From 6a209388ee0f9f638f00a015faf06470f0eb193c Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 29 Apr 2021 22:37:41 +0200 Subject: [PATCH] Use keep_original in pysam.tabix_index to not remove original data --- lib/galaxy/datatypes/tabular.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index 9d50a523433..04518492853 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -823,7 +823,7 @@ class VcfGz(BaseVcf, binary.Binary): index_file = dataset.metadata.spec['tabix_index'].param.new_file(dataset=dataset) try: - pysam.tabix_index(dataset.file_name, index=index_file.file_name, preset='vcf', force=True) + pysam.tabix_index(dataset.file_name, index=index_file.file_name, preset='vcf', keep_original=True, force=True) except Exception as e: raise Exception('Error setting VCF.gz metadata: %s' % (util.unicodify(e))) dataset.metadata.tabix_index = index_file