Switch -a and -b for bedtools coverage

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -164,7 +164,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
       addSummarizable(biopetFlagstatLoose, targetName + "_biopet_flagstat_loose")
       add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose)))
 
-      val bedCov = BedtoolsCoverage(this, inputBam, intervals.bed, depth = true)
+      val bedCov = BedtoolsCoverage(this, intervals.bed, inputBam, depth = true)
       val covStats = CoverageStats(this, targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
       covStats.title = Some("Coverage for " + targetName)
       covStats.subTitle = Some(".")

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

@@ -41,17 +41,11 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
   @Argument(doc = "diffStrand", required = false)
   var diffStrand: Boolean = false
 
-  var inputTag = "-a"
-
-  override def beforeCmd() {
-    if (input.getName.endsWith(".bam")) inputTag = "-abam"
-  }
-
   override def defaultCoreMemory = 4.0
 
   /** Returns command to execute */
   def cmdLine = required(executable) + required("coverage") +
-    required(inputTag, input) +
+    required("-a", input) +
     required("-b", intersectFile) +
     conditional(depth, "-d") +
     conditional(sameStrand, "-s") +
@@ -62,7 +56,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
 object BedtoolsCoverage {
   /** Returns defaul bedtools coverage */
   def apply(root: Configurable, input: File, intersect: File, output: Option[File] = None,
-            depth: Boolean = true, sameStrand: Boolean = false, diffStrand: Boolean = false): BedtoolsCoverage = {
+            depth: Boolean = false, sameStrand: Boolean = false, diffStrand: Boolean = false): BedtoolsCoverage = {
     val bedtoolsCoverage = new BedtoolsCoverage(root)
     bedtoolsCoverage.input = input
     bedtoolsCoverage.intersectFile = intersect