alexsweeten · Oct 12, 2026 · Aug 29, 2026 · Aug 29, 2026 · Aug 29, 2026 · Aug 29, 2026
diff --git a/.gitignore b/.gitignore
@@ -2,7 +2,6 @@
 /node_modules/
 /web/dist/
 /web/node_modules/
-/web/public/examples/Col-CEN_v1.2.fasta
 /web/src/wasm/
 /web/playwright-report/
 /web/test-results/

diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/CITATION.cff b/CITATION.cff
@@ -4,8 +4,8 @@ message: >-
   preferred citation and credit the relevant method papers listed in references.
 title: "ModDotPlot Browser"
 type: software
-version: 1.0.0
-date-released: 2026-10-04
+version: 1.0.2
+date-released: 2026-10-11
 repository-code: "https://github.com/marbl/ModDotPlot-Browser"
 license: MIT-0
 abstract: >-

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,92 @@
+# Contributing to ModDotPlot Browser
+
+> **Note:** This project was generated using ChatGPT 5.6 Sol (ie. vibe-coded) under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
+
+Thank you for improving ModDotPlot Browser. Correct and reproducible scientific output is
+the project's first priority, followed by interactive performance and maintainability.
+
+Start with the [methods reference](docs/METHODS.md), the
+[release checklist](docs/RELEASE_CHECKLIST.md), and the
+[user guide](docs/USER_GUIDE.md).
+
+## Development environment
+
+Use the versions pinned by `rust-toolchain.toml`, `.node-version`, `web/package.json`,
+and both lockfiles. Install `wasm-pack`, then run:
+
+```sh
+npm --prefix web ci
+npm --prefix web run dev
+```
+
+The browser bundle uses only static assets and browser APIs at runtime.
+
+## Before submitting a change
+
+```sh
+cargo fmt --all --check
+cargo clippy --workspace --all-targets -- -D warnings
+cargo test --workspace
+cargo check -p moddotplot-wasm --target wasm32-unknown-unknown
+npm --prefix web run verify
+```
+
+Keep changes modular, document public Rust APIs, and add focused unit tests for both
+successful and erroneous input. Avoid unrelated formatting or generated-file changes.
+
+## Scientific changes
+
+A change is scientific if it affects sequence normalization, coordinates, hashing,
+sketches, cardinality, containment, ANI conversion, strand evidence, sparse correction,
+matrix boundaries, exact mode, missing values, or numeric tile contents.
+
+Scientific changes must:
+
+1. State the invariant or estimator being changed.
+2. Add or update a simple exact/scalar reference implementation when possible.
+3. Differentially test optimized output against that reference.
+4. Include ambiguity, short-range, low-complexity, reverse-complement, and boundary
+   cases relevant to the change.
+5. Quantify approximation error and performance when an estimator changes.
+6. Update `docs/METHODS.md`, `docs/RELEASE_CHECKLIST.md`, the user guide, and the
+   changelog when the decision is durable.
+
+Never loosen a correctness threshold to make an optimization pass without documenting
+and scientifically justifying the changed error model.
+
+The production backend is ntHash2 plus undensified OPH verified winners and HLL p10.
+Exact canonical k-mer containment is the scientific oracle. Rejected minmer, bottom-s,
+alternate-hash, densified, and inverted implementations are historical only and must
+not be restored to the production surface without a reviewed ADR and new validation.
+
+## Browser and renderer changes
+
+Preserve the numeric tile contract and keep coloring in the renderer. Tile keys must
+include every parameter that can change numeric output. A newly selected generation
+must not accept stale tiles, and detailed computation must not delay presentation of a
+complete quick viewport.
+
+Test pure TypeScript state and parsing logic outside WebGL where possible. Renderer
+changes should be manually checked in all supported desktop browser families until the
+automated visual matrix is complete. Inspect pan, zoom, reset, resize, cache eviction,
+self-comparison symmetry, exact zoom, and both color modes.
+
+## Performance work
+
+Benchmark the exact workload affected by the change. Report hardware, browser or
+native target, build profile, input, parameters, elapsed time, and peak memory where
+available. Keep raw machine-readable results beside the Markdown interpretation under
+`docs/benchmarks/`.
+
+An optimization is acceptable only after its numeric output passes the relevant
+reference and statistical gates.
+
+## Documentation and release notes
+
+Update [CHANGELOG.md](CHANGELOG.md) for user-visible changes. Documentation should call
+zero-based and one-based coordinates explicitly, distinguish exact from estimated
+values, and avoid claiming research validation until the gates in
+[release checklist](docs/RELEASE_CHECKLIST.md) are complete.
+
+ModDotPlot Browser is MIT-0 licensed. By contributing, you agree that your contribution is
+provided under that license.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -3,7 +3,7 @@ members = ["crates/core", "crates/wasm"]
 resolver = "2"
 
