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‎CHANGELOG.md‎

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## Changes since v4.1.14 (2026-03-08)
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### bug
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- Fix MM tag ambiguity codes not being recognized
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([#5529](https://github.com/GMOD/jbrowse-components/pull/5529)) @cmdcolin
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- Fix when using refname aliases for chromosome names in displayedRegions list
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([#5522](https://github.com/GMOD/jbrowse-components/pull/5522)) @cmdcolin
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- Fix arc tracks with custom jexl crashing
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([#5513](https://github.com/GMOD/jbrowse-components/pull/5513)) @cmdcolin
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- Fix alignments tracks not being able to vertically scroll since v4.1.4
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([#5512](https://github.com/GMOD/jbrowse-components/pull/5512)) @cmdcolin
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- Fix HTTP 416 errors by replacing http-range-fetcher with simpler fetcher
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([#5505](https://github.com/GMOD/jbrowse-components/pull/5505)) @cmdcolin
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### enhancement
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- Update dependencies
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([#5527](https://github.com/GMOD/jbrowse-components/pull/5527)) @cmdcolin
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- Add debounce to hierarchical search text field
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([#5517](https://github.com/GMOD/jbrowse-components/pull/5517)) @cmdcolin
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- Use Element setHTML if available
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([#5507](https://github.com/GMOD/jbrowse-components/pull/5507)) @cmdcolin
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## Changes since v4.1.13 (2026-02-20)
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### bug

‎SECURITY.md‎

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# Security Policy
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## Reporting a Vulnerability
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Please email [jbrowse2@berkeley.edu](mailto:jbrowse2@berkeley.edu) with a
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description of the vulnerability and steps to reproduce it.

‎agent-docs/OTHER_IDEAS.md‎

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- Track Google Analytics events from users on a fine grained basis. better
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- Ensure `types.refinement` from @jbrowse/mobx-state-tree (see
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~/src/mobx-state-tree) v5.6.0 provides fallbacks when state tree fails to load
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- Map all old "renderer" concepts to new display model settings
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- Ensure all demo sessions load without error
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- Diagonalization: yeast works, grape vs peach unclear
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- Opening reference sequence track with `umd_plugin.js` gives
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`TypeError: Cannot assign to read only property 'metadata'` — need to handle
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frozen objects from extension points logging of species chosen on desktop for
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example
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- Hot module reload breaks canvas features
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- Dockview move to right side not working — non-webgl bug
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### P4.6 UI/UX Ideas (Unscoped)
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- Should not shrink size on linked read resize height
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- Add ability where resize height does actual resize
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- Resize on double-click resize handle
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- Drag entire view to resize
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- Click isoform to expand all
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- Global scrollZoom setting rather than per view
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- Rolling average line plot
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- Zarr VCF support
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- Add legend for alignments
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- Distinguish initialized concepts in linear genome view
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### P2.3 Synteny / Comparative Views
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| Bug | Notes |
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| ----------------------------------------------------- | ------------------------------------------------------------------- |
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| Hs1 vs mm39 synteny — excessively slow, causes freeze | Improved (viewport culling added) — further LOD improvements needed |
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| Zoom to full not working? | **UNCLEAR** — needs verification |
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| Don't colorize indels not working? | **UNCLEAR** — needs verification |
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| Split indels code | Refactoring task |
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| Linked dotplot and synteny view | Idea / future feature |
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| Swap axes dotplot | Idea / future feature |
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| Swap axes linear synteny view | Idea / future feature |
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### P4.2 R/ggplot2 Export System
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**Status:** Very ambitious, branch exists with initial work.
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- Design system to export session to R code generating ggplot images
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- Generic WebGL + ggplot2 system (very speculative)
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- Needs significant planning before implementation
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### P4.4 Automatic Noisiness Scaling for Feature Frequency Thresholds
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Compute a per-track noise estimate (e.g., mean insertion rate across sampled
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positions) during coverage computation and use it to automatically scale the
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`featureFrequencyThreshold` curve. Noisy long-read tracks (PacBio CLR) would get
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stricter thresholds while clean short-read tracks stay unchanged. The data is
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already available in `computePositionFrequencies`; main work is threading the
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stat through the RPC boundary and choosing a good baseline expected noise rate.
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### P4.5 Option to Disable Sub-Pixel Feature Fade
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Add a per-track option to disable the sub-pixel alpha fade that hides
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low-frequency features when zoomed out. High-quality reads (e.g., Illumina,
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PacBio HiFi) have very few sequencing errors, so most mismatches and insertions
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are real variants that users may want to see at all zoom levels regardless of
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frequency. When enabled, features would render at full opacity whenever they are
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present, bypassing both the zoom-based alpha and the frequency-based importance
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scaling.

