jbrowse-plugin-zarr 0.0.0-stage → 0.1.0

package/README.md

@@ -1,3 +1,250 @@
-# Temporary Holding Version
+# jbrowse-plugin-zarr
 
-This version is a temporary placeholder for this package. An operational version to replace this has been submitted for review and is awaiting a staged release.
+Reads multi-sample quantitative signal from a [Zarr v3](https://zarr.dev/) store
+into a JBrowse 2
+[`MultiQuantitativeTrack`](https://jbrowse.org/jb2/docs/user_guides/multiquantitative_track).
+The store holds one samples-by-bins array per resolution level, described by the
+[`jbrowse_signal_matrix`](#store-format) metadata below, so this reads stores
+written for it rather than Zarr in general.
+
+![Copy number for 2504 individuals as a red and blue heatmap, one row per person, over a 190 kb window of human chromosome 17](img/zarr_cohort.png)
+
+Every individual in the 1000 Genomes panel over the CCL3L1 locus, one row each,
+clustered so the copy-number classes separate. White is two copies, red a gain,
+blue a loss. The whole screen is three requests against one store. Built in
+[Population copy number with the 1000 Genomes panel](https://jbrowse.org/jb2-staging/docs/tutorials/population_cnv/),
+this adapter's worked example, which also covers writing the store.
+
+The copy-number values are not ours. They are
+[QuicK-mer2](https://github.com/KiddLab/QuicK-mer2) estimates over the 30x 1000
+Genomes panel, produced by the Kidd lab at the University of Michigan and
+published as the [KiddLab/kmer_1KG](https://github.com/KiddLab/kmer_1KG) track
+hub. If you use them, cite Shen F and Kidd JM,
+[Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2](https://doi.org/10.3390/genes11020141),
+Genes 2020, 11(2):141.
+
+## Why
+
+A multi-sample signal track built from one BigWig per sample is bound by round
+trips, not bytes. Each file needs its header, chrom B-tree and R-tree index
+before it knows where a region's values live, so a screen costs three to four
+sequential requests per sample however small the values are. At 2500 samples
+that is thousands of requests for a few kilobytes of data.
+
+A samples-by-bins array chunked `[all samples, N bins]` answers the same screen
+in one or two chunk reads, whatever the sample count, straight off static
+hosting with no tile server.
+
+### Consider a multi-column bedGraph first
+
+Most of that gain comes from putting every sample in one file, and a
+Tabix-indexed bedGraph with one value column per sample does the same. JBrowse
+reads it with the built-in `BedGraphTabixAdapter`, so it needs no plugin. For
+the 2,504-sample panel on jbrowse.org,
+[jb2bench](https://github.com/cmdcolin/jb2bench) (`scripts/cohort-signal/`)
+measured:
+
+| view                   | 2,504 BigWigs                | this store                  | multi-column bedGraph       |
+| ---------------------- | ---------------------------- | --------------------------- | --------------------------- |
+| 190 kb of chr17        | 15,048 requests, 48 MB, 14 s | 3 requests, 0.19 MB, 0.06 s | 3 requests, 0.31 MB, 0.08 s |
+| all of chr17, 1,500 px | 15,048 requests, 69 MB, 15 s | 40 requests, 9.5 MB, 0.5 s  | 4 requests, 5.9 MB, 1.1 s   |
+
+At a locus the two single-file layouts are the same. The store is ahead only
+when zoomed out: a bedGraph has one bin size, so a whole-chromosome view
+returns every row, and parsing that text is most of its 1.1 s.
