From 31a3766619d1d96159f787518b806bd7df162ac3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 22 Aug 2015 15:28:27 +0200
Subject: [PATCH] Fixed isSorted val
---
.../lumc/sasc/biopet/utils/intervals/BedRecordList.scala | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
index 2f43f7ab5..a0deb868b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
@@ -5,6 +5,7 @@ import java.io.{ PrintWriter, File }
import scala.collection.mutable
import scala.collection.mutable.ListBuffer
import scala.io.Source
+import nl.lumc.sasc.biopet.core.Logging
/**
* Created by pjvan_thof on 8/20/15.
@@ -14,7 +15,10 @@ class BedRecordList(val chrRecords: Map[String, List[BedRecord]]) {
def sort = new BedRecordList(chrRecords.map(x => x._1 -> x._2.sortWith((a, b) => a.start < b.start)))
- lazy val isSorted = this == this.sort
+ lazy val isSorted = {
+ val sorted = this.sort
+ sorted.chrRecords.forall(x => x._2 == chrRecords(x._1))
+ }
def overlapWith(record: BedRecord) = (if (isSorted) this else sort).chrRecords
.getOrElse(record.chr, Nil)
@@ -22,6 +26,7 @@ class BedRecordList(val chrRecords: Map[String, List[BedRecord]]) {
.takeWhile(_.start <= record.end)
def squishBed(strandSensitive: Boolean = true) = BedRecordList.fromList {
+ if (!isSorted) Logging.logger.warn("Running squish bed method on a unsorted bed file may not work correctly")
(for ((chr, records) <- chrRecords; record <- records) yield {
val overlaps = overlapWith(record)
.filterNot(strandSensitive && _.strand != record.strand)
--
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