Add --debug logging flag (#56) and fix RGI-bwt multi-value parsing (#84) - #111
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fmaguire merged 1 commit intoAug 10, 2026
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…ing (pha4ge#84) Issue pha4ge#56: Replace print-to-stderr with Python logging module. Add --debug CLI flag that switches between clean user-facing error messages (WARNING level) and full tracebacks (DEBUG level). Add KeyError catch in input parsing with a helpful message when expected columns are missing. Issue pha4ge#84: Handle RGI-bwt output where reference_gene_length contains semicolon-separated values (e.g., '3561; 3564; 3570') and sequence_identity contains dash-separated ranges (e.g., '92.82 - 100.0'). Extracts the first numeric value instead of crashing with a ValueError. Includes test fixture for RGI-bwt multi-value output and two new tests.
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Issue #56: Replace print-to-stderr with Python logging module. Add --debug CLI flag that switches between clean user-facing error messages (WARNING level) and full tracebacks (DEBUG level). Add KeyError catch in input parsing with a helpful message when expected columns are missing.
Issue #84: Handle RGI-bwt output where reference_gene_length contains semicolon-separated values (e.g., '3561; 3564; 3570') and sequence_identity contains dash-separated ranges (e.g., '92.82 - 100.0'). Extracts the first numeric value instead of crashing with a ValueError.
Includes test fixture for RGI-bwt multi-value output and two new tests.