fix: alignment span slicing drops characters when gaps present#409
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The span slicing in SmithWatermanAligner used len(cu)/len(cv) which includes gap characters, causing the span to include tokens beyond the aligned region. This led to mismatched character display and phoneme transcription. Changes: - align.py: count only non-gap elements when slicing spans - align.py: skip gap chars in edge trimming to prevent over-trimming - console.py: use alignment length for _mark_span loop range - console.py: add bounds check before accessing span/other pointers
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The span slicing in SmithWatermanAligner used len(cu)/len(cv) which
includes gap characters, causing the span to include tokens beyond the
aligned region. This led to mismatched character display and phoneme
transcription.
Changes: