@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/dist/PileupRenderer/renderPerBaseLettering.d.ts

@@ -1,6 +1,6 @@
-import { Region } from '@jbrowse/core/util';
-import { LayoutFeature } from './util';
-export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, }: {
+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;
     region: Region;
@@ -10,4 +10,5 @@ export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, col
     charWidth: number;
     charHeight: number;
     canvasWidth: number;
+    cigarOps: string[];
 }): void;

package/dist/PileupRenderer/renderPerBaseLettering.js

@@ -2,13 +2,11 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderPerBaseLettering = renderPerBaseLettering;
 const util_1 = require("@jbrowse/core/util");
-const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("./util");
-function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, }) {
+function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, cigarOps, }) {
     const heightLim = charHeight - 2;
     const { feature, topPx, heightPx } = feat;
     const seq = feature.get('seq');
-    const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
     const w = 1 / bpPerPx;
     const start = feature.get('start');
     let soffset = 0;
@@ -33,7 +31,6 @@ function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, cont
                 const c = colorForBase[letter];
                 (0, util_2.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/dist/PileupRenderer/renderPerBaseQuality.d.ts

@@ -1,9 +1,10 @@
-import { Region } from '@jbrowse/core/util';
-import { LayoutFeature } from './util';
-export declare function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }: {
+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;
     region: Region;
     bpPerPx: number;
     canvasWidth: number;
+    cigarOps: string[];
 }): void;

package/dist/PileupRenderer/renderPerBaseQuality.js

@@ -2,17 +2,15 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderPerBaseQuality = renderPerBaseQuality;
 const util_1 = require("@jbrowse/core/util");
-const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("./util");
-function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }) {
+function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, cigarOps, }) {
     const { feature, topPx, heightPx } = feat;
     const qual = feature.get('qual') || '';
     const scores = qual.split(' ').map(val => +val);
-    const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
     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/dist/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/dist/PileupRenderer/renderSoftClipping.js

@@ -3,9 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderSoftClipping = renderSoftClipping;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
-// locals
-const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("./util");
+const MismatchParser_1 = require("../MismatchParser");
 function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }) {
     const { feature, topPx, heightPx } = feat;
     const { regions, bpPerPx } = renderArgs;
@@ -14,25 +13,23 @@ function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase
     const mismatches = feature.get('mismatches');
     const seq = feature.get('seq');
     const { charWidth, charHeight } = (0, util_2.getCharWidthHeight)();
-    // Display all bases softclipped off in lightened colors
     if (!(seq && mismatches)) {
         return;
     }
     const heightLim = charHeight - 2;
-    const CIGAR = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
     let seqOffset = 0;
     let refOffset = 0;
-    for (let i = 0; i < CIGAR.length; i += 2) {
-        const op = CIGAR[i + 1];
-        const len = +CIGAR[i];
+    const CIGAR = feature.get('CIGAR');
+    const cigarOps = (0, MismatchParser_1.parseCigar)(CIGAR);
+    for (let i = 0; i < cigarOps.length; i += 2) {
+        const op = cigarOps[i + 1];
+        const len = +cigarOps[i];
         if (op === 'S') {
             for (let k = 0; k < len; k++) {
                 const base = seq[seqOffset + k];
                 const s0 = feature.get('start') - (i === 0 ? len : 0) + refOffset + k;
                 const [leftPx, rightPx] = (0, util_1.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;
                 (0, util_2.fillRect)(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth);
@@ -51,7 +48,6 @@ function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase
             seqOffset += len;
         }
         if (op === 'H') {
-            // do nothing
         }
         if (op === 'D') {
             refOffset += len;

package/dist/PileupRenderer/sortUtil.d.ts

@@ -1,8 +1,3 @@
-import { Feature } from '@jbrowse/core/util';
-interface SortObject {
-    pos: number;
-    type: string;
-    tag?: string;
-}
-export declare const sortFeature: (features: Map<string, Feature>, sortedBy: SortObject) => Map<string, Feature>;
-export {};
+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/dist/PileupRenderer/sortUtil.js

