From 2757c86840f3d2e3d6168c46c65d14eed0d00f3e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Feb 2015 16:31:02 +0100
Subject: [PATCH] Refactor code
---
.../scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala | 13 +++++--------
1 file changed, 5 insertions(+), 8 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
index 85d580890..76f8887cc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
@@ -145,10 +145,8 @@ object VcfFilter extends ToolCommand {
val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().setOutputFile(commandArgs.outputVcf).build)
writer.writeHeader(header)
- val invertedWriter = if (commandArgs.invertedOutputVcf.isDefined)
- Some(new AsyncVariantContextWriter(new VariantContextWriterBuilder().setOutputFile(commandArgs.invertedOutputVcf.get).build))
- else None
- if (invertedWriter.isDefined) invertedWriter.get.writeHeader(header)
+ val invertedWriter = commandArgs.invertedOutputVcf.collect { case x => new VariantContextWriterBuilder().setOutputFile(x).build }
+ invertedWriter.foreach(_.writeHeader(header))
var counterTotal = 0
var counterLeft = 0
@@ -167,16 +165,15 @@ object VcfFilter extends ToolCommand {
inIdSet(record)) {
writer.add(record)
counterLeft += 1
- } else {
- if (invertedWriter.isDefined) invertedWriter.get.add(record)
- }
+ } else
+ invertedWriter.foreach(_.add(record))
counterTotal += 1
if (counterTotal % 100000 == 0) logger.info(counterTotal + " variants processed, " + counterLeft + " left")
}
logger.info(counterTotal + " variants processed, " + counterLeft + " left")
reader.close
writer.close
- if (invertedWriter.isDefined) invertedWriter.get.close()
+ invertedWriter.foreach(_.close())
logger.info("Done")
}
--
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