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4dab984
fix(breakpoint-split-view): fix BND pairing key and consolidate after…
cmdcolin Apr 24, 2026
c73746e
refactor(synteny): drop synthesized query-name fallbacks, note shared…
cmdcolin Apr 24, 2026
b01aafe
fix(synteny): fix SyRI DUP mis-classification and improve plotsr visu…
cmdcolin Apr 24, 2026
5a80e39
refactor(synteny): clean up syri types and simplify model code
cmdcolin Apr 24, 2026
419eeca
fix(synteny): fix stale color descriptions and remove false syri.out …
cmdcolin Apr 24, 2026
54d7903
refactor(synteny, dotplot): coalesce RPC setters, dedup uploads, debo…
cmdcolin Apr 24, 2026
bee976f
fix(synteny, dotplot): guard stale RPC side effects + drop dotplot fe…
cmdcolin Apr 24, 2026
527d110
docs(todo): note dotplot RPC consolidation; merge trailing sections
cmdcolin Apr 24, 2026
ded502e
refactor(breakpoint-split-view): remove redundant alreadySeen sets an…
cmdcolin Apr 24, 2026
0a807b4
refactor(breakpoint-split-view): generalize SVG export to N views, mi…
cmdcolin Apr 24, 2026
68ecaec
docs(breakpoint-split-view): explain sibling-overlay architecture and…
cmdcolin Apr 24, 2026
fcf5de9
refactor(circular-view): simplify types, remove redundant code, fix i…
cmdcolin Apr 24, 2026
b5f3daf
fix(breakpoint-split-view): type safety, nonsense fallback, misleadin…
cmdcolin Apr 24, 2026
d7441e2
refactor(circular-view): remove dead code and consolidate redundant a…
cmdcolin Apr 24, 2026
cb0f3a0
Misc
cmdcolin Apr 24, 2026
caa06a8
fix(mui-v9): update deprecated Typography color shorthands and InputB…
cmdcolin Apr 24, 2026
451fdd0
refactor(dotplot-view): fix infinite loading overlay, delete dead can…
cmdcolin Apr 24, 2026
f2b0a01
refactor(dotplot-view): delete more dead code, fix geometry copy over…
cmdcolin Apr 24, 2026
e352a5b
SAMplot mode
cmdcolin Apr 24, 2026
9978813
Use tsgo
cmdcolin Apr 24, 2026
2445749
fix(variants): defer cluster tree display until cell data reloads wit…
cmdcolin Apr 24, 2026
afdb5a0
docs: wiggle featurePositions are already absolute uint32, remove sta…
cmdcolin Apr 24, 2026
c3cfeb7
Results
cmdcolin Apr 24, 2026
384243f
hierarchy.ts
cmdcolin Apr 24, 2026
e96b810
Start of synteny refactor
cmdcolin Apr 24, 2026
aaa0902
Fix tree sidebar
cmdcolin Apr 24, 2026
2ee39fe
Fix lints
cmdcolin Apr 24, 2026
593d270
Fix some lint
cmdcolin Apr 24, 2026
7c6cdaf
Lint
cmdcolin Apr 24, 2026
f754855
refactor(synteny): extract bp projection helpers, drop straddler feat…
cmdcolin Apr 25, 2026
4b01f36
Refactor tree-sidebar: typed mixin host, iterative leaf walk, SVG pat…
cmdcolin Apr 25, 2026
33ff790
Add PositionedHierarchyNode type, remove ! assertions on x/y coordinates
cmdcolin Apr 25, 2026
328aaa1
refactor(dotplot): port to bp coordinates, mirroring synteny
cmdcolin Apr 25, 2026
02e05f1
Revert "refactor(dotplot): port to bp coordinates, mirroring synteny"
cmdcolin Apr 25, 2026
b9e2ff6
Revert synteny bp+regionIdx refactor (Phase 2+3)
cmdcolin Apr 25, 2026
0b3684e
Remove dead syntenyProjection.ts (only used by its own test)
cmdcolin Apr 25, 2026
eaeba22
Add ADR-010: synteny/dotplot keep pre-projected pixel offsets
cmdcolin Apr 25, 2026
cac4ba8
Clean up stale docs after synteny bp+regionIdx revert
cmdcolin Apr 25, 2026
4d0ecb5
Resizehandle
cmdcolin Apr 25, 2026
0e5b207
Fix stale TODO filename ref (executeSyntenyInstanceData -> executeSyn…
cmdcolin Apr 25, 2026
2c266c5
Fix drawRef culling to check both edges, remove useEffect from settin…