‎agent-docs/PRD.md‎

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# JBrowse 2 WebGL/WebGPU Migration — Project Requirements Document
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**Branch:** `webgl-poc` **Last updated:** 2026-03-17 **Status:** Active
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development — many features working, significant polish and testing needed
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> **Note:** When items are completed, move them to `COMPLETED.md`.
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---
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## Executive Summary
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JBrowse 2 is being migrated from its block-based HTML canvas rendering to a
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unified GPU-accelerated rendering pipeline supporting three backends:
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**WebGPU**, **WebGL 2.0**, and **HTML5 Canvas** (fallback + SVG export). The
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branch has working implementations for most track types with known bugs and gaps
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documented below.
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---
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## Priority 1 — Critical / Blocking
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These issues block production readiness or affect the majority of users.
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### P1.3 Expand Browser Test Suite
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**Requirements:**
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- WebGPU does not work on CI action runners — tests must work with WebGL and
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Canvas fallback
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### P1.4 Demo Session Loading
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- Many shared session links fail to load or load with incorrect settings. This
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is the primary way users encounter the app.
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### Extra ideas
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Make curvy breakpoint split view lines in the alignments track for link
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paired/supp reads
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- Idea: The 'Link supplementary alignments has the concept of connecting reads
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using a single line. But, we have logic in breakpoint split view for properly
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linking the ORIENTATION of the reads using curved lines. evaluate whether we
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can do this in the Linked paired end/supplementary reads mode in the normal
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alignments track. If might be a separate mode from Link supplementary reads,
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like "Link paired/supp reads with curved lines"
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## Priority 4 — Low / Future Enhancements
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### P4.3 Loading old configs
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- Ensure all old renderer configuration settings e.g. PileupRenderer (which were
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all effectively removed) are mapped to new display model settings (e.g. to
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LinearAlignmentsDisplay)
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## Architecture Notes
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### Current Rendering Backends
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```
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┌─────────────────────────────────────────────┐
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│ Track Display Model │
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│ (prepares data, layout) │
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└──────────────┬──────────────────────────────┘
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│
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┌──────────┴──────────┐
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▼ ▼
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┌────────┐ ┌────────┐ ┌────────────┐
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│ WebGPU │ │WebGL2 │ │ Canvas 2D │ ← COMPLETE (all track types)
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│ (WGSL) │ │(GLSL) │ │ (fallback) │
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└────────┘ └────────┘ └────────────┘
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│
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┌────┴────┐
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▼ ▼
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┌────────┐ ┌───────┐
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│ Screen │ │ SVG │ (via SvgCanvas.ts)
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└────────┘ │Export │
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└───────┘
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```
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### Backend Selection
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- `?gpu=webgpu` — force WebGPU
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- `?gpu=webgl` — force WebGL2
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- `?gpu=off` — disable GPU (uses Canvas 2D fallback)
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- Default: auto-detect (WebGPU → WebGL2 → Canvas 2D)
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### Test Infrastructure
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- Puppeteer-based browser tests in `products/jbrowse-web/browser-tests/`
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- **21 test suites** with **~120 test cases** covering: alignments, bigwig,
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variants, synteny, dotplot, HiC, canvas2d-fallback (8 tests: features,
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multi-track, zoom, alignments+coverage, SNP coverage, arcs, sequence, wiggle),
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canvas2d-variants, rendering-backends (16 tests: VCF, GFF3, wiggle, BAM/CRAM
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pileup, SNP coverage, multi-wiggle, SV, JEXL, sequence, alignments+coverage,
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arcs, synteny LGV, synteny linear, dotplot), color-by-tag, wiggle-color,
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workspaces, session-spec, demo-inventory, svg-export, authentication,
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main-thread-rpc, custom-url, redraw, basic-lgv, misc
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- Screenshot comparison via pixelmatch (threshold 0.1)
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- Backend-specific golden snapshots in `__snapshots__/{webgl,webgpu,canvas2d}/`
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- `--backend=webgl|webgpu|canvas2d` flag, `--filter=` for running subsets
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- `compare-backends.ts` for cross-backend visual regression (categories:
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identical, similar <5%, different ≥5%)
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- Unit tests co-located with source (`*.test.ts`) using Jest with jsdom — **157
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tests across 15 suites** in modified plugins
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- Canvas 2D renderer unit tests use mock canvas context pattern (20 tests
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including picking)
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- Density-based feature limit unit tests (7 tests covering all threshold
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scenarios)
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- Strand swap coordinate tests (4 tests covering all strand×reversed
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combinations)
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- `copyView.renameIds()` unit tests (8 tests verifying ID uniqueness)
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- Fetch autorun tests include error recovery via `reload()` flow
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- Interbase indicator tests (7 tests for `computeNoncovCoverage` threshold
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logic, depth boundaries, dominant type selection)
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- Interbase frequency tests (6 tests for `computePositionFrequencies`
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edge/cliff/offset cases)
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- Depth-dependent threshold tests (2 tests for `applyDepthDependentThreshold`
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interbase mode)
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- `featureFrequencyThreshold` tests (5 tests covering step boundaries,
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interpolation, monotonicity)
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- Floating label regression test verifying description data stability across
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zoom levels
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- Browser test runner forwards `[alignments]` and `[webgl-wiggle]` console logs
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for debugging
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## Next Steps
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### Cross-Backend Testing
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1. **Cross-backend visual regression**: Use `compare-backends.ts` to flag
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rendering differences between WebGL and Canvas2D for each track type

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