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eee9b7e
build(svar2): dev-wire svar2-codec path-dep + genoray svar-2 wheel (M6b)
d-laub Jul 3, 2026
2226d2e
feat(svar2): per-hap var_key⋈dense merge + key decode source (gvl M6b)
d-laub Jul 3, 2026
9241ffe
feat(svar2): two-source reconstruct driver via closure source (gvl M6b)
d-laub Jul 3, 2026
26c3fae
feat(svar2): two-source track realign driver (gvl M6b)
d-laub Jul 3, 2026
4af5ac0
feat(svar2): PyO3 fused wrappers for two-source reconstruct/realign (…
d-laub Jul 3, 2026
ed00d48
feat(svar2): additive Python SVAR2 reconstruction adapter (gvl M6b)
d-laub Jul 3, 2026
7fe7a1a
test(svar2): e2e two-source reconstruction vs genoray decode oracle (…
d-laub Jul 3, 2026
bead2cd
docs: spec for SVAR2 gvl MVP validate-and-benchmark session
d-laub Jul 3, 2026
cc085c3
docs: implementation plan for SVAR2 gvl MVP validate+benchmark
d-laub Jul 3, 2026
b4c040c
test: e2e SVAR2 realign_tracks vs SVAR1 pure-Python oracle
d-laub Jul 3, 2026
adf38f3
chore: SVAR2 MVP real-data validation scripts + notes
d-laub Jul 4, 2026
7a572b8
chore: SVAR2 vs SVAR1 gvl benchmark script + results
d-laub Jul 4, 2026
adfc87c
docs: temper SVAR2 benchmark latency claims; record layout + profilin…
d-laub Jul 4, 2026
495b193
docs: SVAR2 profiling follow-up spec (query latency attribution + bui…
d-laub Jul 4, 2026
11c3963
docs: SVAR2 profiling follow-up implementation plan (E1-E4)
d-laub Jul 4, 2026
e587e2c
chore: py-spy folded-stack Python/native self-time splitter
d-laub Jul 4, 2026
3f0ef43
chore: SVAR2 profiling Task 0 — env baseline, symbolized builds, note…
d-laub Jul 4, 2026
f821982
chore: E2 somatic sample-sweep subsample+build sbatch chain (controll…
d-laub Jul 4, 2026
e41ec71
chore: E1 single-path profiling driver for SVAR1/SVAR2 hap query
d-laub Jul 4, 2026
595b952
docs: SVAR2 Dataset wiring design spec (cache overlap results like SV…
d-laub Jul 4, 2026
c7266d6
chore: E1 perf attribution tooling (perf-only DSO split) + park profi…
d-laub Jul 4, 2026
03961eb
docs: fold perf-only/ptrace + compute-reality findings into parked pr…
d-laub Jul 4, 2026
a527fe1
docs: SVAR2 gvl read-bound dataset wiring design spec
d-laub Jul 4, 2026
0b7c6b6
feat(dataset): Svar2Link resolution/fingerprint + Metadata.svar2_link
d-laub Jul 5, 2026
40c5e34
feat(write): _write_from_svar2 6-array ranges cache + dispatch
d-laub Jul 5, 2026
ccad4ee
test(write): lock svar2 cache contents + same-POS tie max_ends parity
d-laub Jul 5, 2026
6397ecf
docs: note latent SVAR1 max_ends same-POS-tie under-extension bug
d-laub Jul 5, 2026
503d245
feat(rust): link genoray_core (query-only) + Svar2Store pyclass
d-laub Jul 5, 2026
c7998a6
feat(svar2): read-bound haplotype kernel (one all-Rust FFI call)
d-laub Jul 5, 2026
1dbfac0
fix(svar2): byte-size split_to_flat presence buffer; cover dense_snp …
d-laub Jul 5, 2026
161d2e7
feat(rust): read-bound svar2 track re-alignment kernel
d-laub Jul 5, 2026
d17c769
feat(rust): read-bound svar2 variants/variant-windows decode
d-laub Jul 5, 2026
b186d23
feat(rust): read-bound svar2 per-hap diffs FFI (for jitter shift comp…
d-laub Jul 6, 2026
2db8f49
feat(dataset): Svar2Haps reconstructor + svar2 read dispatch (haploty…
d-laub Jul 6, 2026
f7423d8
fix(dataset): svar2 min_af/max_af guard + variants jitter guard + cov…
d-laub Jul 6, 2026
0f5b791
feat(dataset): svar2 haplotype-realigned tracks via HapsTracks
d-laub Jul 6, 2026
9bacdac
fix(dataset): guard svar2 FlankSample multi-contig + annotated tracks
d-laub Jul 6, 2026
eb4a783
refactor(dataset): retire svar2 live overlap_batch dispatch (oracle-o…
d-laub Jul 6, 2026
b5bceb7
docs: .svar2 as a write variant source + read-bound wiring (skill, fo…
d-laub Jul 6, 2026
bbc7739
docs(roadmap): SVAR2 read-bound benchmark results (perf DSO split + s…
d-laub Jul 6, 2026
60bdd4b
chore(pre-commit): auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 6, 2026
5989b23
docs(spec): profile & optimize svar2 read-bound Dataset.__getitem__ path
d-laub Jul 6, 2026
074c7e8
docs(plan): svar2 read-bound getitem profiling & optimization (haplot…
d-laub Jul 6, 2026
b943607
docs(plan,spec): parallelize cargo asm phase — subagent per hot fn + …
d-laub Jul 6, 2026
676c525
perf(svar2): live read-bound Dataset.__getitem__ profiling driver + p…
d-laub Jul 6, 2026
9ccc46b