cmdcolin Apr 25, 2026
41963a1
Extract shared utilities from Canvas2D/GPU alignments renderers
cmdcolin Apr 25, 2026
bed12af
Refactor alignments arcs, simplify RPC builders, drop hp-math from JS
cmdcolin Apr 25, 2026
d81d268
Format
cmdcolin Apr 25, 2026
393e6d9
Reduce claude.md wordiness
cmdcolin Apr 25, 2026
1a32b10
Refactor HiC plugin: shared region offsets, inline rotation, fix colo…
cmdcolin Apr 25, 2026
22d96f6
Refactor LD display: inline rotation, share mapLDValue, drop useCallback
cmdcolin Apr 25, 2026
221610b
Clarify untracked() semantics, fix comments, remove redundant bpPerPx…
cmdcolin Apr 25, 2026
7922626
Precompute LD color ramps, drop dead param, remove useCallback from h…
cmdcolin Apr 25, 2026
50869b5
Use void for MobX tracking reads, trim fetchSignal comment
cmdcolin Apr 25, 2026
cc27b3c
Remove dead fallbacks and precompute HiC color ramps
cmdcolin Apr 25, 2026
465aed4
Sync tests with production code, add CLAUDE.md for fetch system
cmdcolin Apr 25, 2026
60defed
Improve HiC rendering: percentile color scaling, fix bugs, type safety
cmdcolin Apr 25, 2026
fb941dd
Rename fetch system variables for clarity across BaseLinearDisplay
cmdcolin Apr 25, 2026
fd07fd4
Fix colormax for log scale too
cmdcolin Apr 25, 2026
5defc9a
Finish maxScore→colorMaxScore rename in HiC plugin
cmdcolin Apr 25, 2026
38d3232
Remove duplicate setSelection in selectFeature
cmdcolin Apr 25, 2026
f8d5e78
Cache featureId/subfeatureId lookups in canvas baseModel
cmdcolin Apr 25, 2026
4c1821f
Dedupe pct helper into alignmentComponentUtils
cmdcolin Apr 25, 2026
a8298de
Drop unused exports from colorUtils
cmdcolin Apr 25, 2026
d1b3f5f
Gate canvas hit-detection label extents on showLabels
cmdcolin Apr 25, 2026
548b317
Extract pileupRowY helper for Canvas2D row→Y formula
cmdcolin Apr 25, 2026
a2f9f27
Unify canvas label width helpers; fix description showLabels gate
cmdcolin Apr 25, 2026
8e3c2c4
Move pendingFileHandleIds into MST session volatile; add FileHandleRe…
cmdcolin Apr 25, 2026
908c359
Widen Canvas2D draw ctx to CanvasLike, extract renderBlocksToCtx
cmdcolin Apr 25, 2026
1a34b7f
SvgCanvas: implement real clip() via <clipPath> + <g clip-path>
cmdcolin Apr 25, 2026
75cb674
Allow Canvas2DAlignmentsRenderer to be constructed without a canvas
cmdcolin Apr 25, 2026
1a2fd90
Revert "Allow Canvas2DAlignmentsRenderer to be constructed without a …
cmdcolin Apr 25, 2026
5697d40
Reapply "Allow Canvas2DAlignmentsRenderer to be constructed without a…
cmdcolin Apr 25, 2026
88a02fc
Document Canvas2DAlignmentsRenderer's bound vs. headless construction…
cmdcolin Apr 25, 2026
8e48721
Lift alignments draw pipeline to a top-level pure function
cmdcolin Apr 25, 2026
1ef83ff
Reversed regions concept
cmdcolin Apr 25, 2026
e7076d3
Use CSS Highlight API for genome search result highlighting
cmdcolin Apr 25, 2026
b7e090f
Unify SVG export draw paths through Canvas2D renderers
cmdcolin Apr 25, 2026
1cd4f1a
Unify SVG export draw paths in canvas + variants plugins
cmdcolin Apr 25, 2026
d0a2a9e
Use shared Ctx2D type from core instead of local Ctx aliases
cmdcolin Apr 25, 2026
6a92a8a
Tidy alignments: SimpleFeature for featureUnderMouse, runHitTest help…
cmdcolin Apr 25, 2026
bd257a9
Unify sashimi arc math between on-screen overlay and SVG export
cmdcolin Apr 25, 2026
0c4eeac
Document SVG export pipeline + sashimi-shared-math in agent-docs
cmdcolin Apr 25, 2026
d6b6f58
