@jbrowse/plugin-alignments 2.17.0 → 2.18.0

package/esm/PileupRenderer/renderMismatches.js

@@ -1,6 +1,6 @@
 import { bpSpanPx, measureText } from '@jbrowse/core/util';
-import { fillRect } from './util';
 import { colord } from '@jbrowse/core/util/colord';
+import { fillRect } from './util';
 export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
     const { bpPerPx, regions } = renderArgs;
     const { heightPx, topPx, feature } = feat;
@@ -9,14 +9,10 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
     const pxPerBp = Math.min(1 / bpPerPx, 2);
     const mismatches = feature.get('mismatches');
     const heightLim = charHeight - 2;
-    // extraHorizontallyFlippedOffset is used to draw interbase items, which are
-    // located to the left when forward and right when reversed
     const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx + 1 : -1;
     if (!mismatches) {
         return;
     }
-    // two pass rendering: first pass, draw all the mismatches except wide
-    // insertion markers
     for (const mismatch of mismatches) {
         const mstart = start + mismatch.start;
         const mlen = mismatch.length;
@@ -34,7 +30,6 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
                 fillRect(ctx, Math.round(leftPx), topPx, widthPx, heightPx, canvasWidth, c);
             }
             if (widthPx >= charWidth && heightPx >= heightLim) {
-                // normal SNP coloring
                 const contrastColor = drawSNPsMuted
                     ? 'black'
                     : contrastForBase[mismatch.base] || 'black';
@@ -83,12 +78,7 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
             }
         }
         else if (mismatch.type === 'skip') {
-            // fix to avoid bad rendering note that this was also related to chrome
-            // bug https://bugs.chromium.org/p/chromium/issues/detail?id=1131528
-            //
-            // also affected firefox ref #1236 #2750
             if (leftPx + widthPx > 0) {
-                // make small exons more visible when zoomed far out
                 const adjustPx = widthPx - (bpPerPx > 10 ? 1.5 : 0);
                 const l = Math.max(0, leftPx);
                 const t = topPx + heightPx / 2 - 1;
@@ -98,7 +88,6 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
             }
         }
     }
-    // second pass, draw wide insertion markers on top
     if (drawIndels) {
         for (const mismatch of mismatches) {
             const mstart = start + mismatch.start;

package/esm/PileupRenderer/renderModifications.d.ts

@@ -1,12 +1,12 @@
+import type { ProcessedRenderArgs } from './types';
+import type { LayoutFeature } from './util';
 import type { Region } from '@jbrowse/core/util';
-import { LayoutFeature } from './util';
-import { RenderArgsWithColor } from './makeImageData';
 export declare function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     region: Region;
     bpPerPx: number;
-    renderArgs: RenderArgsWithColor;
+    renderArgs: ProcessedRenderArgs;
     canvasWidth: number;
     cigarOps: string[];
 }): void;

package/esm/PileupRenderer/renderModifications.js

@@ -1,9 +1,7 @@
 import { bpSpanPx, max, sum } from '@jbrowse/core/util';
-// locals
 import { fillRect } from './util';
-import { alphaColor } from '../shared/util';
 import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
-// render modifications stored in MM tag in BAM
+import { alphaColor } from '../shared/util';
 export function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
     var _a, _b, _c;
     const { feature, topPx, heightPx } = feat;

package/esm/PileupRenderer/renderPerBaseLettering.d.ts

@@ -1,5 +1,5 @@
-import { Region } from '@jbrowse/core/util';
-import { LayoutFeature } from './util';
+import type { LayoutFeature } from './util';
+import type { Region } from '@jbrowse/core/util';
 export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;

package/esm/PileupRenderer/renderPerBaseLettering.js

@@ -28,7 +28,6 @@ export function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBas
                 const c = colorForBase[letter];
                 fillRect(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c);
                 if (w >= charWidth && heightPx >= heightLim) {
-                    // normal SNP coloring
                     ctx.fillStyle = contrastForBase[letter];
                     ctx.fillText(letter, leftPx + (w - charWidth) / 2 + 1, topPx + heightPx);
                 }

package/esm/PileupRenderer/renderPerBaseQuality.d.ts

@@ -1,5 +1,5 @@
-import { Region } from '@jbrowse/core/util';
-import { LayoutFeature } from './util';
+import type { LayoutFeature } from './util';
+import type { Region } from '@jbrowse/core/util';
 export declare function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;