perf(svar2): Python-layer baseline profile (cProfile + pyinstrument)
d-laub Jul 6, 2026
1e28077
perf(svar2): native-layer baseline profile (perf DSO/symbol/callgraph…
d-laub Jul 6, 2026
914a8b9
perf(svar2): skip redundant pre-reconstruct gather for deterministic …
d-laub Jul 6, 2026
ee9c219
perf(svar2): pre-size split_to_flat + decode_variants_from_split allo…
d-laub Jul 6, 2026
cc4ee6e
perf(svar2): compute the pos/ilen ragged reorder index once in varian…
d-laub Jul 6, 2026
fa7ca9a
perf(svar2): re-profile native layer after B1-B3; enumerate cargo-asm…
d-laub Jul 6, 2026
9887390
perf(svar2): decode_variants_from_split asm fix — hoist q=h/ploidy di…
d-laub Jul 6, 2026
7685723
perf(svar2): debug_assert guard for decode_variants_from_split get_un…
d-laub Jul 6, 2026
3a92ec7
perf(svar2): split_to_flat asm fix — hoist q=h/ploidy division out of…
d-laub Jul 6, 2026
e4a37c9
perf(svar2): read-bound getitem optimization results summary
d-laub Jul 6, 2026
5a2283f
docs(svar2): correct stale/imprecise comments in split_to_flat + get_…
d-laub Jul 6, 2026
fb29166
chore(pre-commit): auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 6, 2026
ab868cf
fix(write): copy variant index across filesystems on EXDEV
d-laub Jul 6, 2026
e3c26b4
test(build): adopt vcfixture 0.6 API; fix env LD_LIBRARY_PATH on linux
d-laub Jul 6, 2026
63b8b87
perf(svar2): skip identity row-reorder for single-contig getitem
d-laub Jul 6, 2026
b84a57d
perf(svar2): fuse variant decode, stream-merge from gather
d-laub Jul 6, 2026
a5ee2a3
docs(spec): variant-windows mode for svar2-backed gvl
d-laub Jul 6, 2026
8b71beb
docs(spec): add unphased_union to svar2 variants + variant-windows scope
d-laub Jul 6, 2026
355f91b
docs(plan): svar2 variant-windows + unphased_union implementation plan
d-laub Jul 6, 2026
75db013
feat(svar2): variant-windows read path (ref=window, alt window/allele)
d-laub Jul 6, 2026
22545bf
feat(svar2): unphased_union for variants mode (ploidy-1 fold)
d-laub Jul 7, 2026
3619202
feat(svar2): unphased_union for variant-windows (ploidy-1 fold)
d-laub Jul 7, 2026
c3df9cd
docs(svar2): variant-windows + unphased_union now supported
d-laub Jul 7, 2026
ba871b7
refactor(svar2): hoist Any import + document union guard omission
d-laub Jul 7, 2026
8561b70
refactor(svar2): adopt genoray HapRanges for gather_haps_readbound
d-laub Jul 9, 2026
26d1cac
feat!: consume reconciled genoray chunk_idxs contract (genoray 3.0)
d-laub Jul 9, 2026
8440e9a
feat!: adopt genoray 3.0.0 API (privatized SVAR2 FFI, available_sampl…
d-laub Jul 11, 2026
6893366
docs(svar2): design for routing INFO/FORMAT fields to gvl variants
d-laub Jul 13, 2026
1e9d926
docs(svar2): implementation plan for INFO/FORMAT field routing
d-laub Jul 13, 2026
823b290
chore(svar2): pin genoray main wheel, drop version constraint for dev
d-laub Jul 13, 2026
e286ed5
refactor(svar2): migrate gvl read-bound Rust to genoray Range<usize> API
d-laub Jul 13, 2026
80c4bf0
feat(svar2): Svar2Store retains store_path for field-sidecar paths
d-laub Jul 13, 2026
6a765b6
feat(svar2): field-byte gather with vk_src/dense provenance in split …
d-laub Jul 13, 2026
8ab366f
test(svar2): make field-provenance tests catch sub-stream and stride …
d-laub Jul 13, 2026
55ab671
feat(svar2): decode_variants_from_svar2_readbound returns INFO/FORMAT…
d-laub Jul 13, 2026
70dadbe
feat(svar2): discover store INFO/FORMAT fields and skip SVAR1 lazy-lo…
d-laub Jul 13, 2026
eedbe04
test(svar2): oracle test for INFO/FORMAT field routing (var_key+dense…
d-laub Jul 13, 2026
ce03789
feat(svar2): route INFO/FORMAT fields into RaggedVariants
d-laub Jul 13, 2026
e4c2721
feat(svar2): route INFO/FORMAT fields into variant-windows output
d-laub Jul 13, 2026
39136c4
fix(svar2): honor Dataset.open(var_fields=) and cover multi-contig wi…
d-laub Jul 13, 2026
729489f
docs(svar2): document INFO/FORMAT field routing in variants outputs
d-laub Jul 13, 2026
3405dc3
fix(svar2): validate open(var_fields=), size buffered output, de-dege…
d-laub Jul 13, 2026
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -184,3 +184,4 @@ tests/benchmarks/profiling/*.speedscope.json
tests/benchmarks/profiling/*.memray.bin
tests/benchmarks/profiling/*.flamegraph.html
tests/benchmarks/profiling/*.perf.data
tmp/svar2_mvp/prof_out/
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