Commit bfb88721 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove unused values

parent cedd54be
......@@ -18,23 +18,13 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ PrintWriter, InputStream, File }
import java.util
import htsjdk.samtools.util.Interval
import htsjdk.samtools.{ QueryInterval, SAMRecord, SamReader, SamReaderFactory }
import htsjdk.tribble.AbstractFeatureReader._
import htsjdk.tribble.{ AbstractFeatureReader, TabixFeatureReader }
import htsjdk.tribble.bed.{ BEDFeature, SimpleBEDFeature, BEDCodec, FullBEDFeature }
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
import htsjdk.variant.vcf.{ VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine }
import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.extensions.rscript.ScatterPlot
import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
import scala.collection.JavaConversions._
import scala.collection.JavaConverters._
import scala.collection.mutable
import scala.io.Source
import scala.math._
object RegionAfCount extends ToolCommand {
case class Args(bedFile: File = null,
......@@ -80,12 +70,9 @@ object RegionAfCount extends ToolCommand {
var namesCoding: Double = 0,
var utr: Double = 0,
var utr5: Double = 0,
var utr3: Double = 0,
var exons: Map[String, Double] = Map(),
var intron: Map[String, Double] = Map())
var utr3: Double = 0)
var c = 0
val afCounts = (for (vcfFile <- cmdArgs.vcfFiles.par) yield vcfFile -> {
val reader = new VCFFileReader(vcfFile, true)
val afCounts: mutable.Map[String, AfCounts] = mutable.Map()
......
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