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Preserve distinct original SAM payloads in SV record identity - #444
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coverage: 96.547%. remained the same — fix/sv-original-record-identity into master |
This was referenced Oct 5, 2026
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The selected Sid TPST1::CRCP bulk input contains 32 pairs of original records with the same old
(QNAME, FLAG, RNAME, POS, CIGAR, RG)key but different SAM payloads. Default SV collection silently discarded one; dense mode refused the input. Hash the complete original SAM alignment text for collection and serialized record IDs so both payloads reach the existing placement and cell/UMI ambiguity logic. Exact repeated records still deduplicate, and fragment identities remain unchanged. Record and observation IDs change once. Version 1.44.2.Regressions cover mate fields, MAPQ, sequence, qualities and tags, repeated indexed fetches, default/dense ambiguous labels without extra fragments, and interrupted spool cleanup. The new identity regression fails on released code. The corrected engine scans all 8,148 records in the original bulk subset successfully. Lint and all 5,711 tests pass (97% coverage), including 25 focused tests. CI is running; merge and PyPI deployment follow only after it is green.
Fixes #438. Prerequisite for #433 / #437.