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Mention acceptable compressed VCF file extension in GenomicsDBImport error message #7692

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Feb 23, 2022
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Mention acceptable compressed VCF file extension in GenomicsDBImport error message #7692

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3 changes: 2 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
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