From 90fe82b42ef86f59c5e9db83626c7e9e442cb12f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 19 Aug 2015 17:10:17 +0200
Subject: [PATCH] Combining duplicates records
---
.../lumc/sasc/biopet/tools/RegionAfCount.scala | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 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 51cfd8e38..96446e4d1 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
@@ -27,6 +27,7 @@ import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantC
import htsjdk.variant.variantcontext.{VariantContext, VariantContextBuilder}
import htsjdk.variant.vcf.{VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine}
import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.extensions.rscript.ScatterPlot
import scala.collection.JavaConversions._
import scala.collection.JavaConverters._
@@ -67,7 +68,7 @@ object RegionAfCount extends ToolCommand {
var c = 0
- val afCounts = (for (region <- regions.par) yield region.getName -> {
+ val afCountsRaw = for (region <- regions.par) yield region.getName -> {
val sum = (for (vcfFile <- cmdArgs.vcfFiles.par) yield vcfFile -> {
val reader = new VCFFileReader(vcfFile, true)
val it = reader.query(region.getContig, region.getStart, region.getEnd)
@@ -86,9 +87,22 @@ object RegionAfCount extends ToolCommand {
if (c % 100 == 0) logger.info(s"$c regions done")
sum
- }).toMap
+ }
logger.info(s"Done reading, $c regions")
+ logger.info("Combining duplicates bed records")
+
+ val afCounts: Map[String, Map[File, Double]] = {
+ val combinedAfCounts: mutable.Map[String, mutable.Map[File, Double]] = mutable.Map()
+ for (x <- afCountsRaw) {
+ if (combinedAfCounts.contains(x._1)) {
+ x._2.foreach(y => combinedAfCounts(x._1)(y._1) += y._2)
+ } else combinedAfCounts += x._1 -> mutable.Map(x._2.toList:_*)
+ }
+ combinedAfCounts.map(x => x._1 -> x._2.toMap).toMap
+ }
+
+ logger.info("Writing output file")
val writer = new PrintWriter(cmdArgs.outputFile)
writer.println("\t" + cmdArgs.vcfFiles.map(_.getName).mkString("\t"))
--
GitLab