From b461b79a246f159b1cc9dae2488a213cfea32ad3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 20 Aug 2015 21:02:47 +0200
Subject: [PATCH] Added squish method
---
.../utils/intervals/BedRecordList.scala | 21 ++++++++++++++++---
1 file changed, 18 insertions(+), 3 deletions(-)
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 f734464a3..d2969ec0c 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
@@ -2,9 +2,6 @@ package nl.lumc.sasc.biopet.utils.intervals
import java.io.File
-import htsjdk.samtools.util.Interval
-
-import scala.annotation.tailrec
import scala.collection.mutable
import scala.collection.mutable.ListBuffer
import scala.io.Source
@@ -21,6 +18,24 @@ class BedRecordList(val chrRecords: Map[String, List[BedRecord]]) {
.getOrElse(record.chr, Nil)
.dropWhile(_.end < record.start)
.takeWhile(_.start <= record.end)
+
+ def squishBed(strandSensitive: Boolean = true) = BedRecordList.fromList {
+ (for ((chr, records) <- chrRecords; record <- records) yield {
+ val overlaps = overlapWith(record)
+ .filterNot(strandSensitive && _.strand == record.strand)
+ .filterNot(_.name == record.name)
+ overlaps.foldLeft(List(record))((result, overlap) => {
+ (for (r <- result) yield {
+ (overlap.start < r.start, overlap.end > r.end) match {
+ case (true, true) => Nil
+ case (true, false) => List(r.copy(start = overlap.end + 1))
+ case (false, true) => List(r.copy(end = overlap.start - 1))
+ case (false, false) => List(r.copy(end = overlap.start -1), r.copy(start = overlap.end + 1))
+ }
+ }).flatten
+ })
+ }).flatten
+ }
}
object BedRecordList {
--
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