From 164f4b116ee0dfaf3ab4eb7ca3f1e299315ce6fb Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Tue, 24 Mar 2015 18:01:31 +0100
Subject: [PATCH] Fix error in ExtractAlignedFastq single-end mode where the
input file is rewritten
---
.../scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index 095fb57b7..9620e6bc6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -263,7 +263,7 @@ object ExtractAlignedFastq extends ToolCommand {
case (None, None) => extractReads(memFunc,
new FastqReader(commandArgs.inputFastq1),
- new BasicFastqWriter(commandArgs.inputFastq1))
+ new BasicFastqWriter(commandArgs.outputFastq1))
case (Some(i2), Some(o2)) => extractReads(memFunc,
new FastqReader(commandArgs.inputFastq1),
--
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