Precompute pxPerBp as uniform; arc color LUT; clip simplification
cmdcolin Apr 25, 2026
0fbf149
Fix drawArcsPass leaving stale UBO state for subsequent pileup draws
cmdcolin Apr 25, 2026
f0fb251
Extract visitCigarRenderedSegments to alignments-core; clean up synte…
cmdcolin Apr 25, 2026
990efa1
Apply save/restore UBO pattern to renderFeatureOverlays highlight draw
cmdcolin Apr 25, 2026
4c92375
LDDisplay cleanup: fix uniform-mode guard, drop typed-array copy, naming
cmdcolin Apr 25, 2026
670cb33
Add ExportSvgDisplayTypes tests for wiggle, canvas, and alignments SV…
cmdcolin Apr 25, 2026
f788c49
Done in this round
cmdcolin Apr 25, 2026
66fdb30
Lint and format
cmdcolin Apr 25, 2026
0df1af3
Merge origin/webgl-poc
cmdcolin Apr 25, 2026
910ffac
Ternary
cmdcolin Apr 25, 2026
fcadae5
Fix test failures and suppress expected console.error noise
cmdcolin Apr 26, 2026
b855a98
Disable SNP/CIGAR hit testing beyond ~50kbp zoom level
cmdcolin Apr 26, 2026
bc93cd0
Update todos
cmdcolin Apr 26, 2026
a0c5995
Reduce per-frame work during scroll-zoom
cmdcolin Apr 26, 2026
8398946
Combined wheelstate
cmdcolin Apr 26, 2026
5f5ae58
Dialog usability and copy improvements
cmdcolin Apr 26, 2026
58d3cbc
More dialog fixes; add SubmitDialog wrapper
cmdcolin Apr 26, 2026
45f63c1
Fix MultiWiggle add-track widget mixed-input handling
cmdcolin Apr 26, 2026
6d9d2d3
Third-pass dialog fixes
cmdcolin Apr 26, 2026
ba357ae
MultiWiggle add-track widget: validate submit, reset file input
cmdcolin Apr 26, 2026
cfd509a
Add PluggableComponent helper and use it for widget/about extension p…
cmdcolin Apr 26, 2026
17fd766
Add core BaseExportSvgDialog; consolidate 5 plugin variants
cmdcolin Apr 26, 2026
0c224fc
Fix SetMinMax wording bug in variants; fix ColorByTag misnested actions
cmdcolin Apr 26, 2026
707fb71
Consolidate CollapseIntronsDialog: delete canvas copy, use LGV's
cmdcolin Apr 26, 2026
9fd9991
Use deep imports for CollapseIntronsDialog instead of barrel re-export
cmdcolin Apr 26, 2026
4757891
Move CollapseIntronsDialog into canvas plugin, remove from BaseLinear…
cmdcolin Apr 26, 2026
278813d
Dedupe exon/CDS predicate, add coverage for getTranscripts and featur…
cmdcolin Apr 26, 2026
0cc8b8e
Refactor and harden RPC layer; add RpcClient/RpcServer tests
cmdcolin Apr 26, 2026
84e2a86
Fix tsc errors in RpcClient/RpcServer tests
cmdcolin Apr 26, 2026
d952c7f
Make RpcServer.handler public for test access
cmdcolin Apr 26, 2026
6924407
Fix BedpeImport score type bug; remove any casts and early returns in…
cmdcolin Apr 26, 2026
3098fdd
Use unknown instead of object
cmdcolin Apr 26, 2026
ee37ef2
Changes made:
cmdcolin Apr 26, 2026
c982320
Fix build with error cause
cmdcolin Apr 26, 2026
4d6ca73
Lint
cmdcolin Apr 26, 2026
7e2908d
Optimize synteny RPC: split worker output, drop dead drawRef, precull…
cmdcolin Apr 26, 2026
ad647d4
Pack synteny mates as parallel arrays; bp coords as Uint32
cmdcolin Apr 26, 2026
2b0f82f
Synteny cleanup: remove dead code, hoist constants, simplify hot loop
cmdcolin Apr 26, 2026
fce1a22
Optimize and type-harden variant cell computation
cmdcolin Apr 26, 2026
fa96281
Optimize matrix cells and replace FlatbushItem object array with type…
cmdcolin Apr 26, 2026
230d0e5
Remove globalAlpha usage
cmdcolin Apr 26, 2026
bb0fb1f
Minor optimizations: singleton ABGR cache, Int32Array sampleIndices, …
cmdcolin Apr 26, 2026
aa453ac
HierarchicalTrackSelectorWidget: simplifications and minor fixes
cmdcolin Apr 26, 2026
