From bfb88721edaf278413ef89ce44858102c33fd2a4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 24 Aug 2015 18:26:03 +0200
Subject: [PATCH] Remove unused values
---
.../lumc/sasc/biopet/tools/RegionAfCount.scala | 17 ++---------------
1 file changed, 2 insertions(+), 15 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
index 685a9b5ec..dfbeae419 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
@@ -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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