Merge branch 'develop' into feature-summary

Conflicts:
	public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala

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

@@ -63,8 +63,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
   def biopetScript() {
     add(SamtoolsFlagstat(this, inputBam, swapExt(outputDir, inputBam, ".bam", ".flagstat")))
 
-    val biopetFlagstat = BiopetFlagstat(this, inputBam, swapExt(outputDir, inputBam, ".bam", ".biopetflagstat"),
-      swapExt(outputDir, inputBam, ".bam", ".biopetflagstat.json"))
+    val biopetFlagstat = BiopetFlagstat(this, inputBam, outputDir)
     add(biopetFlagstat)
     addSummarizable(biopetFlagstat, "biopet_flagstat")
 
@@ -92,15 +91,13 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
 
       val strictOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam")
       add(BedtoolsIntersect(this, inputBam, bedFile, strictOutputBam, minOverlap = config("strictintersectoverlap", default = 1.0)), true)
-      add(SamtoolsFlagstat(this, strictOutputBam, swapExt(targetDir, strictOutputBam, ".bam", ".flagstat")))
-      add(BiopetFlagstat(this, strictOutputBam, swapExt(targetDir, strictOutputBam, ".bam", ".biopetflagstat"),
-        swapExt(targetDir, strictOutputBam, ".bam", ".biopetflagstat.json")))
+      add(SamtoolsFlagstat(this, strictOutputBam, targetDir))
+      add(BiopetFlagstat(this, strictOutputBam, targetDir))
 
       val looseOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam")
       add(BedtoolsIntersect(this, inputBam, bedFile, looseOutputBam, minOverlap = config("looseintersectoverlap", default = 0.01)), true)
-      add(SamtoolsFlagstat(this, looseOutputBam, swapExt(targetDir, looseOutputBam, ".bam", ".biopet")))
-      add(BiopetFlagstat(this, looseOutputBam, swapExt(targetDir, looseOutputBam, ".bam", ".biopetflagstat"),
-        swapExt(targetDir, looseOutputBam, ".bam", ".biopetflagstat.json")))
+      add(SamtoolsFlagstat(this, looseOutputBam, targetDir))
+      add(BiopetFlagstat(this, looseOutputBam, targetDir))
 
       val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
       add(BedtoolsCoverage(this, inputBam, bedFile, coverageFile, true), true)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala

@@ -30,10 +30,10 @@ class SamtoolsFlagstat(val root: Configurable) extends Samtools {
 }
 
 object SamtoolsFlagstat {
-  def apply(root: Configurable, input: File, output: File): SamtoolsFlagstat = {
+  def apply(root: Configurable, input: File, outputDir: File): SamtoolsFlagstat = {
     val flagstat = new SamtoolsFlagstat(root)
     flagstat.input = input
-    flagstat.output = output
-    return flagstat
+    flagstat.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".flagstat")
+    flagstat
   }
 }
\ No newline at end of file

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

@@ -52,12 +52,12 @@ class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFuncti
 object BiopetFlagstat extends ToolCommand {
   import scala.collection.mutable.Map
 
-  def apply(root: Configurable, input: File, output: File, summaryFile: File): BiopetFlagstat = {
+  def apply(root: Configurable, input: File, outputDir: File): BiopetFlagstat = {
     val flagstat = new BiopetFlagstat(root)
     flagstat.input = input
-    flagstat.output = output
-    flagstat.summaryFile = summaryFile
-    return flagstat
+    flagstat.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".biopetflagstat")
+    flagstat.summaryFile = new File(outputDir, input.getName.stripSuffix(".bam") + ".biopetflagstat.json")
+    flagstat
   }
 
   case class Args(inputFile: File = null, summaryFile: Option[File] = None, region: Option[String] = None) extends AbstractArgs