5c1561a
FacetedSelector: use CSS Highlight API, fix facet bugs, simplify
cmdcolin Apr 26, 2026
1300374
jbrowse-img: refactor, bug fixes, and tests
cmdcolin Apr 26, 2026
8592349
jbrowse-img: fix README stdout claim, auto-gen epilogue, validate --t…
cmdcolin Apr 26, 2026
360f81b
HierarchicalTrackSelector: apply CSS Highlight API for search text
cmdcolin Apr 26, 2026
0b6c827
Fix lint
cmdcolin Apr 26, 2026
97d907f
dotplot: port synteny optimizations, add executor tests, add SYNC com…
cmdcolin Apr 26, 2026
3c7667f
sv-core: type safety, deduplication, and defensive error handling
cmdcolin Apr 26, 2026
5128182
breakpoint-split-view/alignments: fix SA parsing, remove dead code
cmdcolin Apr 26, 2026
3bcd8db
linear-genome-view: add scalebarOnly mode; linear-comparative-view: c…
cmdcolin Apr 26, 2026
1c19084
ReExports: deduplicate makeStyles shim, remove stale comment
cmdcolin Apr 26, 2026
b837c9d
core: simplify and fix PluginManager, PluginLoader, PhasedScheduler
cmdcolin Apr 26, 2026
dec00e2
core: tighten types in PhasedScheduler and PluginManager
cmdcolin Apr 26, 2026
ec6f1cf
jbrowse-desktop: bug fixes, dead code removal, OpenSequenceDialog ref…
cmdcolin Apr 26, 2026
847bb67
jbrowse-desktop: add tests for OpenSequenceDialogModel
cmdcolin Apr 26, 2026
d5a2eac
app-core/web-core/product-core: bug fixes, dead code removal, type cl…
cmdcolin Apr 26, 2026
f7c5581
jbrowse-cli: refactor add-assembly utils for type safety and clarity
cmdcolin Apr 26, 2026
fef2acb
app-core/core: fix tsc errors for makeStyles params and useWorkspaces…
cmdcolin Apr 26, 2026
bff4c12
jbrowse-cli: refactor remaining commands for type safety and simplifi…
cmdcolin Apr 26, 2026
c722a15
jbrowse-desktop: electron cleanup, fix missing reset IPC handler
cmdcolin Apr 26, 2026
c5f1122
web-core: type BaseWebSession.root via WebRootModelInterface
cmdcolin Apr 26, 2026
de7ecdf
app-core: consolidate Menu and AppSession types, remove duplicate def…
cmdcolin Apr 26, 2026
5a89117
jbrowse-cli: tighten SequenceType union and remove remaining any casts
cmdcolin Apr 26, 2026
e01f753
app-core: replace ViewMenu inline session cast with named ViewMenuSes…
cmdcolin Apr 26, 2026
382be43
Update
cmdcolin Apr 26, 2026
f06eada
jbrowse-desktop: remove unnecessary MST destroy and useEffect from Op…
cmdcolin Apr 26, 2026
c071610
jbrowse-desktop: inline AssemblyConf type and drop unnecessary async …
cmdcolin Apr 26, 2026
84e6e42
jbrowse-desktop: handle onClose errors in OpenSequencePanel instead o…
cmdcolin Apr 26, 2026
968e87a
jbrowse-desktop: revert panel error handling, dialog already surfaces…
cmdcolin Apr 26, 2026
5950e33
plugins/variants: performance optimizations in rendering hot paths
cmdcolin Apr 26, 2026
9b11e12
jbrowse-desktop: replace MST OpenSequenceDialog model with plain Reac…
cmdcolin Apr 26, 2026
8b4e64a
jbrowse-web: simplifications and || to ?? fixes
cmdcolin Apr 26, 2026
1bb4aba
plugins/variants: eliminate ref-count loop and redundant fillStyle sets
cmdcolin Apr 26, 2026
08a94ff
jbrowse-desktop: extract AssemblyConf type to util.ts, move assemblyC…
cmdcolin Apr 26, 2026
8f1c436
jbrowse-desktop: extract AssemblyConf type to util.ts, move assemblyC…
cmdcolin Apr 26, 2026
52e85c7
alignments: flatten ArcsSubModel and SashimiArcsSubModel into display…
cmdcolin Apr 26, 2026
117ad9c
plugins/variants: transfer flatbush buffers zero-copy and cache ABGR→…
cmdcolin Apr 26, 2026
74703f2
plugins/variants: remove premature caches
