From fa54c856b6e0a85868aba388cc2e5892348a099a Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Wed, 25 Mar 2015 10:32:39 +0100
Subject: [PATCH] Properly open and close files in ExtractAlignedFastq
---
.../biopet/tools/ExtractAlignedFastq.scala | 30 ++++++++++++-------
1 file changed, 19 insertions(+), 11 deletions(-)
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 9620e6bc6..501c406c7 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
@@ -261,17 +261,25 @@ object ExtractAlignedFastq extends ToolCommand {
logger.info("Writing to output file(s) ...")
(commandArgs.inputFastq2, commandArgs.outputFastq2) match {
- case (None, None) => extractReads(memFunc,
- new FastqReader(commandArgs.inputFastq1),
- new BasicFastqWriter(commandArgs.outputFastq1))
-
- case (Some(i2), Some(o2)) => extractReads(memFunc,
- new FastqReader(commandArgs.inputFastq1),
- new BasicFastqWriter(commandArgs.outputFastq1),
- new FastqReader(i2),
- new BasicFastqWriter(o2))
-
- case _ => // handled by the command line config check above
+ case (None, None) =>
+ val in = new FastqReader(commandArgs.inputFastq1)
+ val out = new BasicFastqWriter(commandArgs.outputFastq1)
+ extractReads(memFunc, in, out)
+ in.close()
+ out.close()
+
+ case (Some(i2), Some(o2)) =>
+ val in1 = new FastqReader(commandArgs.inputFastq1)
+ val in2 = new FastqReader(i2)
+ val out1 = new BasicFastqWriter(commandArgs.outputFastq1)
+ val out2 = new BasicFastqWriter(o2)
+ extractReads(memFunc, in1, out1, in2, out2)
+ in1.close()
+ in2.close()
+ out1.close()
+ out2.close()
+
+ case _ => ; // handled by the command line config check above
}
}
}
--
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