Fix infinite loop when contig is shorter than read_len#264
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joshfactorial merged 1 commit intoApr 7, 2026
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When read_len exceeds a contig's length, cover_dataset enters an infinite loop because no fragment ever satisfies the length check on line 78, so read_count never increments. Add an early-return guard in generate_reads that skips the contig with a WARNING log instead of hanging. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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When read_len exceeds a contig's length, cover_dataset enters an infinite loop because no fragment ever satisfies the length check on line 78, so read_count never increments. Add an early-return guard in generate_reads that skips the contig with a WARNING log instead of hanging.