package/esm/PileupRenderer/renderPerBaseQuality.js

@@ -6,8 +6,8 @@ export function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth,
     const scores = qual.split(' ').map(val => +val);
     const w = 1 / bpPerPx;
     const start = feature.get('start');
-    let soffset = 0; // sequence offset
-    let roffset = 0; // reference offset
+    let soffset = 0;
+    let roffset = 0;
     for (let i = 0; i < cigarOps.length; i += 2) {
         const len = +cigarOps[i];
         const op = cigarOps[i + 1];

package/esm/PileupRenderer/renderSoftClipping.d.ts

@@ -1,11 +1,11 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Theme } from '@mui/material';
-import { RenderArgsDeserializedWithFeaturesAndLayout } from './PileupRenderer';
-import { LayoutFeature } from './util';
+import type { ProcessedRenderArgs } from './types';
+import type { LayoutFeature } from './util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Theme } from '@mui/material';
 export declare function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
-    renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+    renderArgs: ProcessedRenderArgs;
     config: AnyConfigurationModel;
     colorForBase: Record<string, string>;
     theme: Theme;

package/esm/PileupRenderer/renderSoftClipping.js

@@ -1,4 +1,4 @@
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { bpSpanPx } from '@jbrowse/core/util';
 import { fillRect, getCharWidthHeight } from './util';
 import { parseCigar } from '../MismatchParser';
@@ -10,7 +10,6 @@ export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, color
     const mismatches = feature.get('mismatches');
     const seq = feature.get('seq');
     const { charWidth, charHeight } = getCharWidthHeight();
-    // Display all bases softclipped off in lightened colors
     if (!(seq && mismatches)) {
         return;
     }
@@ -28,8 +27,6 @@ export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, color
                 const s0 = feature.get('start') - (i === 0 ? len : 0) + refOffset + k;
                 const [leftPx, rightPx] = bpSpanPx(s0, s0 + 1, region, bpPerPx);
                 const widthPx = Math.max(minFeatWidth, rightPx - leftPx);
-                // Black accounts for IUPAC ambiguity code bases such as N that
-                // show in soft clipping
                 const baseColor = colorForBase[base] || '#000000';
                 ctx.fillStyle = baseColor;
                 fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth);
@@ -48,7 +45,6 @@ export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, color
             seqOffset += len;
         }
         if (op === 'H') {
-            // do nothing
         }
         if (op === 'D') {
             refOffset += len;

package/esm/PileupRenderer/sortUtil.d.ts

@@ -1,3 +1,3 @@
-import { Feature } from '@jbrowse/core/util';
-import { SortedBy } from '../shared/types';
+import type { SortedBy } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
 export declare const sortFeature: (features: Map<string, Feature>, sortedBy: SortedBy) => Map<string, Feature>;

package/esm/PileupRenderer/sortUtil.js

@@ -4,7 +4,6 @@ export const sortFeature = (features, sortedBy) => {
     const featuresInCenterLine = [];
     const featuresOutsideCenter = [];
     const { pos, type } = sortedBy;
-    // only sort on features that intersect center line, append those outside post-sort
     featureArray.forEach(innerArray => {
         const feature = innerArray;
         const start = feature.get('start');
@@ -37,7 +36,6 @@ export const sortFeature = (features, sortedBy) => {
             }
             break;
         }
-        // first sort all mismatches, then all reference bases at the end
         case 'Base pair': {
             const baseSortArray = [];
             for (const feature of featuresInCenterLine) {
@@ -59,14 +57,13 @@ export const sortFeature = (features, sortedBy) => {
                 const acode = bMismatch === null || bMismatch === void 0 ? void 0 : bMismatch.base.toUpperCase();
                 const bcode = aMismatch === null || aMismatch === void 0 ? void 0 : aMismatch.base.toUpperCase();
                 return acode === bcode && acode === '*'
-                    ? // @ts-expect-error
+                    ?
                         aMismatch.length - bMismatch.length
                     : (acode ? acode.charCodeAt(0) : 0) -
                         (bcode ? bcode.charCodeAt(0) : 0);
             });
             break;
         }
-        // sorts positive strands then negative strands
         case 'Read strand': {
             featuresInCenterLine.sort((a, b) => a.get('strand') <= b.get('strand') ? 1 : -1);
             break;

