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jonperdomoCopilot
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Potential fix for pull request finding
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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contextscore/predict.py

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@@ -546,7 +546,7 @@ def main(argv=None):
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except ValueError as exc:
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logging.error('%s', exc)
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user_message('ANNOVAR setup is required before running prediction.')
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user_message('Example: contextscore --input sample.vcf --output out.vcf --sample_coverage 30 --annovar /path/to/annovar --annovar-db /path/to/humandb')
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user_message('Example: contextscore --input sample.vcf --output out.vcf --sample-coverage 30 --annovar /path/to/annovar --annovar-db /path/to/humandb')
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user_message('Optional: add --model /path/to/model.pkl to override default model resolution.')
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user_message('You can also set ANNOVAR_PATH and ANNOVAR_DB_PATH environment variables.')
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sys.exit(2)

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