From 186b5775c7ad9406f1b1b839593e3ff155481c31 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 24 Aug 2015 11:35:03 +0200
Subject: [PATCH] Move combine method inside class
---
.../sasc/biopet/tools/RegionAfCount.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/SquishBed.scala | 4 +--
.../utils/intervals/BedRecordList.scala | 36 +++++++++----------
3 files changed, 21 insertions(+), 21 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
index 8ba1caabd..81e9283e0 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
@@ -68,7 +68,7 @@ object RegionAfCount extends ToolCommand {
logger.info(s"Combine ${bedRecords.allRecords.size} bed records")
- val combinedBedRecords = BedRecordList.combineOverlap(bedRecords)
+ val combinedBedRecords = bedRecords.combineOverlap
logger.info(s"${combinedBedRecords.allRecords.size} left")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
index 7a424f510..16e518429 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
@@ -39,14 +39,14 @@ object SquishBed extends ToolCommand {
val records = BedRecordList.fromFile(cmdArgs.input)
val length = records.length
- val refLength = BedRecordList.combineOverlap(records).length
+ val refLength = records.combineOverlap.length
logger.info(s"Total bases: $length")
logger.info(s"Total bases on reference: $refLength")
logger.info("Start squishing")
val squishBed = records.squishBed(cmdArgs.strandSensitive).sort
logger.info("Done squishing")
val squishLength = squishBed.length
- val squishRefLength = BedRecordList.combineOverlap(squishBed).length
+ val squishRefLength = squishBed.combineOverlap.length
logger.info(s"Total bases left: $squishLength")
logger.info(s"Total bases left on reference: $squishRefLength")
logger.info(s"Total bases removed from ref: ${refLength - squishRefLength}")
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 029356e5f..351ab6b08 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
@@ -50,6 +50,24 @@ class BedRecordList(val chrRecords: Map[String, List[BedRecord]], header: List[S
}).flatten
}
+ def combineOverlap: BedRecordList = {
+ new BedRecordList(for ((chr, records) <- sort.chrRecords) yield chr -> {
+ def combineOverlap(records: List[BedRecord],
+ newRecords: ListBuffer[BedRecord] = ListBuffer()): List[BedRecord] = {
+ if (records.nonEmpty) {
+ val chr = records.head.chr
+ val start = records.head.start
+ val overlapRecords = records.takeWhile(_.start <= records.head.end)
+ val end = overlapRecords.map(_.end).max
+
+ newRecords += BedRecord(chr, start, end, _originals = overlapRecords)
+ combineOverlap(records.drop(overlapRecords.length), newRecords)
+ } else newRecords.toList
+ }
+ combineOverlap(records)
+ })
+ }
+
def writeToFile(file: File): Unit = {
val writer = new PrintWriter(file)
allRecords.foreach(writer.println)
@@ -91,22 +109,4 @@ object BedRecordList {
throw e
}
}
-
- def combineOverlap(list: BedRecordList): BedRecordList = {
- new BedRecordList(for ((chr, records) <- list.sort.chrRecords) yield chr -> {
- def combineOverlap(records: List[BedRecord],
- newRecords: ListBuffer[BedRecord] = ListBuffer()): List[BedRecord] = {
- if (records.nonEmpty) {
- val chr = records.head.chr
- val start = records.head.start
- val overlapRecords = records.takeWhile(_.start <= records.head.end)
- val end = overlapRecords.map(_.end).max
-
- newRecords += BedRecord(chr, start, end, _originals = overlapRecords)
- combineOverlap(records.drop(overlapRecords.length), newRecords)
- } else newRecords.toList
- }
- combineOverlap(records)
- })
- }
}
\ No newline at end of file
--
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