Combining all into 1 file

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

@@ -98,12 +98,21 @@ object BamStats extends ToolCommand {
    */
   def init(outputDir: File, bamFile: File, referenceDict: SAMSequenceDictionary, binSize: Int, threadBinSize: Int): Unit = {
     val contigsFutures = BedRecordList.fromDict(referenceDict).allRecords.map { contig =>
-      processContig(contig, bamFile, binSize, threadBinSize, outputDir)
-    }
+      contig.chr -> processContig(contig, bamFile, binSize, threadBinSize, outputDir)
+    }.toList
+
+    val stats = waitOnFutures(processUnmappedReads(bamFile) :: contigsFutures.map(_._2))
 
-    val stats = waitOnFutures(processUnmappedReads(bamFile) :: contigsFutures.toList)
+    val statsWriter = new PrintWriter(new File(outputDir, "stats.json"))
+    val statsMap = Map(
+      "total" -> stats.toSummaryMap,
+      "contigs" -> contigsFutures.map(x => x._1 -> x._2.value.get.get.toSummaryMap).toMap
+    )
+    statsWriter.println(ConfigUtils.mapToJson(statsMap).spaces2)
+    statsWriter.close()
+    //stats.writeStatsToFiles(outputDir)
 
-    stats.writeStatsToFiles(outputDir)
+    // FIXME: getting aggregated stats
 
     val clippingHistogram = tsvToMap(new File(outputDir, "clipping.tsv"))
     val mappingQualityHistogram = tsvToMap(new File(outputDir, "mapping_quality.tsv"))
@@ -157,11 +166,7 @@ object BamStats extends ToolCommand {
       .grouped((region.length.toDouble / binSize).ceil.toInt / (region.length.toDouble / threadBinSize).ceil.toInt)
       .map(scatters => processThread(scatters, bamFile))
       .toList
-    val stats = waitOnFutures(scattersFutures, Some(region.chr))
-    val contigDir = new File(outputDir, "contigs" + File.separator + region.chr)
-    contigDir.mkdirs()
-    stats.writeStatsToFiles(contigDir)
-    stats
+    waitOnFutures(scattersFutures, Some(region.chr))
   }
 
   /**

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

@@ -15,6 +15,7 @@
 package nl.lumc.sasc.biopet.tools.bamstats
 
 import java.io.{ File, PrintWriter }
+import nl.lumc.sasc.biopet.utils.sortAnyAny
 
 import scala.collection.mutable
 
@@ -49,6 +50,11 @@ class Counts[T](_counts: Map[T, Long] = Map[T, Long]())(implicit ord: Ordering[T
     writer.close()
   }
 
+  def toSummaryMap = {
+    val values = counts.keySet.toList.sortWith(sortAnyAny)
+    Map("values" -> values, "counts" -> values.map(counts(_)))
+  }
+
   override def equals(other: Any): Boolean = {
     other match {
       case c: Counts[T] => this.counts == c.counts

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

@@ -58,4 +58,17 @@ case class Stats(flagstat: FlagstatCollector = new FlagstatCollector(),
     this._5_ClippingHistogram.writeToTsv(new File(outputDir, "5_prime_clipping.tsv"))
     this._3_ClippingHistogram.writeToTsv(new File(outputDir, "3_prime_clipping.tsv"))
   }
+
+  def toSummaryMap = {
+    Map(
+      "flagstats" -> flagstat.toSummaryMap,
+      "mapping_quality" -> mappingQualityHistogram.toSummaryMap,
+      "insert_size" -> insertSizeHistogram.toSummaryMap,
+      "clipping" -> clippingHistogram.toSummaryMap,
+      "left_clipping" -> leftClippingHistogram.toSummaryMap,
+      "right_clipping" -> rightClippingHistogram.toSummaryMap,
+      "5_prime_clipping" -> _5_ClippingHistogram.toSummaryMap,
+      "3_prime_clipping" -> _3_ClippingHistogram.toSummaryMap
+    )
+  }
 }

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

@@ -201,6 +201,15 @@ class FlagstatCollector {
     buffer.toString()
   }
 
+  def toSummaryMap = {
+    val sortedKeys = names.keys.toArray.sorted
+    Map(
+      "keys" -> sortedKeys.map(names(_)),
+      "total" -> totalCounts,
+      "cross_counts" -> crossCounts
+    )
+  }
+
   def +=(other: FlagstatCollector): FlagstatCollector = {
     require(this.names == other.names)
     //require(this.functions == other.functions)