cmdcolin Apr 26, 2026
95ff676
alignments: tighten ArcColorByType usage and fix preexisting lint errors
cmdcolin Apr 26, 2026
4ef0bcc
plugins/variants: replace per-cell string arrays with compact indexed…
cmdcolin Apr 26, 2026
8bf9a57
plugins/variants: inline cellHitInfo, use non-null assertions
cmdcolin Apr 26, 2026
b871dbe
alignments: move ArcColorByType to shared/types, rename arcColorByTyp…
cmdcolin Apr 26, 2026
bd54483
[skip ci] repo-wide: apply prefer-nullish-coalescing lint rule
cmdcolin Apr 26, 2026
ed915d3
wheel: fix zoomDivisor last-wins coalescing bug, add tests
cmdcolin Apr 27, 2026
30f610a
alignments/canvas/lgv: several refactors and fixes
cmdcolin Apr 27, 2026
405a266
alignments: extract chain metadata + paired insert size, drop redunda…
cmdcolin Apr 27, 2026
d600778
variants: migrate to standard fetchRegions pipeline, unify with other…
cmdcolin Apr 27, 2026
d486c35
variants: derive hasPhased / sampleInfo / featuresVolatile from cellData
cmdcolin Apr 27, 2026
ca0fe7a
Fix vertical scroll
cmdcolin Apr 27, 2026
c334499
Fix test errors
cmdcolin Apr 27, 2026
d682a00
stats: fix featureCount optionality, remove unsafe casts, tighten types
cmdcolin Apr 27, 2026
79b0b9a
canvas renderSvg test: wrap in <svg> for correct React namespace, des…
cmdcolin Apr 27, 2026
8f9d381
types: remove unnecessary casts in comparative-adapters and variants
cmdcolin Apr 27, 2026
78cbc92
lgv: guard keyboardHandler against Node.js environments
cmdcolin Apr 27, 2026
6b8a3d8
types: remove unnecessary casts in packages/core
cmdcolin Apr 27, 2026
0917cc5
types: replace Object.assign in BaseBlock with explicit typed constru…
cmdcolin Apr 27, 2026
b86617c
canvas: derive regionTooLarge to fix banner flicker on small zoom
cmdcolin Apr 27, 2026
6ef6828
Type improvements
cmdcolin Apr 27, 2026
15eeb8d
docs: describe imperative vs. derived regionTooLarge in ARCHITECTURE
cmdcolin Apr 27, 2026
f1a138d
Merge origin/main
cmdcolin Apr 27, 2026
ae268f1
Update @jbrowse/core exports
cmdcolin Apr 27, 2026
d683ab4
Actions-up
cmdcolin Apr 27, 2026
9dc62d2
Cleanup and bug fixes in plugins/bed
cmdcolin Apr 28, 2026
268318d
Cleanup and bug fixes in plugins/dotplot-view
cmdcolin Apr 28, 2026
b9e2b78
Cleanup and bug fixes in plugins/data-management
cmdcolin Apr 28, 2026
df162c2
Remove manual memo/useCallback/useMemo in data-management; React Comp…
cmdcolin Apr 28, 2026
fdca08d
Simplify TrackLabel and TrackCategory components
cmdcolin Apr 28, 2026
5a75238
Bug fixes and cleanup in plugins/breakpoint-split-view
cmdcolin Apr 28, 2026
d9c6ce1
Simplify findMatchingAlt to use find() instead of Map
cmdcolin Apr 28, 2026
85c6fa9
Extract and fix diagonalizeRegions to packages/core
cmdcolin Apr 28, 2026
869f106
Minimize re-renders in hierarchical track list on track toggle
cmdcolin Apr 28, 2026
6a0926f
Further perf improvements in hierarchical track list
cmdcolin Apr 28, 2026
3f5658f
Update packages
cmdcolin Apr 28, 2026
dbb66ba
Fix incorrect views.length assertion in LinearSyntenyView model test
cmdcolin Apr 28, 2026
2ce3823
Add noEmit:true to root tsconfig, noEmit:false to build configs
cmdcolin Apr 28, 2026
e212cc7
Simplify ElidedBlock and fix totalBp double-filter
cmdcolin Apr 28, 2026
73f7901
Simplify and clean up plugins/arc
cmdcolin Apr 28, 2026
9f739d3
Optimize calculateStaticBlocks and calculateDynamicBlocks
cmdcolin Apr 28, 2026
29cd327
Fix pre-existing TypeScript errors across codebase
