Review fixes: signed-u8 guard, dense-subset byte budget, and lcp_array - #8

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BenjaminDEMAILLE wants to merge 20 commits into

COMBINE-lab:mainfrom

BenjaminDEMAILLE:fix/rob-review

Commits on Aug 13, 2026

feat: radix-seeded prefix doubling for the plain in-memory SA

BenjaminDEMAILLE
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claude
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ffe3680
feat: `verify_sa`, an O(n) independent suffix-array check

BenjaminDEMAILLE
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claude
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148f266
perf: parallelise grouping and rank publication in the doubling path

BenjaminDEMAILLE
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9a39247
bench: add a reproducible chr21 harness

BenjaminDEMAILLE
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claude
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9369034
docs: document the fast path, and correct two stale claims

BenjaminDEMAILLE
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claude
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cda07cb
perf: replace the seed comparison sort with an MSD counting sort

BenjaminDEMAILLE
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f5ef8e2
feat: extend the doubling path to subsets and to in-memory sample sort

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claude
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fe411d8
docs: refresh the fast-path numbers and coverage

BenjaminDEMAILLE
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14f3107
perf: rank the alphabet before packing keys

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ef6a78b
docs: record the alphabet-ranking result

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f9c42c9
perf: pack keys with a SWAR gather over a pre-ranked text

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83f721e
docs: refresh in-memory numbers after the SWAR key packing

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cd28bfb
perf: drop the per-group allocation and prepass from doubling rounds

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54b6c57
docs: refresh in-memory numbers after the doubling-round cleanup

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3400b1c
refactor: drop the external-memory seed from the doubling module

BenjaminDEMAILLE
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5101601
perf: stop materialising the seed key array, and narrow the group bounds

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94921f6
bench: add an ACGT-start filter to the benchmark CLI

BenjaminDEMAILLE
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b53d097
feat: make the dense-subset full-SA path an explicit byte budget

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claude
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f823bee
feat: `lcp_array`, deriving the LCP array from the suffix array in O(n)

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04ae2e2
fix: keep the signed-symbol guard covered on the surviving path

BenjaminDEMAILLE
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252b0aa

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Review fixes: signed-u8 guard, dense-subset byte budget, and lcp_array - #8

Review fixes: signed-u8 guard, dense-subset byte budget, and lcp_array#8
BenjaminDEMAILLE wants to merge 20 commits into
COMBINE-lab:mainfrom
BenjaminDEMAILLE:fix/rob-review

Commits on Aug 13, 2026

feat: radix-seeded prefix doubling for the plain in-memory SA

feat: `verify_sa`, an O(n) independent suffix-array check

perf: parallelise grouping and rank publication in the doubling path

bench: add a reproducible chr21 harness

docs: document the fast path, and correct two stale claims

perf: replace the seed comparison sort with an MSD counting sort

feat: extend the doubling path to subsets and to in-memory sample sort

docs: refresh the fast-path numbers and coverage

perf: rank the alphabet before packing keys

docs: record the alphabet-ranking result

perf: pack keys with a SWAR gather over a pre-ranked text

docs: refresh in-memory numbers after the SWAR key packing

perf: drop the per-group allocation and prepass from doubling rounds

docs: refresh in-memory numbers after the doubling-round cleanup

refactor: drop the external-memory seed from the doubling module

perf: stop materialising the seed key array, and narrow the group bounds

bench: add an ACGT-start filter to the benchmark CLI

feat: make the dense-subset full-SA path an explicit byte budget

feat: `lcp_array`, deriving the LCP array from the suffix array in O(n)

fix: keep the signed-symbol guard covered on the surviving path