fix: --skip-no-m6a skips all reads when MSP annotations are missing#102
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fix: --skip-no-m6a skips all reads when MSP annotations are missing#102
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…nnotations The skip condition incorrectly combined m6A emptiness with MSP count, causing all reads to be skipped when the BAM had m6A calls (MM/ML tags) but no pre-computed MSP annotations (as tag). This affected ONT data where dorado provides m6A calls but fiberseq MSP/nucleosome tags are absent. Fixes #100 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
--skip-no-m6aflag inft fireincorrectly skipped all reads when the BAM had valid m6A calls (MM/ML tags) but no pre-computed MSP annotations (astag)rec.m6a.annotations.is_empty() || n_msps == 0conflated "no m6A" with "no MSPs", causing all ONT reads (which have m6A from dorado but no fiberseq MSP tags) to be skipped--skip-no-m6aonly checks m6A presence, MSP count is checked separately by--min-msp, and the division-by-zero guard for average MSP size is scoped to when--min-ave-msp-size > 0Fixes #100
Test plan
cargo test)🤖 Generated with Claude Code