Init commit for bamstats

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

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
+
+/**
+  * Created by pjvanthof on 25/05/16.
+  */
+object BamStats extends ToolCommand {
+  case class Args(outputDir: File = null,
+                  bamFile: File = null,
+                  reference: File = null,
+                  binSize: Int = 10000,
+                  threadBinSize: Int = 10000000) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('R', "reference") required () valueName "<file>" action { (x, c) =>
+      c.copy(reference = x)
+    }
+    opt[File]('o', "outputDir") required () valueName "<directory>" action { (x, c) =>
+      c.copy(outputDir = x)
+    }
+    opt[File]('b', "bam") required () valueName "<file>" action { (x, c) =>
+      c.copy(bamFile = x)
+    }
+    opt[Int]("binSize") required () valueName "<int>" action { (x, c) =>
+      c.copy(binSize = x)
+    }
+  }
+
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+
+    val regions = BedRecordList.fromReference(cmdArgs.reference)
+      .scatter(cmdArgs.binSize)
+      .sorted
+      .chrRecords.flatMap { case (chr, regions) =>
+        val numberThreads = cmdArgs.threadBinSize / cmdArgs.binSize
+        regions.grouped(numberThreads).map(BedRecordList.fromList(_))
+      }.par
+
+    for (regionList <- regions) {
+      require(regionList.chrRecords.size == 1, "A thread can only have 1 contig")
+      val chr = regionList.chrRecords.head._1
+      val start = regionList.allRecords.map(_.start).min + 1
+      val end = regionList.allRecords.map(_.end).max
+    }
+  }
+}