Moving flagstats from bamstats to summary

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

@@ -82,10 +82,6 @@ class BamMetrics(val root: Configurable) extends QScript
   def biopetScript() {
     add(SamtoolsFlagstat(this, inputBam, outputDir))
 
-    val biopetFlagstat = BiopetFlagstat(this, inputBam, outputDir)
-    add(biopetFlagstat)
-    addSummarizable(biopetFlagstat, "biopet_flagstat")
-
     val bamStats = new BamStats(this)
     bamStats.bamFile = inputBam
     bamStats.outputDir = new File(outputDir, "bamstats")

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala

@@ -2,14 +2,18 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Input
 
+import scala.collection.JavaConversions._
+
 /**
   * Created by pjvanthof on 18/11/2016.
   */
-class BamStats(val root: Configurable) extends ToolCommandFunction with Reference {
+class BamStats(val root: Configurable) extends ToolCommandFunction with Reference with Summarizable {
   def toolObject = nl.lumc.sasc.biopet.tools.bamstats.BamStats
 
   @Input(required = true)
@@ -27,6 +31,13 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
   override def defaultCoreMemory = 5.0
   override def dictRequired = true
 
+  def flagstatSummaryFile(implicit contig: Option[String] = None): File = {
+    contig match {
+      case Some(contig) => new File(outputDir, "contigs" + File.separator + contig + File.separator + "flagstats.summary.json")
+      case _ => new File(outputDir, "flagstats.summary.json")
+    }
+  }
+
   override def beforeGraph() {
     super.beforeGraph()
     jobOutputFile = new File(outputDir, ".bamstats.out")
@@ -41,4 +52,13 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
     optional("--binSize", binSize) +
     optional("--threadBinSize", threadBinSize)
 
+
+  def summaryFiles: Map[String, File] = Map()
+
+  def summaryStats: Map[String, Any] = Map(
+    "flagstats" -> ConfigUtils.fileToConfigMap(flagstatSummaryFile),
+    "flagstats_per_contig" -> referenceDict.getSequences.map {
+      c => c.getSequenceName -> ConfigUtils.fileToConfigMap(flagstatSummaryFile(Some(c.getSequenceName)))
+    }.toMap
+  )
 }