+
+### Per-base signal
+
+Copy number changes slowly and repeats across samples, so one bedGraph row
+stands for a long stretch. Per-base signal does neither. For 100 ENCODE
+ATAC-seq fold-change tracks over chr1:10–20 Mb at their native resolution, the
+same jb2bench script (`SET=perbase`) measured:
+
+| view   | 100 BigWigs                 | this store                 | multi-column bedGraph       |
+| ------ | --------------------------- | -------------------------- | --------------------------- |
+| 1 kb   | 692 requests, 2.3 MB, 0.9 s | 7 requests, 0.05 MB, 0.1 s | 3 requests, 1.0 MB, 0.2 s   |
+| 100 kb | 674 requests, 5.8 MB, 0.9 s | 46 requests, 2.1 MB, 0.2 s | 4 requests, 6.5 MB, 1.5 s   |
+| 1 Mb   | 600 requests, 5.2 MB, 1.0 s | 46 requests, 2.4 MB, 0.4 s | 14 requests, 51 MB, 11 s    |
+| 10 Mb  | 600 requests, 3.2 MB, 0.9 s | 46 requests, 2.1 MB, 0.2 s | 111 requests, 502 MB, 109 s |
+
+A hundred samples rarely share a value at adjacent bases, so the bedGraph keeps
+9.0 million rows for 10 million bases after merging equal ones, and every view
+reads all of them. The store reads a coarser level instead. The BigWigs have
+zoom levels too and hold near 1 s, at 600–700 requests a screen.
+
+The store is the largest of the three on disk: 1.0 GB against 634 MB for the
+BigWigs and 495 MB for the bedGraph. Its 10 bp level with min and max is 390 MB
+of that, more than the 1 bp level, so start the pyramid coarser if disk
+matters more than views around 10–50 kb.
+
+Use this plugin for per-base signal across many samples, for genome-wide views
+of a large cohort, or when the [summary levels](#summary-levels) matter at
+coarse zoom. For binned data viewed at a locus, a multi-column bedGraph is
+simpler, smaller (178 MB against this store's 662 MB for the whole-genome
+copy-number panel) and needs no plugin.
+
+## Install
+
+Needs JBrowse 5. Install it from the
+[plugin store](https://jbrowse.org/jb2/docs/user_guides/plugin_store), or name
+it in a config by its store name, which resolves to the newest release the host
+supports (see
+[configuring plugins](https://jbrowse.org/jb2/docs/config_guides/plugins)):
+
+```json
+{
+  "plugins": [{ "storePlugin": "Zarr" }],
+  "tracks": [
+    {
+      "type": "MultiQuantitativeTrack",
+      "trackId": "cohort_signal",
+      "name": "Cohort signal",
+      "assemblyNames": ["hg38"],
+      "adapter": {
+        "type": "MultiWiggleZarrAdapter",
+        "uri": "https://example.com/cohort.zarr"
+      },
+      "displayDefaults": { "defaultRendering": "multirowdensity" }
+    }
+  ]
+}
+```
+
+The adapter config is the store's location and nothing else. Sample names, bin
+size and resolution levels come from the store's own metadata.
+
+## Store format
+
+A Zarr v3 group whose root attributes carry a `jbrowse_signal_matrix` object,
+plus one `float32` array per resolution level:
+
+```json
+{
+  "jbrowse_signal_matrix": {
+    "version": 2,
+    "samples": [{ "name": "HG00551", "group": "PUR" }],
+    "decimals": 2,
+    "levels": [
+      {
+        "path": "bin1000",
+        "binSize": 1000,
+        "refs": {
+          "chr17": { "start": 35000000, "binOffset": 0, "numBins": 2500 }
+        }
+      },
+      {
+        "path": "bin10000",
+        "binSize": 10000,
+        "minPath": "bin10000_min",
+        "maxPath": "bin10000_max",
+        "refs": {
+          "chr17": { "start": 35000000, "binOffset": 0, "numBins": 250 }
+        }
+      }
+    ]
+  }
+}
+```
+
+Each level array is shaped `[samples, bins]`, C order, with every refName laid
+end to end on the bin axis at its own `binOffset`. `start` is the genomic
+coordinate of that refName's first bin, so a store can cover one window of one
+chromosome rather than a whole genome. Unmeasured bins are the array's `NaN`
+fill value and are dropped rather than drawn as zero.
+
+Chunk each level with the whole sample axis inside one chunk,
+`[all samples, 256 bins]` or thereabouts. This is the opposite of the natural
+per-sample layout, and it is what the format buys: split the samples across
+chunks instead and a screenful costs a read per sample again.
+
+Levels are a resolution pyramid: the adapter reads the coarsest level whose bins
+are still no wider than a screen pixel.
