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main
May 28, 2026
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Merge pull request #20 from logannye/rosalind/docs-readme-refresh
Logan Nye MD committed
aa35243
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docs(readme): refresh for bounded whole-genome variants --index
Logan Nye committed
ab4b270
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Merge pull request #19 from logannye/rosalind/phase-b4-variants-index
Logan Nye MD committed
b39dcbe
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feat(cli): variants --index memory receipt + record-only --memory-budget-mb
Logan Nye committed
6d1f0b1
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style(call): rustfmt reflow of the whole_genome working-set assertion
Logan Nye committed
38c6518
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feat(cli): variants --index — bounded multi-contig calling over the persisted index
Logan Nye committed
324d489
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feat(call): bounded whole-genome germline drive over a sorted stream + ReferenceView
Logan Nye committed
1659f25
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feat(io/bam): StreamingBamSource — bounded, sort-guarded BAM read source
Logan Nye committed
8223187
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docs(plan): Phase B4 — bounded whole-genome variant calling over the persisted index
Logan Nye committed
c7c89d1
May 27, 2026
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docs(spec): Phase B4 — bounded whole-genome variant calling over the persisted index
Logan Nye committed
01355ae
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Merge pull request #18 from logannye/rosalind/phase-b4a-reference-view
Logan Nye MD committed
31c97c3
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feat(genomics/index/view): ReferenceView — zero-copy reference access from the index
Logan Nye committed
61143ec
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docs(plan): Phase B4a — ReferenceView (self-contained reference access) plan
Logan Nye committed
da3d1f6
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docs(spec): Phase B4a — self-contained reference access (ReferenceView) design
Logan Nye committed
913b993
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Merge pull request #17 from logannye/rosalind/phase-b3c-index-cli
Logan Nye MD committed
48ecde9
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test(cli): B3c determinism + self-contained gates; docs(readme): build-once → query
Logan Nye committed
bdce9c5
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feat(cli): rosalind locate — load + exact-match query a prebuilt index
Logan Nye committed
9d8fed4
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feat(cli): rosalind index — build + persist a reference index
Logan Nye committed
c06d993
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feat(genomics/index/report): build estimate + receipt + plan-line helpers
Logan Nye committed
7b5f5db
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docs(plan): Phase B3c — rosalind index + load (CLI) implementation plan
Logan Nye committed
e4df07b
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docs(spec): Phase B3c — rosalind index + load (CLI) design
Logan Nye committed
caec338
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Merge pull request #16 from logannye/rosalind/phase-b3b-zerocopy-index
Logan Nye MD committed
990ae07
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harden(genomics/index): reject non-8-aligned block offsets at open
Logan Nye committed
45a6097
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test(index): B3b persistence gates + docs/index-format.md
Logan Nye committed
4738988
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harden(genomics/index/view): validate block records + rate consistency
Logan Nye committed
9f91384
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feat(genomics/index/view): zero-copy FmIndexView + GenomeIndexView + equivalence gate
Logan Nye committed
16d8877
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feat(genomics/index/io): IndexReader::open parses the FM-index sections
Logan Nye committed
41f2fe9
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feat(genomics/index/io): deterministic GenomeIndex serializer
Logan Nye committed
d0a9024
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feat(genomics/index/format): extend SectionKind for the FM-index sections
Logan Nye committed
ceabf16
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feat(genomics): pub(crate) serialization accessors + shared rank primitives
Logan Nye committed
a68182e