@@ -7,7 +7,6 @@ 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');
@@ -40,36 +39,34 @@ const sortFeature = (features, sortedBy) => {
             }
             break;
         }
-        // first sort all mismatches, then all reference bases at the end
         case 'Base pair': {
             const baseSortArray = [];
-            featuresInCenterLine.forEach(feature => {
+            for (const feature of featuresInCenterLine) {
                 const mismatches = feature.get('mismatches');
-                mismatches.forEach(mismatch => {
+                for (const m of mismatches) {
                     const start = feature.get('start');
-                    const offset = start + mismatch.start + 1;
-                    const consuming = mismatch.type === 'insertion' || mismatch.type === 'softclip';
-                    const len = consuming ? 0 : mismatch.length;
+                    const offset = start + m.start + 1;
+                    const consuming = m.type === 'insertion' || m.type === 'softclip';
+                    const len = consuming ? 0 : m.length;
                     if (pos >= offset && pos < offset + len) {
-                        baseSortArray.push([feature.id(), mismatch]);
+                        baseSortArray.push([feature.id(), m]);
                     }
-                });
-            });
+                }
+            }
             const baseMap = new Map(baseSortArray);
             featuresInCenterLine.sort((a, b) => {
                 const aMismatch = baseMap.get(a.id());
                 const bMismatch = baseMap.get(b.id());
                 const acode = bMismatch === null || bMismatch === void 0 ? void 0 : bMismatch.base.toUpperCase();
                 const bcode = aMismatch === null || aMismatch === void 0 ? void 0 : aMismatch.base.toUpperCase();
-                if (acode === bcode && acode === '*') {
-                    // @ts-expect-error
-                    return aMismatch.length - bMismatch.length;
-                }
-                return ((acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0));
+                return acode === bcode && acode === '*'
+                    ?
+                        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/dist/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/dist/PileupRenderer/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/dist/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/dist/PileupRenderer/util.js

@@ -23,7 +23,7 @@ function getColorBaseMap(theme) {
         C: bases.C.main,
         G: bases.G.main,
         T: bases.T.main,
-        deletion: '#808080', // gray
+        deletion: '#808080',
     };
 }
 function getContrastBaseMap(theme) {
@@ -38,8 +38,6 @@ function shouldDrawSNPsMuted(type) {
 function shouldDrawIndels() {
     return true;
 }
-// get width and height of chars the height is an approximation: width letter M
-// is approximately the height
 function getCharWidthHeight() {
     const charWidth = (0, util_1.measureText)('A');
     const charHeight = (0, util_1.measureText)('M') - 2;

package/dist/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/dist/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -4,13 +4,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const operators_1 = require("rxjs/operators");
+const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const rxjs_2 = require("rxjs");
-// locals
-const generateCoverageBins_1 = __importDefault(require("./generateCoverageBins"));
+const operators_1 = require("rxjs/operators");
 const util_1 = require("../util");
+const generateCoverageBins_1 = require("./generateCoverageBins");
 class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configure() {
         var _a, _b;
@@ -38,14 +37,19 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { subadapter } = await this.configure();
-            const feats = await (0, rxjs_2.firstValueFrom)(subadapter.getFeatures(region, opts).pipe((0, operators_1.toArray)()));
-            const { bins, skipmap } = await (0, generateCoverageBins_1.default)(feats, region, opts, arg => this.fetchSequence(arg));
+            const features = await (0, rxjs_2.firstValueFrom)(subadapter.getFeatures(region, opts).pipe((0, operators_1.toArray)()));
+            const { bins, skipmap } = await (0, generateCoverageBins_1.generateCoverageBins)({
+                features,
+                region,
+                opts,
+                fetchSequence: (region) => this.fetchSequence(region),
+            });
             bins.forEach((bin, index) => {
                 const start = region.start + index;
                 observer.next(new simpleFeature_1.default({
                     id: `${this.id}-${start}`,
                     data: {
-                        score: bin.total,
+                        score: bin.depth,
                         snpinfo: bin,
                         start,
                         end: start + 1,
@@ -53,7 +57,6 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     },
                 }));
             });
-            // make fake features from the coverage
             Object.entries(skipmap).forEach(([key, skip]) => {
                 observer.next(new simpleFeature_1.default({
                     id: key,
@@ -63,12 +66,12 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                         end: skip.end,
                         strand: skip.strand,
                         score: skip.score,
-                        xs: skip.xs,
+                        effectiveStrand: skip.effectiveStrand,
                     },
                 }));
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     async getMultiRegionFeatureDensityStats(regions, opts) {
         const { subadapter } = await this.configure();
@@ -78,6 +81,6 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const { subadapter } = await this.configure();
         return subadapter.getRefNames(opts);
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = SNPCoverageAdapter;

package/dist/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/dist/SNPCoverageAdapter/configSchema.js

@@ -1,15 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config SNPCoverageAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (0, configuration_1.ConfigurationSchema)('SNPCoverageAdapter', {
-    /**
-     * #slot
-     * normally refers to a BAM or CRAM adapter
-     */
     subadapter: {
         type: 'frozen',
         defaultValue: null,

package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts

@@ -1,13 +1,13 @@
-import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { Bin, SkipMap } from './util';
-export default function generateCoverageBins(features: Feature[], region: Region, opts: {
-    bpPerPx?: number;
-    colorBy?: {
-        type: string;
-        tag?: string;
-    };
-}, fetchSequence: (arg: Region) => Promise<string>): Promise<{
-    bins: Bin[];
+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;
+    opts: Opts;
+    fetchSequence: (arg: Region) => Promise<string>;
+}): Promise<{
+    bins: PreBaseCoverageBin[];
     skipmap: SkipMap;
 }>;