+
+### Summary levels
+
+A level may name two sibling arrays holding the min and max of the finer bins
+each of its bins averages, the same thing a BigWig zoom record carries beside
+its mean. They are the same shape and chunking as the level itself:
+
+- `minPath` and `maxPath` are optional and always travel together. One without
+  the other is rejected, because the display would draw a whisker against the
+  mean on the other side and it would read as real asymmetry in the data.
+- The finest level has neither: it has nothing below it to summarize.
+- Their presence is the feature test, not `version`. A store written before v2
+  has none, and a reader that predates them opens `path` and behaves as before.
+
+Without them a zoomed-out view can only show a mean, and anything narrower than
+a coarse bin averages back into the baseline at exactly the zoom someone would
+be scanning for it. With them, the multi-wiggle display's `mark.extent`
+`min-max` and `encoding.y.field` `minScore` or `maxScore` do what they do for a
+BigWig. A view at a summary level reads all three arrays whatever it draws, as a
+BigWig ships its zoom record whole, so changing either setting redraws without
+a refetch.
+
+The min and max are over the store's own finer bins, not over whatever the input
+was. If the finest level is itself an aggregate of something finer, the whiskers
+describe the store, not the source.
+
+### Size
+
+Two knobs, both read-side transparent, so neither needs a reader to know:
+
+- **`chunk-bins`** trades requests against overfetch, not total bytes: a view
+  needs the bins it needs. 256 leaves under 20% edge overfetch on a typical
+  view; going much smaller multiplies requests to save very little.
+- **Stored precision** is usually the bigger lever. gzip on this layout is
+  mostly matching repeated values rather than modelling a distribution, so the
+  number of distinct values dominates. Quantizing copy number to 0.01 roughly
+  halves a store; it does nothing for genuinely continuous data. Record what was
+  used in `decimals` — provenance only, since the values arrive already rounded.
+
+The coarse levels are not the cheap ones. Averaging manufactures distinct values
+and destroys the repetition gzip was feeding on, so a level with a third of the
+bins is not a third of the bytes. Measure before assuming.
+
+Write one with
+[`build_signal_zarr.ts`](https://github.com/GMOD/jbrowse-components/blob/main/scripts/build_signal_zarr.ts),
+which packs a list of BigWigs into this layout and takes both knobs as flags.
+
+## Codecs
+
+This build ships zarrita's own codecs (`bytes`, `gzip`, `zlib`, `transpose`,
+`crc32c`) and stubs the numcodecs ones (`blosc`, `lz4`, `zstd`), which are
+1.35 MB of wasm against a 52 KB plugin. A store compressed with one of those
+fails with a message naming the codec rather than silently misreading. Write
+stores with gzip.
+
+That is less of a compromise than it looks. On a 2504-sample copy-number chunk,
+gzip-9 gets 9.9x and zstd-9 gets 11.4x, so the wasm buys 13%. A byte-shuffle
+filter ahead of either makes it _worse_, by 73%: shuffle helps floats that vary
+smoothly in their mantissa, and this layout's wins come from long runs of
+identical values that shuffle splits across four distant regions of the buffer.
+Reducing stored precision beats every codec choice here, and costs no bytes on
+the wire to support.
+
+## Develop
+
+```bash
+pnpm install
+pnpm test          # vitest, adapter round trip against an in-memory store
+pnpm start         # esbuild watch, serves dist/out.js on :9000
+pnpm build         # dist/jbrowse-plugin-zarr.umd.production.min.js
+```
+
+Point a JBrowse config's plugin `url` at `http://localhost:9000/dist/out.js` to
+develop against the watch build.
+
+## Release
+
+```bash
+pnpm version patch # lint, typecheck, test, build, then push the v* tag
+```
+
+The tag publishes to npm from CI by trusted publishing, and the plugin store
+takes it from npm at its next update.
+
+`pnpm betabuild` still pushes an unreleased build to
+`https://jbrowse.org/demos/zarr/jbrowse-plugin-zarr.umd.production.min.js` for
+trying a change in a config before releasing it. It re-downloads the entry point
+through CloudFront afterwards and fails if it does not match what was just
+built.

