From 59ae18bdb6cde4bc1af22e8cda437629d255678e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 22 Aug 2015 16:15:17 +0200
Subject: [PATCH] Switch to originals
---
.../main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala | 3 +--
.../src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala | 1 -
2 files changed, 1 insertion(+), 3 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 0435f9d6d..ad29bd5f7 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
@@ -89,8 +89,7 @@ object RegionAfCount extends ToolCommand {
case a: util.ArrayList[_] => a.map(_.toString.toDouble).toArray
case s => Array(s.toString.toDouble)
}).sum
- bedRecords
- .overlapWith(BedRecord(variant.getContig, variant.getStart, variant.getEnd))
+ region.originals
.map(_.name.getOrElse("error"))
.distinct
.foreach(name => afCounts += name -> (afCounts.getOrElse(name, 0.0) + sum))
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
index 73daabbc6..e90c3b1da 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
@@ -4,7 +4,6 @@ import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
-import nl.lumc.sasc.biopet.utils.intervals.BedRecord
/**
* Created by pjvanthof on 22/08/15.
--
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