From a81d6298faf93bc718be4b351b402655f119ce24 Mon Sep 17 00:00:00 2001 From: pichuan Date: Tue, 25 Aug 2020 11:35:00 -0700 Subject: [PATCH] This change will address the real issue in https://github.com/google/deepvariant/issues/334, where the sample name for empty VCFs became `default` if we don't specify it. PiperOrigin-RevId: 328370355 --- deepvariant/postprocess_variants.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/deepvariant/postprocess_variants.py b/deepvariant/postprocess_variants.py index fb8ff81d..1b294501 100644 --- a/deepvariant/postprocess_variants.py +++ b/deepvariant/postprocess_variants.py @@ -1055,6 +1055,11 @@ def main(argv=()): if record is None: logging.info('call_variants_output is empty. Writing out empty VCF.') sample_name = dv_constants.DEFAULT_SAMPLE_NAME + if FLAGS.sample_name: + logging.info( + '--sample_name is set in postprocess_variant. Using %s as the ' + 'sample name.', FLAGS.sample_name) + sample_name = FLAGS.sample_name variant_generator = iter([]) else: sample_name = _extract_single_sample_name(record)