Reclassify taxonomy#1093
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- reclassify: run EM only; remove low-abundance target dropping. EM iterations now print a '-' progress dash and a "Converged after N iterations." message. - abundance: user controls dropping via --drop (renamed from --drop-percentage, default 0 = disabled). - abundance: add breadth_of_coverage column, computed from CIGAR backtrace M positions (fraction of target covered by >=1 read residue), with a span-based fallback when no backtrace is present.
- default reclassify lambda 1.0 -> 0.25, alpha 1.0 -> 0.5. - clarify the shared parameter-definition comment (drop/taxonomy are abundance-only, not reclassify options). - reclassify -h: describe it as EM-only, dropping moved to 'mmseqs abundance --drop'. - abundance -h: mention breadth of coverage and add a --drop usage example.
reclassify: resultToBuffer was passing hasOrfPosition into the `compress` argument, re-compressing an already-compressed CIGAR into garbage (e.g. "46M" -> "0M14161M") and dropping the ORF-position columns. Pass compress=false and forward hasOrfPosition to its correct slot so the backtrace round-trips and ORF columns are preserved. abundance: rewrite breadth/mapped_length to count covered residues on a per-target boolean map bounded to [0, targetLength), so mapped_length can never exceed target_length by construction (removed the Interval/merge/clamp machinery). Add phase logging and progress bars, and drop the redundant score field from TargetHitRef to cut peak memory. Parameters: stop registering the unused EM flags (--lambda/--alpha/--gamma /--max-iter/--tol) for the abundance command; abundance does not run EM. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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