From 7d201c9d53ee634ad95266b1a140b4f6629bd292 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 May 2016 16:34:28 +0200
Subject: [PATCH] Adding logging
---
.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
index 50bdf0f42..82c016856 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
@@ -84,7 +84,10 @@ object VepNormalizer extends ToolCommand {
logger.debug("Wrote header to file")
normalize(reader, writer, newInfos, commandArgs.mode, commandArgs.removeCSQ)
- } else writer.writeHeader(header)
+ } else {
+ logger.debug("No variants found, skipping normalize step")
+ writer.writeHeader(header)
+ }
writer.close()
logger.debug("Closed writer")
reader.close()
--
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