jbrowse-plugin-zarr 0.0.1 → 0.1.0

package/README.md

@@ -175,8 +175,11 @@ its mean. They are the same shape and chunking as the level itself:
 
 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, `summaryScoreMode` (`whiskers`, `min`, `max`) in
-the multi-wiggle display does what it does for a BigWig.
+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

package/dist/MultiWiggleZarrAdapter/MultiWiggleZarrAdapter.d.ts

@@ -8,8 +8,10 @@ export interface RawFeatureArrays {
     starts: Int32Array;
     ends: Int32Array;
     scores: Float32Array;
-    minScores: Float32Array | undefined;
-    maxScores: Float32Array | undefined;
+    summary?: {
+        minScores: Float32Array;
+        maxScores: Float32Array;
+    };
     count: number;
 }
 interface WiggleOptions extends BaseOptions {
@@ -18,7 +20,6 @@ interface WiggleOptions extends BaseOptions {
     sources?: {
         name: string;
     }[];
-    summaryScoreMode?: string;
 }
 export default class MultiWiggleZarrAdapter extends BaseFeatureDataAdapter {
     static capabilities: string[];

package/dist/MultiWiggleZarrAdapter/MultiWiggleZarrAdapter.js

@@ -17,8 +17,6 @@ const EMPTY_RAW = {
     starts: new Int32Array(0),
     ends: new Int32Array(0),
     scores: new Float32Array(0),
-    minScores: undefined,
-    maxScores: undefined,
     count: 0,
 };
 // The subtree filter in the clustering sidebar narrows the source list the
@@ -36,8 +34,9 @@ function slabToRaw(slab, sampleIndex) {
     const lo = sampleIndex * stride + offset;
     const hi = lo + numBins;
     const row = values.subarray(lo, hi);
-    const minRow = mins === null || mins === void 0 ? void 0 : mins.subarray(lo, hi);
-    const maxRow = maxs === null || maxs === void 0 ? void 0 : maxs.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])) {
@@ -73,8 +72,7 @@ function slabToRaw(slab, sampleIndex) {
             starts: gridStarts,
             ends: gridEnds,
             scores: row,
-            minScores: minRow,
-            maxScores: maxRow,
+            summary: rowSummary,
             count,
         };
     }
@@ -83,8 +81,10 @@ function slabToRaw(slab, sampleIndex) {
     const scores = new Float32Array(count);
     // Allocated only on a summary level, so a base-resolution read still transfers
     // three arrays rather than five.
-    const minScores = minRow ? new Float32Array(count) : undefined;
-    const maxScores = maxRow ? new Float32Array(count) : undefined;
+    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];
@@ -95,16 +95,16 @@ function slabToRaw(slab, sampleIndex) {
             // 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 (minScores && maxScores) {
-                const min = minRow[i];
-                const max = maxRow[i];
-                minScores[out] = Number.isNaN(min) ? score : min;
-                maxScores[out] = Number.isNaN(max) ? score : max;
+            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, minScores, maxScores, count };
+    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`
@@ -231,12 +231,15 @@ class MultiWiggleZarrAdapter extends BaseFeatureDataAdapter {
             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;
-        // `avg` draws the mean and nothing else, and it is the default, so reading
-        // the summary arrays there triples the bytes for a screenful to buy a pair
-        // the consumer allocates, fills and then discards.
-        const wantSummary = minPath && maxPath && opts.summaryScoreMode !== 'avg';
-        const paths = [level.path, ...(wantSummary ? [minPath, maxPath] : [])];
+        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);

package/dist/MultiWiggleZarrAdapter/MultiWiggleZarrAdapter.js.map

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package/dist/MultiWiggleZarrAdapter/MultiWiggleZarrAdapter.test.js

