Adding methods to agregate stats

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

@@ -51,7 +51,7 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
   }
 
   /** Function to write 1 specific general field */
-  def writeField2(field: String, chr: String = "total"): Map[String, Array[Any]] = {
+  def getField(field: String, chr: String = "total"): Map[String, Array[Any]] = {
 
     val data = this.generalStats.getOrElse(chr, mutable.Map[String, mutable.Map[Any, Int]]()).getOrElse(field, mutable.Map[Any, Int]())
     val rows = for (key <- data.keySet.toArray.sortWith(sortAnyAny)) yield {
@@ -82,7 +82,7 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
   }
 
   /** Function to write 1 specific genotype field */
-  def writeGenotypeField2(samples: List[String], field: String, chr: String = "total"): Map[String, Map[String, Any]] = {
+  def getGenotypeField(samples: List[String], field: String, chr: String = "total"): Map[String, Map[String, Any]] = {
     val keySet = (for (sample <- samples) yield this.samplesStats(sample).genotypeStats.getOrElse(chr, Map[String, Map[Any, Int]]()).getOrElse(field, Map[Any, Int]()).keySet).fold(Set[Any]())(_ ++ _)
 
     (for (sample <- samples) yield sample -> {
@@ -91,6 +91,26 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[String, mutable.M
       ).toMap
     }).toMap
   }
+
+  /** This will generate stats for one contig */
+  def getContigStats(contig: String, samples: List[String], genotypeFields:  List[String], infoFields: List[String]): Map[String, Any] = {
+    Map(
+      "genotype" -> genotypeFields.map(f => f -> getGenotypeField(samples, f, contig)).toMap,
+      "info" -> infoFields.map(f => f -> getField(f, contig))
+    )
+  }
+
+  /** This will generate stats for total */
+  def getTotalStats(samples: List[String], genotypeFields:  List[String], infoFields: List[String]) =
+    getContigStats("total", samples, genotypeFields, infoFields)
+
+  /** This will generate stats for total and contigs separated */
+  def getAllStats(contigs: List[String], samples: List[String], genotypeFields:  List[String], infoFields: List[String]): Map[String, Any] = {
+    Map(
+      "contigs" -> contigs.map(c => c -> getContigStats(c, samples, genotypeFields, infoFields)).toMap,
+      "total" -> getTotalStats(samples, genotypeFields, infoFields)
+    )
+  }
 }
 
 object Stats {

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala

@@ -195,7 +195,7 @@ object VcfStats extends ToolCommand {
     }
 
     // Triple for loop to not keep all bins in memory
-    val statsFutures = (for (intervals <- Random.shuffle(intervals).grouped(intervals.size / (if (intervals.size > 10) 4 else 1)).toList) yield Future {
+    val statsFutures = for (intervals <- Random.shuffle(intervals).grouped(intervals.size / (if (intervals.size > 10) 4 else 1)).toList) yield Future {
       val chunkStats = for (intervals <- intervals.grouped(25)) yield {
         val binStats = for (interval <- intervals.par) yield {
           val reader = new VCFFileReader(cmdArgs.inputFile, true)
@@ -243,7 +243,7 @@ object VcfStats extends ToolCommand {
         binStats.toList.fold(createStats)(_ += _)
       }
       chunkStats.toList.fold(createStats)(_ += _)
-    })
+    }
     val stats = statsFutures.foldLeft(createStats) { case (a,b) => a += Await.result(b, Duration.Inf) }
 
     logger.info("Done reading vcf records")