From 0e3d6e9f8163333454c716cfbb90a07e51f4c3da Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 23 Aug 2015 11:55:42 +0200
Subject: [PATCH] Change _originals to val
---
.../sasc/biopet/utils/intervals/BedRecord.scala | 17 ++++++-----------
.../biopet/utils/intervals/BedRecordList.scala | 4 +---
2 files changed, 7 insertions(+), 14 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 543e41509..4c50cc857 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
@@ -14,9 +14,8 @@ case class BedRecord(chr: String,
rgbColor: Option[(Int, Int, Int)] = None,
blockCount: Option[Int] = None,
blockSizes: Array[Int] = Array(),
- blockStarts: Array[Int] = Array()) {
-
- protected[intervals] var _originals: List[BedRecord] = Nil
+ blockStarts: Array[Int] = Array(),
+ protected[intervals] val _originals: List[BedRecord] = Nil) {
def originals(nested: Boolean = false): List[BedRecord] = {
if (_originals.isEmpty) List(this)
@@ -32,10 +31,8 @@ case class BedRecord(chr: String,
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-$exonNumber"))
- record._originals :+= this
- record
+ BedRecord(chr, start + blockStarts(i), start + blockStarts(i) + blockSizes(i),
+ name.map(_ + s"_exon-$exonNumber"), _originals = List(this))
}))
} else None
@@ -45,10 +42,8 @@ case class BedRecord(chr: String,
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-$intronNumber"))
- record._originals :+= this
- record
+ BedRecord(chr, start + start + blockStarts(i) + blockSizes(i) + 1, start + blockStarts(i + 1) - 1,
+ name.map(_ + s"_intron-$intronNumber"), _originals = List(this))
}))
} else None
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 ed2c873d3..906f90df1 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
@@ -83,9 +83,7 @@ object BedRecordList {
val overlapRecords = records.takeWhile(_.start <= records.head.end)
val end = overlapRecords.map(_.end).max
- val newRecord = BedRecord(chr, start, end)
- newRecord._originals = overlapRecords
- newRecords += newRecord
+ newRecords += BedRecord(chr, start, end, _originals = overlapRecords)
combineOverlap(records.drop(overlapRecords.length), newRecords)
} else newRecords.toList
}
--
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