From 35315f22ec4208b18f489adfd810df080fda1ba2 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 24 Aug 2015 11:23:25 +0200
Subject: [PATCH] switch exons en introns to simple lists
---
.../nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
index b8f5e680c..a3be5ebf9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
@@ -26,25 +26,25 @@ case class BedRecord(chr: String,
def length = end - start + 1
lazy val exons = if (blockCount.isDefined && blockSizes.length > 0 && blockStarts.length > 0) {
- Some(BedRecordList.fromList(for (i <- 0 to blockCount.get) yield {
+ Some(for (i <- 0 to blockCount.get) yield {
val exonNumber = strand match {
case Some(false) => blockCount.get - i
case _ => i + 1
}
BedRecord(chr, start + blockStarts(i), start + blockStarts(i) + blockSizes(i),
name.map(_ + s"_exon-$exonNumber"), _originals = List(this))
- }))
+ })
} else None
lazy val introns = if (blockCount.isDefined && blockSizes.length > 0 && blockStarts.length > 0) {
- Some(BedRecordList.fromList(for (i <- 0 to (blockCount.get - 1)) yield {
+ Some(for (i <- 0 to (blockCount.get - 1)) yield {
val intronNumber = strand match {
case Some(false) => blockCount.get - i
case _ => i + 1
}
BedRecord(chr, start + start + blockStarts(i) + blockSizes(i) + 1, start + blockStarts(i + 1) - 1,
name.map(_ + s"_intron-$intronNumber"), _originals = List(this))
- }))
+ })
} else None
lazy val utr5 = (strand, thickStart, thickEnd) match {
--
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