cmdcolin Apr 28, 2026
121dfc7
Convert blockTypes from class hierarchy to discriminated union
cmdcolin Apr 28, 2026
2ebb6fa
Dedupe block factory args in calculate{Static,Dynamic}Blocks
cmdcolin Apr 28, 2026
ce6c50b
Fix linked-read bezier overlay region indexing and refactor
cmdcolin Apr 28, 2026
7f47c59
Trim BlockSet API surface
cmdcolin Apr 28, 2026
b29816d
Remove dead parentRegion field, narrow variant to literal
cmdcolin Apr 28, 2026
806a3f8
Tidy block code: fuse totalBp loop, un-export BlockData, fix stale co…
cmdcolin Apr 28, 2026
04aaab4
Step 1 — Extracted shared traversal into components/computeLinkedRead…
cmdcolin Apr 28, 2026
d840095
Update exports
cmdcolin Apr 28, 2026
6efaa85
Fix linkedReadBezier mode correctness, gate linked-read line computat…
cmdcolin Apr 28, 2026
d7f782b
Modularize modifications
cmdcolin Apr 29, 2026
146db19
Finish modification feature colocation; raise shaders/ folder
cmdcolin Apr 29, 2026
1f81620
Document feature colocation plan for steps 2-5
cmdcolin Apr 29, 2026
737d719
Refactors
cmdcolin Apr 29, 2026
b6dc33b
Simplifications
cmdcolin Apr 29, 2026
c89223f
Hit-test type layering fix — Created shared/hitTestTypes.ts (CigarCoo…
cmdcolin Apr 29, 2026
bf7fe2b
sync() dead ensureRegion calls — uploadReads already populates the re…
cmdcolin Apr 29, 2026
4a7df62
Style refactors — inline styles → makeStyles, finer observer granularity
cmdcolin Apr 29, 2026
87e708f
Format
cmdcolin Apr 29, 2026
db5e31d
Bump deps
cmdcolin Apr 29, 2026
7d14808
Fix missing inter-region padding due to bpPerPx float drift
cmdcolin Apr 29, 2026
0671912
Simplify calculateStaticBlocks: block-number end checks, remove dead …
cmdcolin Apr 29, 2026
7872227
Fix infinite fetch loop in MultiVariantDisplay
cmdcolin Apr 29, 2026
ee0e6a5
Remove debug logging from MultiVariantDisplay fetch loop fix
cmdcolin Apr 29, 2026
f8af66e
Refactor variant sources: extract sourcesBase, share makeHaplotypeSou…
cmdcolin Apr 29, 2026
a0735e2
Clean up nrow: remove stale fallback to sourcesVolatile
cmdcolin Apr 29, 2026
d2bfc0f
Alignments: colocate small utilities, split alignmentComponentUtils
cmdcolin Apr 29, 2026
7fb3b15
Remove dead ReducedFeature interface from shared/types.ts
cmdcolin Apr 29, 2026
241f3db
Document sampleInfo hazard on sourcesWithoutLayout
cmdcolin Apr 29, 2026
f7fda38
Variants: clean up dead code, casts, and style issues
cmdcolin Apr 29, 2026
0a6ae5e
MultiLGVSynteny: raise shaders/ and split types into shared/
cmdcolin Apr 29, 2026
a9f08dd
MultiLGVSynteny: split coverage family into per-feature folders
cmdcolin Apr 29, 2026
84b96c1
MultiLGVSynteny: split CIGAR family into per-feature folders
cmdcolin Apr 29, 2026
8c5a815
MultiLGVSynteny: split fill feature; retire multiSyntenyGpuData.ts
cmdcolin Apr 29, 2026
f3e358d
MultiLGVSynteny: move colorUtils to shared/ and tidy imports
cmdcolin Apr 29, 2026
bbb5565
MultiLGVSynteny: align structure/naming with plugin-alignments
cmdcolin Apr 29, 2026
b7c6892
MultiLGVSynteny: standardize backend interface to match alignments
cmdcolin Apr 29, 2026
af538c6
Graph plan
cmdcolin Apr 30, 2026
54f7975
plugins/bed: tighten types and fix isBedMethylFeature edge case
cmdcolin Apr 30, 2026
af88e06
Continued refactoring
cmdcolin Apr 30, 2026
1431468
[skip ci] Update
cmdcolin Apr 30, 2026
9fcccc7
GfaTabixAdapter: cache reverse name map, partition helper, doc consol…
cmdcolin Apr 30, 2026
f5bc5dd
Snaps
cmdcolin Apr 30, 2026
85c9f74
