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Merge pull request #11913 from mvdbeek/keep_original_keep_data

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[21.01] Use keep_original in pysam.tabix_index to not remove original data
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Marius van den Beek
2021-05-03 11:44:19 +02:00
committed by GitHub
parent 31c67a2420 6a209388ee
commit 26049fa684
1 changed files with 1 additions and 1 deletions
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lib/galaxy/datatypes/tabular.py
+1 -1
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@@ -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