 [workspace.package]
-version = "1.0.0"
+version = "1.0.2"
 edition = "2024"
 license = "MIT-0"
 repository = "https://github.com/marbl/ModDotPlot-Browser"

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 
 **Live application:** [marbl.github.io/ModDotPlot-Browser](https://marbl.github.io/ModDotPlot-Browser/)
 
-> **Note:** This project was generated by ChatGPT 5.6 Sol under the direction of Adam Phillippy and Alex Sweeten. It is intended to be used for exploratory purposes only. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
+> **Note:** This project was generated using ChatGPT 5.6 Sol (ie. vibe-coded) under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
 
 ## Documentation
 

diff --git a/SBOM.cdx.json b/SBOM.cdx.json
@@ -6,7 +6,7 @@
     "component": {
       "type": "application",
       "name": "moddotplot-interactive",
-      "version": "1.0.0",
+      "version": "1.0.2",
       "licenses": [
         {
           "license": {

diff --git a/assets/example-data/Col-CEN_v1.2.fasta.gz b/assets/example-data/Col-CEN_v1.2.fasta.gz
diff --git a/docs/CITATIONS.md b/docs/CITATIONS.md
@@ -1,6 +1,6 @@
 # Citations
 
-> **Note:** This project was generated by ChatGPT 5.6 Sol under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
+> **Note:** This project was generated using ChatGPT 5.6 Sol (ie. vibe-coded) under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
 
 ## Preferred citation
 

diff --git a/docs/DEPLOYMENT.md b/docs/DEPLOYMENT.md
@@ -1,6 +1,6 @@
 # Local installation and HPC deployment
 
-> **Note:** This project was generated by ChatGPT 5.6 Sol under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
+> **Note:** This project was generated using ChatGPT 5.6 Sol (ie. vibe-coded) under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
 
 `ModDotPlot Browser` is a static Rust/WebAssembly web application. After it has been
 built, it does not require an application server or database. A web server only
@@ -124,9 +124,8 @@ The deployable website is written to:
 web/dist/
 ```
 
-The build also runs the TypeScript tests, prepares the bundled *Arabidopsis thaliana*
-example, generates the WebAssembly bindings, checks the documentation contracts, and
-updates the software dependency inventory.
+The build also runs the TypeScript tests, generates the WebAssembly bindings, checks
+the documentation contracts, and updates the software dependency inventory.
 
 ### 5. Launch locally
 
@@ -261,24 +260,24 @@ Package the generated static site:
 
 ```bash
 tar -C web/dist \
-  -czf moddotplot-browser-v1.0.0-dist.tar.gz \
+  -czf moddotplot-browser-v1.0.2-dist.tar.gz \
   .
 ```
 
 Copy it to the HPC system:
 
 ```bash
-scp moddotplot-browser-v1.0.0-dist.tar.gz \
+scp moddotplot-browser-v1.0.2-dist.tar.gz \
   USER@login.cluster.example.edu:/path/to/destination/
 ```
 
 On the HPC system:
 
 ```bash
-mkdir -p /path/to/moddotplot-browser-v1.0.0
+mkdir -p /path/to/moddotplot-browser-v1.0.2
 
