Commit 39ee5e10 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix bug on missing index

parent 693e61b8
......@@ -67,7 +67,7 @@ object VcfFilter {
if (inputVcf == null) throw new IllegalStateException("No inputVcf, use -I")
if (outputVcf == null) throw new IllegalStateException("No outputVcf, use -o")
val reader = new VCFFileReader(inputVcf)
val reader = new VCFFileReader(inputVcf, false)
val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().setOutputFile(outputVcf).build)
writer.writeHeader(reader.getFileHeader)
for (record <- reader) {
......
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