From e4d581c070f5d76f5c4b651705ff0bace8077970 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Wed, 23 Feb 2022 14:28:11 -0500 Subject: [PATCH] Mention acceptable VCF file extension in GenomicsDBImport Resolves #7691 --- .../hellbender/tools/genomicsdb/GenomicsDBImport.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java index f2e5938301a..f68309565cf 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java @@ -514,7 +514,8 @@ private static void assertIntervalsCoverEntireContigs(GenomicsDBImporter importe private static void assertVariantFileIsCompressedAndIndexed(final Path path) { if (!path.toString().toLowerCase().endsWith(FileExtensions.COMPRESSED_VCF)) { throw new UserException("Input variant files must be block compressed vcfs when using " + - BYPASS_FEATURE_READER + ", but " + path.toString() + " does not appear to be"); + BYPASS_FEATURE_READER + ", but " + path.toString() + " does not end with " + + "the standard file extension " + FileExtensions.COMPRESSED_VCF); } Path indexPath = path.resolveSibling(path.getFileName() + FileExtensions.COMPRESSED_VCF_INDEX); IOUtils.assertFileIsReadable(indexPath);