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Deduplicate query-name storage in bounded recovery - #108

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iskandr merged 1 commit into
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fix/107-compact-read-receipts
Oct 2, 2026
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iskandr merged 1 commit into
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fix/107-compact-read-receipts

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@iskandr

@iskandr iskandr commented Oct 2, 2026

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Bounded partner recovery repeated the full seed query-name list in every acquisition receipt and samtools input file. A four-platform Sid pilot accumulated 6.15 GB of JSON and 2.26 GB of query-name text around 1.55 GB of BAMs; the 461 text files contained only 15 distinct lists (68.7 MB).

Store query-name lists once as verified content-addressed assets, shared by disk receipts and samtools -N inputs. Public in-memory receipts, selected records, semantic requests and cache identities stay unchanged. Legacy receipts remain readable offline. Add verified receipt dependency pins and explicit, round-trip-checked offline cache compaction; original BAMs/indexes and recorded command-input paths are preserved. Compact caches require osteosarc 0.15.2 or newer.

Validation: 403 tests pass, including original-record preservation, offline legacy reuse/compaction, shared assets, corruption rejection and interrupted publication. Ruff and strict MkDocs pass. Version 0.15.2.

Fixes #107. Unblocks openvax/isovar#433.

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iskandr merged commit a1ac4a3 into main Oct 2, 2026
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Deduplicate query-name assets in bounded recovery receipts and cache files

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