package/esm/PileupRenderer/types.d.ts

@@ -0,0 +1,26 @@
+import type { ColorBy, ModificationTypeWithColor, SortedBy } from '../shared/types';
+import type { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import type { Feature } from '@jbrowse/core/util';
+import type { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
+export interface LayoutFeature {
+    heightPx: number;
+    topPx: number;
+    feature: Feature;
+}
+export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
+    colorBy?: ColorBy;
+    colorTagMap?: Record<string, string>;
+    visibleModifications?: Record<string, ModificationTypeWithColor>;
+    sortedBy?: SortedBy;
+    showSoftClip: boolean;
+    highResolutionScaling: number;
+}
+export interface ProcessedRenderArgs extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+    layout: BaseLayout<Feature>;
+    regionSequence: string | undefined;
+}
+export interface PreProcessedRenderArgs extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+    layout: BaseLayout<Feature>;
+}

package/esm/PileupRenderer/types.js

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

package/esm/PileupRenderer/util.d.ts

@@ -1,5 +1,5 @@
-import { Feature } from '@jbrowse/core/util';
-import { Theme } from '@mui/material';
+import type { Feature } from '@jbrowse/core/util';
+import type { Theme } from '@mui/material';
 export declare function fillRect(ctx: CanvasRenderingContext2D, l: number, t: number, w: number, h: number, cw: number, color?: string): void;
 export declare function getColorBaseMap(theme: Theme): {
     A: string;

package/esm/PileupRenderer/util.js

@@ -15,7 +15,7 @@ export function getColorBaseMap(theme) {
         C: bases.C.main,
         G: bases.G.main,
         T: bases.T.main,
-        deletion: '#808080', // gray
+        deletion: '#808080',
     };
 }
 export function getContrastBaseMap(theme) {
@@ -30,8 +30,6 @@ export function shouldDrawSNPsMuted(type) {
 export function shouldDrawIndels() {
     return true;
 }
-// get width and height of chars the height is an approximation: width letter M
-// is approximately the height
 export function getCharWidthHeight() {
     const charWidth = measureText('A');
     const charHeight = measureText('M') - 2;

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -1,6 +1,7 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
 export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     protected configure(): Promise<{
         subadapter: BaseFeatureDataAdapter;

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -1,9 +1,8 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { toArray } from 'rxjs/operators';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { firstValueFrom } from 'rxjs';
-// locals
+import { toArray } from 'rxjs/operators';
 import { fetchSequence } from '../util';
 import { generateCoverageBins } from './generateCoverageBins';
 export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
@@ -53,7 +52,6 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
                     },
                 }));
             });
-            // make fake features from the coverage
             Object.entries(skipmap).forEach(([key, skip]) => {
                 observer.next(new SimpleFeature({
                     id: key,
@@ -68,7 +66,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
                 }));
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     async getMultiRegionFeatureDensityStats(regions, opts) {
         const { subadapter } = await this.configure();
@@ -78,5 +76,5 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
         const { subadapter } = await this.configure();
         return subadapter.getRefNames(opts);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/SNPCoverageAdapter/configSchema.d.ts

@@ -1,8 +1,4 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * normally refers to a BAM or CRAM adapter
-     */
     subadapter: {
         type: string;
         defaultValue: null;

package/esm/SNPCoverageAdapter/configSchema.js

@@ -1,13 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config SNPCoverageAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('SNPCoverageAdapter', {
-    /**
-     * #slot
-     * normally refers to a BAM or CRAM adapter
-     */
     subadapter: {
         type: 'frozen',
         defaultValue: null,

package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts

@@ -1,10 +1,7 @@
-import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { ColorBy, PreBaseCoverageBin, SkipMap } from '../shared/types';
-interface Opts {
-    bpPerPx?: number;
-    colorBy?: ColorBy;
-}
+import type { Opts } from './util';
+import type { PreBaseCoverageBin, SkipMap } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
+import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
 export declare function generateCoverageBins({ fetchSequence, features, region, opts, }: {
     features: Feature[];
     region: Region;
@@ -14,4 +11,3 @@ export declare function generateCoverageBins({ fetchSequence, features, region,
     bins: PreBaseCoverageBin[];
     skipmap: SkipMap;
 }>;
-export {};