Start on basecounter

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+
+import htsjdk.samtools.{SAMRecord, SamReaderFactory}
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
+
+import scala.collection.JavaConversions._
+import scala.collection.mutable
+
+/**
+  * Created by pjvanthof on 22/01/16.
+  */
+object BaseCounter extends ToolCommand {
+  case class Args(bedFile: File = null,
+                  outputDir: File = null,
+                  bamFile: File = null) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]("bedFile") required () valueName "<file>" action { (x, c) =>
+      c.copy(bedFile = x)
+    }
+    opt[File]('o', "outputDir") required () valueName "<file>" action { (x, c) =>
+      c.copy(outputDir = x)
+    }
+    opt[File]('b', "bam") required () valueName "<file>" action { (x, c) =>
+      c.copy(bamFile = x)
+    }
+  }
+
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException(""))
+
+    val bedrecords = BedRecordList.fromFile(cmdArgs.bedFile).combineOverlap
+
+    val counts = for (region <- bedrecords.allRecords) yield {
+      val bamReader = SamReaderFactory.makeDefault.open(cmdArgs.bamFile)
+      val interval = region.toSamInterval
+      val samIterator = bamReader.queryOverlapping(interval.getContig, interval.getStart, interval.getEnd)
+      for (samRecord <- samIterator) samRecordToCounts(samRecord, region.originals())
+    }
+  }
+
+  def samRecordToCounts(samRecord: SAMRecord, bedRecords: List[BedRecord]): Unit = {
+    samRecord.getAlignmentBlocks.foreach { x =>
+      val bedStart = x.getReferenceStart - 1
+      val bedEnd = bedStart + x.getLength
+    }
+  }
+}