@@ -111,10 +111,18 @@ const WRONG_SHAPE_STORE = {
     '/zarr.json': groupMetadata([LEVELS[0]]),
     '/bin100/zarr.json': JSON.stringify(arrayMetadata(NUM_BINS, 2)),
 };
+// s2's middle coarse bin unmeasured, so s2 takes the copying path on a
+// summary level, where s1 and s3 view the slab
+const GAPPED_COARSE_VALUES = COARSE_VALUES.map((v, i) => i === COARSE_BINS + 1 ? Number.NaN : v);
+const GAPPED_SUMMARY_STORE = {
+    ...SUMMARY_STORE,
+    ...chunkFiles('bin200', GAPPED_COARSE_VALUES, COARSE_BINS),
+};
 const STORES = {
     'test.zarr': STORE,
     'wrongshape.zarr': WRONG_SHAPE_STORE,
     'summary.zarr': SUMMARY_STORE,
+    'gappedsummary.zarr': GAPPED_SUMMARY_STORE,
 };
 function makeAdapter(store = 'test.zarr') {
     return new MultiWiggleZarrAdapter(configSchema.create({ uri: `http://localhost/${store}` }));
@@ -278,8 +286,20 @@ test('a summary level returns the min and max beside the mean', async () => {
     });
     const s1 = result[0].raws[0];
     expect([...s1.scores]).toEqual([0.5, 2.5, 4.5]);
-    expect([...s1.minScores]).toEqual([0, 2, 4]);
-    expect([...s1.maxScores]).toEqual([1, 3, 5]);
+    expect([...s1.summary.minScores]).toEqual([0, 2, 4]);
+    expect([...s1.summary.maxScores]).toEqual([1, 3, 5]);
+});
+// @jbrowse/plugin-wiggle reads a bin's extremes off `summary` alone, so a flat
+// minScores/maxScores pair is dropped there without a word: no whiskers, and a
+// y field of minScore or maxScore plots the mean.
+test('the extremes travel as one summary, the shape the host reads', async () => {
+    const adapter = makeAdapter('summary.zarr');
+    const result = await adapter.getMultiSourceFeatureArraysMulti([REGION], {
+        bpPerPx: 200,
+    });
+    const s1 = result[0].raws[0];
+    expect(Object.keys(s1).sort()).toEqual(['count', 'ends', 'scores', 'starts', 'summary'].sort());
+    expect(Object.keys(s1.summary).sort()).toEqual(['maxScores', 'minScores']);
 });
 // The bin whose second input was unmeasured: a summary over one value is that
 // value three times, not a range reaching down to the fill.
@@ -290,8 +310,19 @@ test('a partly unmeasured coarse bin summarizes only what it measured', async ()
     });
     const s2 = result[1].raws[0];
     expect([...s2.scores]).toEqual([10.5, 12, 14.5]);
-    expect([...s2.minScores]).toEqual([10, 12, 14]);
-    expect([...s2.maxScores]).toEqual([11, 12, 15]);
+    expect([...s2.summary.minScores]).toEqual([10, 12, 14]);
+    expect([...s2.summary.maxScores]).toEqual([11, 12, 15]);
+});
+test('a gapped sample on a summary level keeps the extremes of the bins it keeps', async () => {
+    const adapter = makeAdapter('gappedsummary.zarr');
+    const result = await adapter.getMultiSourceFeatureArraysMulti([REGION], {
+        bpPerPx: 200,
+    });
+    const s2 = result[1].raws[0];
+    expect([...s2.starts]).toEqual([1000, 1400]);
+    expect([...s2.scores]).toEqual([10.5, 14.5]);
+    expect([...s2.summary.minScores]).toEqual([10, 14]);
+    expect([...s2.summary.maxScores]).toEqual([11, 15]);
 });
 // Presence of the paths is the feature test, not the version number: the finest
 // level of a v2 store has nothing under it to summarize and declares neither.
@@ -301,8 +332,7 @@ test('the finest level of a summary store reports no summary', async () => {
         bpPerPx: 1,
     });
     expect([...result[0].raws[0].scores]).toEqual([0, 1, 2, 3, 4, 5]);
-    expect(result[0].raws[0].minScores).toBeUndefined();
-    expect(result[0].raws[0].maxScores).toBeUndefined();
+    expect(result[0].raws[0].summary).toBeUndefined();
 });
 test('a level declaring one of minPath/maxPath is rejected', () => {
     expect(() => parseSignalMatrixMetadata({
@@ -421,27 +451,16 @@ test('a region the level does not cover comes back empty, not wrong', async () =
     expect(result[0].raws[0].count).toBe(0);
     expect([...result[0].raws[1].scores]).toEqual([0, 1, 2, 3, 4, 5]);
 });
-// avg is the default and draws the mean alone, so the summary arrays are two
-// thirds of a screenful's bytes bought for nothing. Unknown still means read
-// them: an older caller sends no mode at all.
-test('avg mode does not read the summary arrays', async () => {
-    const adapter = makeAdapter('summary.zarr');
-    const result = await adapter.getMultiSourceFeatureArraysMulti([REGION], {
+// The host sends no summary mode: one fetch serves the mean, the extremes and
+// the band around them, so switching the y field or the extent re-encodes
+// without a refetch.
+test('a summary level reads the extremes under the options the host sends', async () => {
+    const result = await makeAdapter('summary.zarr').getMultiSourceFeatureArraysMulti([REGION], {
         bpPerPx: 200,
-        summaryScoreMode: 'avg',
+        resolution: 1,
+        sources: [{ name: 's1' }],
     });
-    expect([...result[0].raws[0].scores]).toEqual([0.5, 2.5, 4.5]);
-    expect(result[0].raws[0].minScores).toBeUndefined();
-    expect(result[0].raws[0].maxScores).toBeUndefined();
-});
-test('max mode still reads them, and so does a caller that sends no mode', async () => {
-    for (const opts of [
-        { bpPerPx: 200, summaryScoreMode: 'max' },
-        { bpPerPx: 200 },
-    ]) {
-        const result = await makeAdapter('summary.zarr').getMultiSourceFeatureArraysMulti([REGION], opts);
-        expect([...result[0].raws[0].minScores]).toEqual([0, 2, 4]);
-        expect([...result[0].raws[0].maxScores]).toEqual([1, 3, 5]);
-    }
+    expect([...result[0].raws[0].summary.minScores]).toEqual([0, 2, 4]);
+    expect([...result[0].raws[0].summary.maxScores]).toEqual([1, 3, 5]);
 });
 //# sourceMappingURL=MultiWiggleZarrAdapter.test.js.map

package/dist/MultiWiggleZarrAdapter/MultiWiggleZarrAdapter.test.js.map

@@ -1 +1 @@
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