Fix SquishBed

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala

@@ -4,13 +4,16 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.ToolCommand
 import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
+import nl.lumc.sasc.biopet.utils.intervals.BedRecord
 
 /**
  * Created by pjvanthof on 22/08/15.
  */
 object SquishBed extends ToolCommand {
 
-  case class Args(input: File = null, output: File = null) extends AbstractArgs
+  case class Args(input: File = null,
+                  output: File = null,
+                  strandSensitive: Boolean = false) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     opt[File]('I', "input") required () valueName "<file>" action { (x, c) =>
@@ -19,6 +22,9 @@ object SquishBed extends ToolCommand {
     opt[File]('o', "output") required () unbounded () valueName "<file>" action { (x, c) =>
       c.copy(output = x)
     }
+    opt[Unit]('s', "strandSensitive") unbounded () valueName "<file>" action { (x, c) =>
+      c.copy(strandSensitive = true)
+    }
   }
 
   /**
@@ -30,7 +36,8 @@ object SquishBed extends ToolCommand {
 
     if (!cmdArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + cmdArgs.input)
 
-    val records = BedRecordList.fromFile(cmdArgs.input).squishBed()
-
+    val records = BedRecordList.fromFile(cmdArgs.input).sort
+    val squishBed = records.squishBed(cmdArgs.strandSensitive).sort
+    squishBed.writeToFile(cmdArgs.output)
   }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala

@@ -12,9 +12,11 @@ import scala.io.Source
 class BedRecordList(val chrRecords: Map[String, List[BedRecord]]) {
   def allRecords = for (chr <- chrRecords; record <- chr._2) yield record
 
-  def sort = new BedRecordList(chrRecords.map(x => x._1 -> x._2.sortBy(_.start)))
+  def sort = new BedRecordList(chrRecords.map(x => x._1 -> x._2.sortWith((a, b) => a.start < b.start)))
 
-  def overlapWith(record: BedRecord) = chrRecords
+  lazy val isSorted = this == this.sort
+
+  def overlapWith(record: BedRecord) = (if (isSorted) this else sort).chrRecords
     .getOrElse(record.chr, Nil)
     .dropWhile(_.end < record.start)
     .takeWhile(_.start <= record.end)
@@ -22,18 +24,23 @@ class BedRecordList(val chrRecords: Map[String, List[BedRecord]]) {
   def squishBed(strandSensitive: Boolean = true) = BedRecordList.fromList {
     (for ((chr, records) <- chrRecords; record <- records) yield {
       val overlaps = overlapWith(record)
-        .filterNot(strandSensitive && _.strand == record.strand)
+        .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
-      })
+      if (overlaps.isEmpty) {
+        List(record)
+      } else {
+        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
   }