From 2b62e2914637eca80c19a33e958f91ca8b29584c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 24 Aug 2015 13:37:40 +0200
Subject: [PATCH] Sets utrs to None when not existing
---
.../nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala | 8 +++++---
1 file changed, 5 insertions(+), 3 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 29b5a7d7a..a7222a93b 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
@@ -17,7 +17,7 @@ case class BedRecord(chr: String,
blockStarts: Array[Int] = Array(),
protected[intervals] val _originals: List[BedRecord] = Nil) {
- def originals(nested: Boolean = false): List[BedRecord] = {
+ def originals(nested: Boolean = true): List[BedRecord] = {
if (_originals.isEmpty) List(this)
else if (nested) _originals.flatMap(_.originals(true))
else _originals
@@ -48,8 +48,10 @@ case class BedRecord(chr: String,
} else None
lazy val utr5 = (strand, thickStart, thickEnd) match {
- case (Some(true), Some(tStart), Some(tEnd)) => Some(BedRecord(chr, start, tStart - 1, name.map(_ + "_utr5")))
- case (Some(false), Some(tStart), Some(tEnd)) => Some(BedRecord(chr, tEnd + 1, end, name.map(_ + "_utr5")))
+ case (Some(true), Some(tStart), Some(tEnd)) if (tStart > start && tEnd < end) =>
+ Some(BedRecord(chr, start, tStart - 1, name.map(_ + "_utr5")))
+ case (Some(false), Some(tStart), Some(tEnd)) if (tStart > start && tEnd < end) =>
+ Some(BedRecord(chr, tEnd + 1, end, name.map(_ + "_utr5")))
case _ => None
}
--
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