Adding mapping quality and clipping stats to summary

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

@@ -9,6 +9,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Input
 
 import scala.collection.JavaConversions._
+import scala.io.Source
 
 /**
   * Created by pjvanthof on 18/11/2016.
@@ -31,13 +32,17 @@ 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 = {
+  def getOutputFile(name: String, 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")
+      case Some(contig) => new File(outputDir, "contigs" + File.separator + contig + File.separator + name)
+      case _ => new File(outputDir, name)
     }
   }
 
+  def flagstatSummaryFile(contig: Option[String] = None): File = getOutputFile("flagstats.summary.json", contig)
+  def mappingQualityFile(contig: Option[String] = None): File = getOutputFile("mapping_quality.tsv", contig)
+  def clipingFile(contig: Option[String] = None): File = getOutputFile("clipping.tsv", contig)
+
   override def beforeGraph() {
     super.beforeGraph()
     jobOutputFile = new File(outputDir, ".bamstats.out")
@@ -56,9 +61,29 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
   def summaryFiles: Map[String, File] = Map()
 
   def summaryStats: Map[String, Any] = Map(
-    "flagstats" -> ConfigUtils.fileToConfigMap(flagstatSummaryFile),
+    "flagstats" -> ConfigUtils.fileToConfigMap(flagstatSummaryFile()),
     "flagstats_per_contig" -> referenceDict.getSequences.map {
       c => c.getSequenceName -> ConfigUtils.fileToConfigMap(flagstatSummaryFile(Some(c.getSequenceName)))
-    }.toMap
+    }.toMap,
+    "mapping_quality" -> BamStats.tsvToMap(mappingQualityFile()),
+    "clipping" -> BamStats.tsvToMap(clipingFile())
   )
 }
+
+object BamStats {
+  def tsvToMap(tsvFile: File): Map[String, Array[Int]] = {
+    val reader = Source.fromFile(tsvFile)
+    val it = reader.getLines()
+    val header = it.next().split("\t")
+    val arrays = header.zipWithIndex.map(x => x._2 -> (x._1 -> Array[Int]()))
+    for (line <- it) {
+      val values = line.split("\t")
+      require(values.size == header.size, s"Line does not have the number of field as header: $line")
+      for (array <- arrays) {
+        array._2._2 :+ values(array._1)
+      }
+    }
+    reader.close()
+    arrays.map(_._2).toMap
+  }
+}
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