Rewrite readFeature to avoid using pattern matching #75
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Rajkumar-D
reviewed
Dec 9, 2025
Comment on lines
+220
to
+225
| if (!accession.isEmpty() | ||
| && !source.isEmpty() | ||
| && !name.isEmpty() | ||
| && (strand.equals("+") || strand.equals("-") || strand.equals(".") || strand.equals("?")) | ||
| && isValidNumber(start_str) | ||
| && isValidNumber(end_str)) { |
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So this will silently ignore the lines that are not valid.
Better to log the ignored lines
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Reduces validation & transformation time by half. Using the ensembl gnenes.gff file the validation time decreases from 3m40s to 1m