From 2d4da7d9ff0e2113e28d79178748815abef715f5 Mon Sep 17 00:00:00 2001 From: Binglan Li Date: Wed, 6 Mar 2024 18:06:54 -0800 Subject: [PATCH] fix(preprocessor): improve message for gVCF Fix-for: #174 --- preprocessor/pharmcat_vcf_preprocessor.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/preprocessor/pharmcat_vcf_preprocessor.py b/preprocessor/pharmcat_vcf_preprocessor.py index c894cc7a0..1ce77a0f0 100644 --- a/preprocessor/pharmcat_vcf_preprocessor.py +++ b/preprocessor/pharmcat_vcf_preprocessor.py @@ -155,7 +155,8 @@ for file in m_vcf_files: if preprocessor.is_gvcf_file(file): print('%s is a gVCF file, which is not currently supported.\n' - 'The PharmCAT VCF Preprocessor will support block gVCF in the future.' % str(file)) + 'See https://github.com/PharmGKB/PharmCAT/issues/79 for details.\n' + 'If this is not a gVCF file, use -G to bypass.' % str(file)) sys.exit(1) m_samples: List[str] = []