From 57145398db85026fe7544bc246d497482e98af7b Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 31 Oct 2014 18:37:41 +0100
Subject: [PATCH] Fix for BAM query sorting order
---
.../scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index 8ceb27793..e56202dfa 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -93,10 +93,10 @@ object ExtractAlignedFastq extends ToolCommand {
}
val queries: Array[QueryInterval] = iv.toList
- // sort Interval
- .sortBy(x => (x.getSequence, x.getStart, x.getEnd))
// transform to QueryInterval
.map(x => new QueryInterval(getSequenceIndex(x.getSequence), x.getStart, x.getEnd))
+ // sort Interval
+ .sortBy(x => (x.referenceIndex, x.start, x.end))
// cast to array
.toArray
--
GitLab