From 792cb0053406a1492d77944173610ed02ebab672 Mon Sep 17 00:00:00 2001 From: Ivar Grytten Date: Wed, 9 Mar 2022 12:56:07 +0100 Subject: [PATCH] Added tabix indexing of variant file to fix bug where file was not indexed --- src/python/bin/multigrmpy.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/python/bin/multigrmpy.py b/src/python/bin/multigrmpy.py index 70fcf63..424af3b 100644 --- a/src/python/bin/multigrmpy.py +++ b/src/python/bin/multigrmpy.py @@ -57,6 +57,7 @@ def load_graph_description(args): for record in [record for record_block in records for record in record_block]: vcf_with_event_ids_file.write(record) + pysam.tabix_index(vcf_with_event_ids_path, preset="vcf", force=True) logging.info("Saving: %s.", converted_json_path) with gzip.open(converted_json_path, "wt") as converted_json_file: json.dump(event_list, converted_json_file, sort_keys=True, indent=4, separators=(',', ': '))