package/dist/MultiWiggleZarrAdapter/MultiWiggleZarrAdapter.d.ts

@@ -0,0 +1,50 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { SignalMatrixMetadata } from './signalMatrixMetadata';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
+import type { Observable } from 'rxjs';
+import type { Array as ZarrArray, DataType, FetchStore, Group as ZarrGroup } from 'zarrita';
+export interface RawFeatureArrays {
+    starts: Int32Array;
+    ends: Int32Array;
+    scores: Float32Array;
+    summary?: {
+        minScores: Float32Array;
+        maxScores: Float32Array;
+    };
+    count: number;
+}
+interface WiggleOptions extends BaseOptions {
+    bpPerPx?: number;
+    resolution?: number;
+    sources?: {
+        name: string;
+    }[];
+}
+export default class MultiWiggleZarrAdapter extends BaseFeatureDataAdapter {
+    static capabilities: string[];
+    private setupP?;
+    private setupPre;
+    setup(opts?: BaseOptions): Promise<{
+        meta: SignalMatrixMetadata;
+        group: ZarrGroup<FetchStore>;
+        arrays: Map<string, Promise<ZarrArray<DataType, FetchStore>>>;
+    }>;
+    private openArray;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    private placeRegion;
+    private planFetch;
+    private fetchRegionSlabs;
+    getMultiSourceFeatureArraysMulti(regions: Region[], opts?: WiggleOptions): Promise<{
+        source: string;
+        raws: RawFeatureArrays[];
+    }[]>;
+    getSources(_regions: Region[]): Promise<{
+        source: string;
+        name: string;
+        group?: string;
+        color?: string;
+    }[]>;
+    getFeatures(region: Region, opts?: WiggleOptions): Observable<Feature>;
+}
+export {};

package/dist/MultiWiggleZarrAdapter/MultiWiggleZarrAdapter.js

@@ -0,0 +1,336 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, updateStatus } from '@jbrowse/core/util';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { parseSignalMatrixMetadata, pickLevel } from './signalMatrixMetadata';
+import { openZarrGroup, zarritaP } from '../zarrStore';
+const EMPTY_SLAB = {
+    numBins: 0,
+    binSize: 1,
+    start: 0,
+    stride: 0,
+    offset: 0,
+    values: new Float32Array(0),
+    mins: undefined,
+    maxs: undefined,
+};
+const EMPTY_RAW = {
+    starts: new Int32Array(0),
+    ends: new Int32Array(0),
+    scores: new Float32Array(0),
+    count: 0,
+};
+// The subtree filter in the clustering sidebar narrows the source list the
+// display sends down, so this is a real user-driven filter and not just the
+// full list echoed back. `undefined` means "no filter", which is not the same
+// as an empty one.
+function wantedNames(sources) {
+    return (sources === null || sources === void 0 ? void 0 : sources.length) ? new Set(sources.map(s => s.name)) : undefined;
+}
+// A bin the converter never wrote (no k-mers, a gap, or outside the store's
+// covered window) comes back as the array's NaN fill value. Dropping those keeps
+// an unmeasured region visibly empty rather than drawing it as zero coverage.
+function slabToRaw(slab, sampleIndex) {
+    const { numBins, binSize, start, stride, offset, values, mins, maxs } = slab;
+    const lo = sampleIndex * stride + offset;
+    const hi = lo + numBins;
+    const row = values.subarray(lo, hi);
+    const rowSummary = mins && maxs
+        ? { minScores: mins.subarray(lo, hi), maxScores: maxs.subarray(lo, hi) }
+        : undefined;
+    let count = 0;
+    for (let i = 0; i < numBins; i++) {
+        if (!Number.isNaN(row[i])) {
+            count++;
+        }
+    }
+    // The whole row is measured, which is the ordinary case for a binned store
+    // and universal at the coarse levels (a 1Mb bin is empty only where the
+    // reference is). Then the bin grid is the region's own, identical for every
+    // sample, and the values are already a contiguous run of the slab: hand back
+    // one shared grid and three views instead of five fresh arrays per sample.
+    //
+    // This is what decides whether a cohort renders at all. The interface is one
+    // RawFeatureArrays per sample PER REGION, so a 24-contig view of 2504 samples
+    // asks for 60,096 of them; copying meant ~300,000 typed arrays for a frame
+    // holding 31 MB of actual values, and the tab died before it drew. Sharing is
+    // safe because the consumer copies into its own buffers
+    // (processFeaturesFromArrays) and the transferable collector dedupes the
+    // buffers, so 2504 views of one slab transfer once rather than 2504 times.
