class BaseCounterTest extends TestNGSuite with Matchers {
     assert(ab.exists(x => x._1 == "geneB" && x._2.start == 201 && x._2.end == 210))
     assert(ab.exists(x => x._1 == "geneB" && x._2.start == 221 && x._2.end == 250))
   }
+
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  @Test
+  def testMain: Unit = {
+    val outputDir = Files.createTempDir()
+    outputDir.deleteOnExit()
+    val prefix = "test"
+    val bamFile = new File(resourcePath("/empty.bam"))
+    val refflat = new File(resourcePath("/chrQ.refflat"))
+    main(Array("-o", outputDir.getAbsolutePath, "-p", prefix,
+      "-b", bamFile.getAbsolutePath, "-r", refflat.getAbsolutePath))
+    outputDir.list().size shouldBe 34
+  }
 }
 
 object BaseCounterTest {