No overwrite of the total.json anymore

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala

@@ -165,7 +165,7 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[Any, Int]] = muta
                      sampleDistributions: List[String],
                      contig: Option[String]): Unit = {
     outputDir.mkdirs()
-    this.writeToFile(new File(outputDir, "stats.json"),
+    this.writeToFile(new File(outputDir, s"${contig.getOrElse("total")}.json"),
                      samples,
                      genotypeFields,
                      infoFields,

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala

@@ -110,11 +110,11 @@ object VcfStats extends ToolCommand {
 
     val completeStatsJson = regions
       .flatMap(_.map(_.chr))
-      .foldLeft(ConfigUtils.fileToConfigMap(new File(cmdArgs.outputDir, "stats.json"))) {
+      .foldLeft(ConfigUtils.fileToConfigMap(new File(cmdArgs.outputDir, "total.json"))) {
         case (map, contig) =>
           val contigMap = ConfigUtils.fileToConfigMap(
             new File(cmdArgs.outputDir,
-                     "contigs" + File.separator + contig + File.separator + "stats.json"))
+                     "contigs" + File.separator + contig + File.separator + s"$contig.json"))
           ConfigUtils.mergeMaps(map, contigMap)
       }