+    if (count === numBins) {
+        let { gridStarts, gridEnds } = slab;
+        if (!gridStarts || !gridEnds) {
+            gridStarts = new Int32Array(numBins);
+            gridEnds = new Int32Array(numBins);
+            for (let i = 0; i < numBins; i++) {
+                gridStarts[i] = start + i * binSize;
+                gridEnds[i] = start + (i + 1) * binSize;
+            }
+            slab.gridStarts = gridStarts;
+            slab.gridEnds = gridEnds;
+        }
+        return {
+            starts: gridStarts,
+            ends: gridEnds,
+            scores: row,
+            summary: rowSummary,
+            count,
+        };
+    }
+    const starts = new Int32Array(count);
+    const ends = new Int32Array(count);
+    const scores = new Float32Array(count);
+    // Allocated only on a summary level, so a base-resolution read still transfers
+    // three arrays rather than five.
+    const summary = rowSummary && {
+        minScores: new Float32Array(count),
+        maxScores: new Float32Array(count),
+    };
+    let out = 0;
+    for (let i = 0; i < numBins; i++) {
+        const score = row[i];
+        if (!Number.isNaN(score)) {
+            starts[out] = start + i * binSize;
+            ends[out] = start + (i + 1) * binSize;
+            scores[out] = score;
+            // The converter writes all three from the same set of finer bins, so a
+            // NaN here would mean a torn store; fall back to the mean rather than
+            // emit a NaN the renderer would carry into its scale.
+            if (summary) {
+                const min = rowSummary.minScores[i];
+                const max = rowSummary.maxScores[i];
+                summary.minScores[out] = Number.isNaN(min) ? score : min;
+                summary.maxScores[out] = Number.isNaN(max) ? score : max;
+            }
+            out++;
+        }
+    }
+    return { starts, ends, scores, summary, count };
+}
+// Checked rather than trusted, because the failure is silent otherwise: a level
+// with fewer rows than the metadata claims makes the last samples' `subarray`
+// run off the end, and `Number.isNaN(undefined)` is false, so those rows come
+// back as full-length runs of NaN-scored features instead of an error.
+async function openLevelArray(group, path, numSamples) {
+    const zarr = await zarritaP;
+    const array = await zarr.open.v3(group.resolve(path), { kind: 'array' });
+    const { shape } = array;
+    if (shape.length !== 2 || shape[0] !== numSamples) {
+        throw new Error(`signal matrix level "${path}" is shaped [${shape.join(', ')}], expected [${numSamples}, bins] to match the ${numSamples} samples in the store metadata`);
+    }
+    return array;
+}
+// A samples-by-bins quantitative matrix in a Zarr v3 store: one chunk holds
+// every sample over a span of bins, so a screenful of a 2500-sample cohort is a
+// couple of range requests instead of the 3-4 sequential index reads per file
+// that a BigWig-per-sample track pays. The store's own attributes carry the
+// sample list, bin size and resolution levels — see signalMatrixMetadata.ts.
+class MultiWiggleZarrAdapter extends BaseFeatureDataAdapter {
+    async setupPre(opts) {
+        const { statusCallback = () => { } } = opts !== null && opts !== void 0 ? opts : {};
+        const group = await updateStatus('Downloading zarr metadata', statusCallback, () => openZarrGroup({
+            adapterName: 'MultiWiggleZarrAdapter',
+            location: this.getConf('zarrLocation'),
+            pluginManager: this.pluginManager,
+        }));
+        return {
+            group,
+            meta: parseSignalMatrixMetadata(group.attrs),
+            arrays: new Map(),
+        };
+    }
+    async setup(opts) {
+        var _a;
+        (_a = this.setupP) !== null && _a !== void 0 ? _a : (this.setupP = this.setupPre(opts).catch((e) => {
+            this.setupP = undefined;
+            throw e;
+        }));
+        return this.setupP;
+    }
+    // One open per array for the life of the adapter: opening an array is its own
+    // metadata read, and the level is re-picked on every navigation. Keyed by
+    // path rather than by level so a level's mean/min/max are three cache entries
+    // and the summary pair is only ever opened on a level that declares it.
