From 97d996953c8a3bd0810a192ad16d08536efdb22c Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 9 Apr 2015 10:25:38 +0200
Subject: [PATCH] set sequence dicttionary for vepnormalizer
---
.../scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
index a10882b81..7945cfbf9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
@@ -90,6 +90,11 @@ object VepNormalizer extends ToolCommand {
logger.debug("Parsing header")
val new_infos = parseCsq(header)
header.setWriteCommandLine(true)
+
+ val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().
+ setOutputFile(output).setReferenceDictionary(header.getSequenceDictionary)
+ build())
+
for (info <- new_infos) {
val tmpheaderline = new VCFInfoHeaderLine(info, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "A VEP annotation")
header.addMetaDataLine(tmpheaderline)
@@ -97,9 +102,7 @@ object VepNormalizer extends ToolCommand {
logger.debug("Header parsing done")
logger.debug("Writing header to file")
- val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().
- setOutputFile(output).
- build())
+
writer.writeHeader(header)
logger.debug("Wrote header to file")
--
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