GRAPH_PLAN: re-rank backlog post-refactor; add bubble preprocess regr…
cmdcolin Apr 30, 2026
a455253
More updates
cmdcolin Apr 30, 2026
e9c5cae
CLeanup docs
cmdcolin Apr 30, 2026
8426f52
Wow
cmdcolin May 1, 2026
2971805
agent-docs: rewrite graph plan — reference coords, tabix-only, tests
cmdcolin May 1, 2026
63adfde
agent-docs: fix timing gaps and faidx bottleneck note in graph plan
cmdcolin May 1, 2026
5e7e840
agent-docs: remove network bottleneck speculation from graph plan
cmdcolin May 1, 2026
b72c311
agent-docs: add chr20 validation gate to every phase
cmdcolin May 1, 2026
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Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
---
name: WebGL/WebGPU Migration
description:
Active migration to GPU-accelerated rendering with three backends (WebGPU,
WebGL2, Canvas 2D). Tracks progress on PRD items.
type: project
---

Branch: `webgl-poc`, PRD at repo root `/PRD.md`

## Completed (as of 2026-03-19)

- **P1.1 Canvas 2D Fallback**: All 10 track types have Canvas 2D fallback
renderers
- **P1.2 Data Fetching**: Replaced legacy `staticRegions` with viewport-based
`mergedVisibleRegions` + 50% buffer; integrated `isCacheValid()` for wiggle
resolution re-fetch; error recovery on zoom
- **P1.4 Session Migration**: Snapshot migration for old display types and
property names — `migrateWiggleSnapshot`, `migrateAlignmentsSnapshot`,
`migrateSessionSnapshot`/`migrateConfigSnapshot` (49 tests total). Wired into
session loading and config loading paths.
- **P2.1 Alignments**: Mapping quality legend, outline when compact, arc alpha
fix, linked read snapshot migration
- **P2.2 Wiggle**: Cross-hatches (displayCrossHatches toggle + SVG overlay)
- **Effective Track Config**: `effectiveTrackConfig` getter on displays bakes
session overrides into track config snapshots for "Copy config" in About track
dialog (14 tests)
- **Tests**: 63+ new tests across 5 suites

## Architecture: Config Override Pattern

Display models have `*Setting` properties (e.g., `colorSetting`) that override
config slots. Getters merge them:
`get color() { return self.colorSetting ?? getConf(self, 'color') }`. The
`effectiveTrackConfig` getter iterates config slots and compares against display
getters to produce a config snapshot with overrides baked in. Plan to simplify
this in `CONFIG_SIMPLIFICATION.md`.

## Next Priority Items

- P2.3: Hs1 vs mm39 synteny excessively slow
- P3.1: Closing track errors (getContainingView throws on detached model)
- P1.3: Expand browser test suite
- Add `effectiveTrackConfig` override to remaining display types

**Why:** These are the highest-impact remaining issues per PRD analysis. **How
to apply:** Check PRD.md for full item list and demo inventory status.
6 changes: 3 additions & 3 deletions .github/workflows/publish.yml
Original file line number Diff line number Diff line change
Expand Up @@ -13,13 +13,13 @@ jobs:
id-token: write
contents: read
steps:
- uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
with:
persist-credentials: false
- uses: pnpm/action-setup@41ff72655975bd51cab0327fa583b6e92b6d3061 # v4.2.0
- uses: pnpm/action-setup@fc06bc1257f339d1d5d8b3a19a8cae5388b55320 # v5.0.0
with:
version: 10
- uses: actions/setup-node@6044e13b5dc448c55e2357c09f80417699197238 # v6.2.0
- uses: actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
with:
node-version: '24'
cache: pnpm
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