+    async openArray(path, opts) {
+        const { group, arrays, meta } = await this.setup(opts);
+        let arrayP = arrays.get(path);
+        if (!arrayP) {
+            // The rejection is not kept. A failed open is usually a transient fetch,
+            // and the level is re-picked on every navigation, so caching it would
+            // leave that zoom level broken for the life of the adapter with no way
+            // back short of reloading the page.
+            arrayP = openLevelArray(group, path, meta.samples.length).catch((e) => {
+                arrays.delete(path);
+                throw e;
+            });
+            arrays.set(path, arrayP);
+        }
+        return arrayP;
+    }
+    async getRefNames(opts) {
+        const { meta } = await this.setup(opts);
+        return [...new Set(meta.levels.flatMap(l => Object.keys(l.refs)))];
+    }
+    // Where one region lands on a level's flat bin axis, or undefined if the
+    // level does not cover it.
+    placeRegion(region, level) {
+        const span = level.refs[region.refName];
+        if (!span) {
+            return undefined;
+        }
+        const { binSize } = level;
+        const first = Math.max(0, Math.floor((region.start - span.start) / binSize));
+        const last = Math.min(span.numBins, Math.ceil((region.end - span.start) / binSize));
+        return last <= first
+            ? undefined
+            : {
+                from: span.binOffset + first,
+                to: span.binOffset + last,
+                start: span.start + first * binSize,
+            };
+    }
+    // Merge the placed regions into as few reads as the layout allows.
+    //
+    // Every refName sits end to end on one bin axis in karyotype order, so a
+    // multi-region view is usually a contiguous run of it and a whole-genome view
+    // always is: 24 contigs at the coarsest level are ~3100 adjacent bins, which
+    // is a dozen chunks. Asking per region instead turns that into 24 slices, and
+    // 72 once a summary level triples them, for bytes the store would have handed
+    // over in one pass.
+    //
+    // Two runs merge when the gap between them is under a chunk, because that
+    // chunk is fetched either way. That is the whole rule: it never reads a chunk
+    // it would not have read, so two far-apart windows stay two reads and do not
+    // drag the space between them along.
+    planFetch(placed, chunkBins) {
+        const order = placed
+            .map((_, i) => i)
+            .sort((a, b) => placed[a].from - placed[b].from);
+        const runs = [];
+        for (const i of order) {
+            const { from, to } = placed[i];
+            const last = runs.at(-1);
+            if (last && from - last.to <= chunkBins) {
+                last.to = Math.max(last.to, to);
+            }
+            else {
+                runs.push({ from, to });
+            }
+        }
+        return runs;
+    }
+    async fetchRegionSlabs(regions, opts = {}) {
+        var _a;
+        const { bpPerPx = 0, resolution = 1 } = opts;
+        const { meta } = await this.setup(opts);
+        const resolutionMultiplier = this.getConf('resolutionMultiplier');
+        // One level for the whole call: bpPerPx describes the view, not a region.
+        const level = pickLevel(meta.levels, (bpPerPx / resolution) * resolutionMultiplier);
+        const placed = regions.map(region => this.placeRegion(region, level));
+        const present = placed.filter(p => p !== undefined);
+        if (!present.length) {
+            return regions.map(() => EMPTY_SLAB);
+        }
+        const zarr = await zarritaP;
+        // Read whenever the level declares them, as the host's BigWig adapter
+        // ships every summary its file holds: the host sends no summary mode, and
+        // one fetch serves the mean, the extremes and the band between them, so
+        // switching the y field or the extent re-encodes without a refetch.
+        const { minPath, maxPath } = level;
+        const paths = [
+            level.path,
+            ...(minPath && maxPath ? [minPath, maxPath] : []),
+        ];
+        const arrays = await Promise.all(paths.map(p => this.openArray(p, opts)));
+        const chunkBins = (_a = arrays[0].chunks[1]) !== null && _a !== void 0 ? _a : 1;
+        const runs = this.planFetch(present, chunkBins);
+        // Every read of every run at once: they are independent range requests and
+        // the point of the layout is that a screenful is a couple of them.
