fix(sketch): wire piscem hit positions into sketch mappings#1022
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Sketch (pseudoalignment) mappings were constructed with ref_pos=0, fw_pos=-1,
rc_pos=-1, read_len=0 — discarding the positions piscem already computes in
SimpleHit (pos / mate_pos / fragment_length). Consequences:
- `--sketch --writeMappings` wrote POS=1 (i.e. ref_pos 0) for every record;
- `--sketch` with --seqBias/--gcBias collected bias context from position 0 of
every transcript (a positionally-degenerate, meaningless model);
- the orphan/single-end ambiguous-fragment FLD term could not fire in sketch
mode (it keys on fw_pos/rc_pos).
Populate ref_pos / fw_pos / rc_pos / read_len / r1_pos / r2_pos from the hit's
approximate positions, mirroring selective alignment's conventions: single-end
and orphans use the mate's leftmost (ref_pos = orientation-aware 5' end), and a
concordant pair uses the fragment 5' START / 3' END for the positional models.
These positions are approximate (k-mer-anchor: ref_pos - read_pos), which is
inherent to sketch mode.
Sketch quant.sf is unchanged on concordant data (positions don't alter eq-class
membership); SAM POS is now realistic (e.g. 17/149 with TLEN 183, 2298 distinct
positions vs 1 before); sketch+bias is now position-aware. Full workspace tests
+ clippy green; real-data sketch mapping rate stable.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01B7JMur5DmDpECddErpi2JS
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01B7JMur5DmDpECddErpi2JS
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Sketch mappings discarded the positions piscem already computes (SimpleHit.pos/mate_pos/fragment_length), so
--sketch --writeMappingswrote POS=1 for every record, sketch bias collected from position 0 (degenerate), and the orphan ambiguous-fragment FLD term couldn't fire.This wires ref_pos/fw_pos/rc_pos/read_len/r1_pos/r2_pos from the hit positions (approximate k-mer-anchor coords), mirroring selective-alignment conventions.
Validation: sketch quant.sf unchanged on concordant data (positions don't alter eq-classes); SAM POS now realistic (17/149, TLEN 183, 2298 distinct vs 1); sketch+bias now position-aware; full workspace tests + clippy green; real-data sketch mapping rate stable (~92.6%).
🤖 Generated with Claude Code