From f365755d45a3bbcc388e821a527e3d5b8441adbc Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 24 Aug 2015 11:17:34 +0200
Subject: [PATCH] Added utr features
---
.../lumc/sasc/biopet/utils/intervals/BedRecord.scala | 12 ++++++++++++
1 file changed, 12 insertions(+)
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 9a798fbaf..b8f5e680c 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
@@ -47,6 +47,18 @@ case class BedRecord(chr: String,
}))
} else None
+ lazy val utr5 = (strand, thickStart, thickEnd) match {
+ case (Some("+"), Some(tStart), Some(tEnd)) => Some(BedRecord(chr, start, tStart - 1, name.map(_ + "_utr5")))
+ case (Some("-"), Some(tStart), Some(tEnd)) => Some(BedRecord(chr, tEnd + 1, end, name.map(_ + "_utr5")))
+ case _ => None
+ }
+
+ lazy val utr3 = (strand, thickStart, thickEnd) match {
+ case (Some("-"), Some(tStart), Some(tEnd)) => Some(BedRecord(chr, start, tStart - 1, name.map(_ + "_utr3")))
+ case (Some("+"), Some(tStart), Some(tEnd)) => Some(BedRecord(chr, tEnd + 1, end, name.map(_ + "_utr3")))
+ case _ => None
+ }
+
override def toString = {
def arrayToOption[T](array: Array[T]): Option[Array[T]] = {
if (array.isEmpty) None
--
GitLab