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…and add missing wide format header column `centered_query_start` and `centered_query_end` were off by 1 on the minus strand because the half-open interval [start, end) was negated as [-end, -start) instead of the correct [-end+1, -start+1). This caused m6a positions to index into the wrong base when users sliced `query_sequence[-centered_query_end:]` for minus strand reads. The fix converts to inclusive coordinates before negation and back to exclusive after, matching the existing correct logic in `apply_offset_helper()`. Also adds the missing `fire_qual` column name to the wide format header so the header column count (22) matches the data. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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centered_query_startandcentered_query_endwere off by 1 on the minus strand because the half-open interval [start, end) was negated as [-end, -start) instead of the correct [-end+1, -start+1). This caused m6a positions to index into the wrong base when users slicedquery_sequence[-centered_query_end:]for minus strand reads. The fix converts to inclusive coordinates before negation and back to exclusive after, matching the existing correct logic inapply_offset_helper().Also adds the missing
fire_qualcolumn name to the wide format header so the header column count (22) matches the data.