Adding flagstats as tsv

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

@@ -103,6 +103,9 @@ object BamStats extends ToolCommand {
 
     val stats = waitOnFutures(processUnmappedReads(bamFile) :: contigsFutures.map(_._2))
 
+    stats.flagstat.writeAsTsv(new File(outputDir, "flagstats.tsv"))
+    stats.insertSizeHistogram
+
     val statsWriter = new PrintWriter(new File(outputDir, "bamstats.json"))
     val totalStats = stats.toSummaryMap
     val statsMap = Map(

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala

@@ -43,7 +43,7 @@ class Counts[T](_counts: Map[T, Long] = Map[T, Long]())(implicit ord: Ordering[T
   }
 
   /** Write histogram to a tsv/count file */
-  def writeToTsv(file: File): Unit = {
+  def writeHistogramToTsv(file: File): Unit = {
     val writer = new PrintWriter(file)
     writer.println("value\tcount")
     counts.keys.toList.sorted.foreach(x => writer.println(s"$x\t${counts(x)}"))

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

@@ -50,13 +50,13 @@ case class Stats(flagstat: FlagstatCollector = new FlagstatCollector(),
   def writeStatsToFiles(outputDir: File): Unit = {
     this.flagstat.writeReportToFile(new File(outputDir, "flagstats"))
     this.flagstat.writeSummaryTofile(new File(outputDir, "flagstats.summary.json"))
-    this.mappingQualityHistogram.writeToTsv(new File(outputDir, "mapping_quality.tsv"))
-    this.insertSizeHistogram.writeToTsv(new File(outputDir, "insert_size.tsv"))
-    this.clippingHistogram.writeToTsv(new File(outputDir, "clipping.tsv"))
-    this.leftClippingHistogram.writeToTsv(new File(outputDir, "left_clipping.tsv"))
-    this.rightClippingHistogram.writeToTsv(new File(outputDir, "right_clipping.tsv"))
-    this._5_ClippingHistogram.writeToTsv(new File(outputDir, "5_prime_clipping.tsv"))
-    this._3_ClippingHistogram.writeToTsv(new File(outputDir, "3_prime_clipping.tsv"))
+    this.mappingQualityHistogram.writeHistogramToTsv(new File(outputDir, "mapping_quality.tsv"))
+    this.insertSizeHistogram.writeHistogramToTsv(new File(outputDir, "insert_size.tsv"))
+    this.clippingHistogram.writeHistogramToTsv(new File(outputDir, "clipping.tsv"))
+    this.leftClippingHistogram.writeHistogramToTsv(new File(outputDir, "left_clipping.tsv"))
+    this.rightClippingHistogram.writeHistogramToTsv(new File(outputDir, "right_clipping.tsv"))
+    this._5_ClippingHistogram.writeHistogramToTsv(new File(outputDir, "5_prime_clipping.tsv"))
+    this._3_ClippingHistogram.writeHistogramToTsv(new File(outputDir, "3_prime_clipping.tsv"))
   }
 
   def toSummaryMap = {

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala

@@ -32,6 +32,12 @@ class FlagstatCollector {
   protected[FlagstatCollector] var totalCounts: Array[Long] = Array()
   protected[FlagstatCollector] var crossCounts = Array.ofDim[Long](1, 1)
 
+  def writeAsTsv(file: File): Unit = {
+    val writer = new PrintWriter(file)
+    names.foreach(x => writer.println(x._2 + "\t" + totalCounts(x._1)))
+    writer.close()
+  }
+
   def loadDefaultFunctions() {
     addFunction("All", record => true)
     addFunction("Mapped", record => !record.getReadUnmappedFlag)

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala

@@ -86,7 +86,7 @@ class CountsTest extends TestNGSuite with Matchers {
     val tsvFile = File.createTempFile("counts.", ".tsv")
     tsvFile.deleteOnExit()
 
-    c1.writeToTsv(tsvFile)
+    c1.writeHistogramToTsv(tsvFile)
 
     val reader = Source.fromFile(tsvFile)
     reader.getLines().toList shouldBe List("value\tcount", "1\t1", "2\t2", "3\t3")

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala

@@ -64,7 +64,7 @@ class HistogramTest extends TestNGSuite with Matchers {
     val tsvFile = File.createTempFile("counts.", ".tsv")
     tsvFile.deleteOnExit()
 
-    c1.writeToTsv(tsvFile)
+    c1.writeHistogramToTsv(tsvFile)
 
     val reader = Source.fromFile(tsvFile)
     reader.getLines().toList shouldBe List("value\tcount", "1\t1", "2\t2", "3\t3")