+        const blocks = await Promise.all(runs.map(async (run) => {
+            const selection = [null, zarr.slice(run.from, run.to)];
+            const datas = await Promise.all(arrays.map(async (array, i) => {
+                const { data } = await zarr.get(array, selection);
+                if (!(data instanceof Float32Array)) {
+                    throw new Error(`signal matrix level "${paths[i]}" must be float32, got ${array.dtype}`);
+                }
+                return data;
+            }));
+            return { run, values: datas[0], mins: datas[1], maxs: datas[2] };
+        }));
+        return placed.map(p => {
+            if (!p) {
+                return EMPTY_SLAB;
+            }
+            const block = blocks.find(b => b.run.from <= p.from && p.to <= b.run.to);
+            return {
+                numBins: p.to - p.from,
+                binSize: level.binSize,
+                start: p.start,
+                stride: block.run.to - block.run.from,
+                offset: p.from - block.run.from,
+                values: block.values,
+                mins: block.mins,
+                maxs: block.maxs,
+            };
+        });
+    }
+    async getMultiSourceFeatureArraysMulti(regions, opts = {}) {
+        var _a;
+        const { meta } = await this.setup(opts);
+        const wanted = wantedNames(opts.sources);
+        const slabs = await updateStatus('Downloading signal matrix', (_a = opts.statusCallback) !== null && _a !== void 0 ? _a : (() => { }), () => this.fetchRegionSlabs(regions, opts));
+        return meta.samples
+            .map((sample, sampleIndex) => ({ sample, sampleIndex }))
+            .filter(({ sample }) => !wanted || wanted.has(sample.name))
+            .map(({ sample, sampleIndex }) => ({
+            source: sample.name,
+            raws: slabs.map(slab => slab.numBins ? slabToRaw(slab, sampleIndex) : EMPTY_RAW),
+        }));
+    }
+    async getSources(_regions) {
+        const { meta } = await this.setup();
+        return meta.samples.map(sample => ({ ...sample, source: sample.name }));
+    }
+    // The feature-object path, which the multiwiggle render never takes — it uses
+    // the typed arrays above. This is what clustering (getScoreMatrix) reads, and
+    // it costs one SimpleFeature per sample per bin, so it emits straight off the
+    // slab rather than building per-sample typed arrays it would immediately throw
+    // away.
+    getFeatures(region, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { meta } = await this.setup(opts);
+            const wanted = wantedNames(opts.sources);
+            const [slab] = await this.fetchRegionSlabs([region], opts);
+            const { numBins, binSize, start, stride, offset, values } = slab;
+            const { refName } = region;
+            for (const [sampleIndex, sample] of meta.samples.entries()) {
+                if (wanted && !wanted.has(sample.name)) {
+                    continue;
+                }
+                const lo = sampleIndex * stride + offset;
+                const row = values.subarray(lo, lo + numBins);
+                for (let i = 0; i < numBins; i++) {
+                    const score = row[i];
+                    if (Number.isNaN(score)) {
+                        continue;
+                    }
+                    const featureStart = start + i * binSize;
+                    observer.next(new SimpleFeature({
+                        // refName included: getFeaturesInMultipleRegions concatenates
+                        // regions, and two of them can hold the same bin coordinate on
+                        // different contigs.
+                        uniqueId: `${sample.name}-${refName}-${featureStart}`,
+                        refName,
+                        start: featureStart,
+                        end: featureStart + binSize,
+                        score,
+                        source: sample.name,
+                    }));
+                }
+            }
+            observer.complete();
+        }, opts.signal);
+    }
+}
+MultiWiggleZarrAdapter.capabilities = ['hasResolution'];
+export default MultiWiggleZarrAdapter;
+//# sourceMappingURL=MultiWiggleZarrAdapter.js.map

package/dist/MultiWiggleZarrAdapter/MultiWiggleZarrAdapter.js.map

@@ -0,0 +1 @@
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package/dist/MultiWiggleZarrAdapter/MultiWiggleZarrAdapter.test.d.ts

@@ -0,0 +1 @@
+export {};