Fix alignment display coordinates across row wraps (#26)#37
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nathanweeks wants to merge 2 commits into
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Fix alignment display coordinates across row wraps (#26)#37nathanweeks wants to merge 2 commits into
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The --showalignment row-boundary coordinates were wrong whenever a
display unit straddled the wrap column:
- a codon split across the wrap (dna2protein) mis-numbered the row,
since the marker recorded the unit's start rather than the position
of the last character actually shown; interpolate proportionally
across the unit instead, and emit a marker per crossed boundary so a
single over-wide unit (eg an intron label under a small
--alignmentwidth) no longer desyncs later rows.
- the non-advancing sequence (eg the cDNA across a target intron in
est2genome) was reported one base too high, as a zero-advance unit
used the next base position rather than the last one emitted.
Add dna2protein and est2genome alignment-display regression tests.
Assisted-by: Claude:claude-opus-4-8
Track row-start coordinates separately from row-end coordinates when a display unit spans a row wrap. This keeps split 3-letter amino-acid labels on the same residue and prevents compressed introns from making contiguous genome coordinates jump. Extend dna2protein and est2genome alignment tests for the target side. assisted-by: Claude-Code:claude-opus-4-8 Assisted-by: Codex:gpt-5.5
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The --showalignment row-boundary coordinates were wrong whenever a display unit straddled the wrap column:
a codon split across the wrap (dna2protein) mis-numbered the row, since the marker recorded the unit's start rather than the position of the last character actually shown; interpolate proportionally across the unit instead, and emit a marker per crossed boundary so a single over-wide unit (eg an intron label under a small --alignmentwidth) no longer desyncs later rows.
the non-advancing sequence (eg the cDNA across a target intron in est2genome) was reported one base too high, as a zero-advance unit used the next base position rather than the last one emitted.
Add dna2protein and est2genome alignment-display regression tests.