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lines changed Original file line number Diff line number Diff line change 41
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CLINVAR_SUBMISSION_SUMMARY_URL = (
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'ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/submission_summary.txt.gz'
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)
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+ MIN_HT_PARTITIONS = 2000
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logger = get_logger (__name__ )
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@@ -127,7 +128,7 @@ def download_and_import_latest_clinvar_vcf(
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drop_samples = True ,
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skip_invalid_loci = True ,
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contig_recoding = reference_genome .contig_recoding (include_mt = True ),
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- min_partitions = 2000 ,
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+ min_partitions = MIN_HT_PARTITIONS ,
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force_bgz = True ,
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)
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mt = mt .annotate_globals (version = _parse_clinvar_release_date (tmp_file .name ))
@@ -192,5 +193,5 @@ def download_and_import_clinvar_submission_summary() -> hl.Table:
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'ReportedPhenotypeInfo' : hl .tstr ,
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},
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missing = '-' ,
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- min_partitions = 3 , # recommended 2-4 partitions per core
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+ min_partitions = MIN_HT_PARTITIONS ,
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)
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