-tar -xzf /path/to/destination/moddotplot-browser-v1.0.0-dist.tar.gz \
-  -C /path/to/moddotplot-browser-v1.0.0
+tar -xzf /path/to/destination/moddotplot-browser-v1.0.2-dist.tar.gz \
+  -C /path/to/moddotplot-browser-v1.0.2
 ```
 
 The extracted directory is the complete static website. It can be published through
@@ -423,12 +422,11 @@ The static server should:
 - Serve `.wasm` files using the MIME type `application/wasm`.
 - Support HTTP byte-range requests.
 - Preserve `Range`, `Content-Range`, and `Content-Length` headers.
-- Serve bundled `.gz` files as binary files without automatically adding a
-  `Content-Encoding` header.
 - Permit JavaScript module workers.
 - Use HTTPS for a remotely shared deployment.
 
-Byte-range support is important for indexed access to the bundled example FASTA.
+The example button streams Col-CEN from GitHub, so deployed pages must allow outbound
+HTTPS requests to that host through their Content Security Policy.
 
 ### Open OnDemand
 

diff --git a/docs/METHODS.md b/docs/METHODS.md
@@ -1,6 +1,6 @@
 # Methods
 
-> **Note:** This project was generated by ChatGPT 5.6 Sol under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
+> **Note:** This project was generated using ChatGPT 5.6 Sol (ie. vibe-coded) under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
 
 ## How the algorithm works
 
@@ -165,9 +165,9 @@ At this resolution:
 - Reverse-complement matches produce reverse diagonals.
 - Reverse-complement-palindromic *k*-mers have neutral direction evidence.
 
-The default exact view colors matches by the corresponding base from the X sequence.
-An identity-colored exact view is also available. Changing exact-view colors does not
-change the underlying exact match matrix.
+The exact view colors matches by the corresponding base from the X sequence. Exact
+containment values remain part of the scientific provenance, but the redundant
+identity-colored exact display is not exposed.
 
 ## How this differs from the published ModDotPlot algorithm
 

diff --git a/docs/PRIVACY.md b/docs/PRIVACY.md
@@ -1,6 +1,6 @@
 # Privacy and local data handling
 
-> **Note:** This project was generated by ChatGPT 5.6 Sol under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
+> **Note:** This project was generated using ChatGPT 5.6 Sol (ie. vibe-coded) under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
 
 ModDotPlot Browser is designed to process genomic data locally in the user's browser.
 
@@ -10,6 +10,9 @@ The current application:
 
 * reads FASTA, FAI, GZI, BED, GFF3, and GTF files, including gzip- and BGZF-compressed
   sequence and annotation versions where supported, through browser file APIs;
+* can, only when a user submits a URL, fetch an HTTPS FASTA or FASTA.gz response
+  directly from that remote host and stream it through the local parser, including
+  adjacent FAI/GZI indexes and bounded byte ranges when the host provides them;
 * parses and sketches sequences in a dedicated Web Worker and WebAssembly instance;
 * renders numeric results through WebGL2;
 * makes no application API calls;
@@ -20,8 +23,14 @@ The current application:
 The built application is a set of static files. It still requires HTTP or HTTPS
 hosting because browsers restrict module workers and WebAssembly on `file://` pages.
 The hosting provider can observe normal requests for the application files, including
-IP address and browser metadata according to that provider's policy. Loaded genomic
-files are not part of those requests.
+IP address and browser metadata according to that provider's policy. Locally selected
+genomic files are not part of those requests.
+
+For a user-requested URL import, the remote data host receives a normal browser GET
+request and can observe request metadata such as IP address and browser headers under
+that host's policy. ModDotPlot Browser omits credentials and referrer information from
+this request, does not proxy the sequence through the application host, and does not
+send the parsed sequence elsewhere. The host must permit cross-origin requests (CORS).
 
 ## Memory and lifetime
 

diff --git a/docs/RELEASE_CHECKLIST.md b/docs/RELEASE_CHECKLIST.md
@@ -1,8 +1,8 @@
 # Release checklist
 
-> **Note:** This project was generated by ChatGPT 5.6 Sol under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
+> **Note:** This project was generated using ChatGPT 5.6 Sol (ie. vibe-coded) under the direction of Adam Phillippy and Alex Sweeten. For analyses intended for publication, please use the official [ModDotPlot CLI](https://github.com/marbl/ModDotPlot) and cite the [ModDotPlot paper](https://doi.org/10.1093/bioinformatics/btae493).
 
-This checklist applies to the v1.0.0 release. The browser remains intended for
+This checklist applies to the v1.0.2 release. The browser remains intended for
 exploratory use; analyses intended for publication should use the official ModDotPlot CLI.
 
 ## Source and identity
@@ -66,8 +66,10 @@ npm --prefix web run verify
 - [x] Confirm no monotonic live-cache growth during a fixed pan/zoom trace.
 - [x] Clearly retain the 1 Gb input value as an upper bound rather than a laptop
   performance guarantee until sharding/spill validation is complete.
-- [x] Run the generated million-record annotation parser/publication gate and enforce
-  explicit per-file byte and matching-record admission limits.
+- [x] Run the generated million-feature annotation parser/publication gate and enforce
+  explicit per-file byte and retained-feature admission limits.
+- [x] Import the official CHM13 v2.0 RefSeq Liftoff v5.3 GFF across all 24 chromosomes
+  without treating collapsed exon, CDS, and UTR rows as separately retained features.
 
 ## Reproducibility and distribution gate
 
@@ -103,4 +105,4 @@ npm --prefix web run verify
 - [ ] Create and verify an annotated tag from a clean tree as the final source action.
 - [ ] Produce source/binary archives, checksums, provenance, release notes, and known
   limitations under the local ignored `release-artifacts/` directory.
-- [ ] Push the verified v1.0.0 release commit to the `main` branch.
+- [ ] Push the verified v1.0.2 release commit to the `main` branch.