From 59fb76fbaff9944f9d3cc9e12bd749b3a059929a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 5 Jul 2016 15:44:01 +0200
Subject: [PATCH] posible to get list from dict now
---
.../sasc/biopet/utils/intervals/BedRecordList.scala | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
index 2cfb86e50..08788a294 100644
--- a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
+++ b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
@@ -14,12 +14,12 @@
*/
package nl.lumc.sasc.biopet.utils.intervals
-import java.io.{ PrintWriter, File }
+import java.io.{ File, PrintWriter }
+import htsjdk.samtools.SAMSequenceDictionary
import htsjdk.samtools.reference.FastaSequenceFile
import scala.collection.JavaConversions._
-
import scala.collection.mutable
import scala.collection.mutable.ListBuffer
import scala.io.Source
@@ -154,8 +154,13 @@ object BedRecordList {
def fromReference(file: File) = {
val referenceFile = new FastaSequenceFile(file, true)
+ val dict = referenceFile.getSequenceDictionary
+ referenceFile.close()
+ fromDict(dict)
+ }
- fromList(for (contig <- referenceFile.getSequenceDictionary.getSequences) yield {
+ def fromDict(dict: SAMSequenceDictionary) = {
+ fromList(for (contig <- dict.getSequences) yield {
BedRecord(contig.getSequenceName, 0, contig.getSequenceLength)
})
}
--
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