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Fix bug that results in an empty Vapor report #754

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merged 2 commits into from
Jan 6, 2025
Merged

Fix bug that results in an empty Vapor report #754

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34a90da
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kjaisingh Dec 4, 2024
46b629f
Conditionally get dict fields if they exist
kjaisingh Dec 5, 2024
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9 changes: 5 additions & 4 deletions src/sv_utils/src/sv_utils/report_confident_irs_vapor_variants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -223,7 +223,8 @@ def main(argv: Optional[List[Text]] = None) -> get_truth_overlap.ConfidentVarian
vapor_support_old = vapor_rec['p_non_ref_old'] > 1 - arguments.vapor_min_precision
vapor_support_genotyped = vapor_rec['p_non_ref_genotyped'] > 1 - arguments.vapor_min_precision
vapor_support_read_threshold = vapor_rec['p_non_ref_read_threshold'] > 1 - arguments.vapor_min_precision
if vapor_support_old or vapor_support_genotyped or vapor_support_read_threshold:
vapor_support = vapor_support_old or vapor_support_genotyped or vapor_support_read_threshold
if vapor_support:
vapor_support_gt = vapor_rec[genomics_io.Keys.gt]
vapor_support_gq = vapor_rec[genomics_io.Keys.gq]
vapor_support_reads = vapor_rec[genomics_io.Keys.vapor_read_scores]
Expand Down Expand Up @@ -259,9 +260,9 @@ def main(argv: Optional[List[Text]] = None) -> get_truth_overlap.ConfidentVarian
sample,
record.info['SVTYPE'],
record.info['SVLEN'],
record.samples[sample]['GT'][0],
record.samples[sample]['GT'][1],
record.samples[sample]['GQ'],
record.samples[sample].get('GT', ['N/A', 'N/A'])[0],
record.samples[sample].get('GT', ['N/A', 'N/A'])[1],
record.samples[sample].get('GQ', 'N/A'),
vapor_support_gt,
vapor_support_gq,
vapor_support_reads,
Expand Down
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