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docs(2.1.0): note sketch reference-position wiring
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01B7JMur5DmDpECddErpi2JS
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docs/release-notes-2.1.0.md

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@@ -193,6 +193,15 @@ toward SA's 51.8 k).
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flag, the transcript mate is recovered as an orphan (only when the other mate's
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hits are entirely decoys). On the subset above this recovers +8,270 fragments
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(92.6 % → 92.9 %), matching SA mode's `--allowDecoyOrphans` effect.
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- **Sketch mappings now carry their reference positions.** The port previously
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discarded the positions piscem computes for each pseudoalignment hit, so
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`--sketch --writeMappings` wrote `POS=1` for every record, sketch `--seqBias`/
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`--gcBias` collected bias context from position 0 of every transcript (a
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degenerate model), and the orphan/single-end ambiguous-fragment-length term
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could not fire. Sketch mappings now populate the approximate hit positions
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(k-mer-anchor `ref_pos − read_pos`), so SAM output, bias context, and the
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ambiguous FLD term all work. Sketch `quant.sf` is unchanged on concordant data
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(positions do not alter equivalence-class membership).
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## Mapper allocation/perf
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