From 2f23e35323063cda0ca075b2634a7b284f52f461 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 22 Jul 2016 14:26:23 +0200
Subject: [PATCH] Added check for outputDir
---
.../main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
index 014718a9b..e9817cc90 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
@@ -57,7 +57,11 @@ object BaseCounter extends ToolCommand {
//Sets picard logging level
htsjdk.samtools.util.Log.setGlobalLogLevel(htsjdk.samtools.util.Log.LogLevel.valueOf(logger.getLevel.toString))
+ require(cmdArgs.outputDir.exists(), s"Output dir does not exist: ${cmdArgs.outputDir}")
+ require(cmdArgs.outputDir.isDirectory, s"Output dir is not a dir: ${cmdArgs.outputDir}")
+
logger.info("Start reading RefFlat file")
+
val bamReader = SamReaderFactory.makeDefault().open(cmdArgs.bamFile)
val geneReader = GeneAnnotationReader.loadRefFlat(cmdArgs.refFlat, bamReader.getFileHeader.getSequenceDictionary)
bamReader.close()
--
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