From 1f4aead0af92e5d66d9c8ea3bae9ac37d9c03e88 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 22 Aug 2015 13:50:07 +0200
Subject: [PATCH] Adding exons and introns
---
.../biopet/utils/intervals/BedRecord.scala | 30 +++++++++++++++++++
1 file changed, 30 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 320a98a1e..55f5907cc 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
@@ -16,6 +16,36 @@ case class BedRecord(chr: String,
blockSizes: Array[Int] = Array(),
blockStarts: Array[Int] = Array()) {
+ protected[intervals] var _originals: List[BedRecord] = Nil
+
+ def originals = _originals
+
+ lazy val exons = if (blockCount.isDefined && blockSizes.length > 0 && blockStarts.length > 0) {
+ Some(BedRecordList.fromList(for (i <- 0 to blockCount.get) yield {
+ val exonNumber = strand match {
+ case Some(false) => blockCount.get - i
+ case _ => i + 1
+ }
+ val record = BedRecord(chr, start + blockStarts(i), start + blockStarts(i) + blockSizes(i),
+ name.map(_ + s"_exon-$exonNumber"))
+ record._originals :+= this
+ record
+ }))
+ } else None
+
+ lazy val introns = if (blockCount.isDefined && blockSizes.length > 0 && blockStarts.length > 0) {
+ Some(BedRecordList.fromList(for (i <- 0 to (blockCount.get - 1)) yield {
+ val intronNumber = strand match {
+ case Some(false) => blockCount.get - i
+ case _ => i + 1
+ }
+ val record = BedRecord(chr, start + start + blockStarts(i) + blockSizes(i) + 1, start + blockStarts(i + 1) - 1,
+ name.map(_ + s"_intron-$intronNumber"))
+ record._originals :+= this
+ record
+ }))
+ } else None
+
//TODO: Complete bed line output
override def toString = {
s"$chr\t$start\t$end"
--
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