Commit 97d99695 authored by Sander Bollen's avatar Sander Bollen
Browse files

set sequence dicttionary for vepnormalizer

parent e7ed7e5f
......@@ -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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