@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/dist/SNPCoverageAdapter/processMismatches.js

@@ -0,0 +1,58 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.processMismatches = processMismatches;
+const util_1 = require("./util");
+function processMismatches({ feature, region, bins, skipmap, }) {
+    var _a;
+    const fstart = feature.get('start');
+    const fstrand = feature.get('strand');
+    const mismatches = (_a = feature.get('mismatches')) !== null && _a !== void 0 ? _a : [];
+    for (const mismatch of mismatches) {
+        const mstart = fstart + mismatch.start;
+        const mlen = (0, util_1.mismatchLen)(mismatch);
+        const mend = mstart + mlen;
+        for (let j = mstart; j < mstart + mlen; j++) {
+            const epos = j - region.start;
+            if (epos >= 0 && epos < bins.length) {
+                const bin = bins[epos];
+                const { base, altbase, type } = mismatch;
+                const interbase = (0, util_1.isInterbase)(type);
+                if (type === 'deletion' || type === 'skip') {
+                    (0, util_1.inc)(bin, fstrand, 'delskips', type);
+                    bin.depth--;
+                }
+                else if (!interbase) {
+                    (0, util_1.inc)(bin, fstrand, 'snps', base);
+                    bin.ref.entryDepth--;
+                    bin.ref[fstrand]--;
+                    bin.refbase = altbase;
+                }
+                else {
+                    (0, util_1.inc)(bin, fstrand, 'noncov', type);
+                }
+            }
+        }
+        if (mismatch.type === 'skip') {
+            const tags = feature.get('tags');
+            const xs = (tags === null || tags === void 0 ? void 0 : tags.XS) || (tags === null || tags === void 0 ? void 0 : tags.TS);
+            const ts = tags === null || tags === void 0 ? void 0 : tags.ts;
+            const effectiveStrand = xs === '+'
+                ? 1
+                : xs === '-'
+                    ? -1
+                    : (ts === '+' ? 1 : xs === '-' ? -1 : 0) * fstrand;
+            const hash = `${mstart}_${mend}_${effectiveStrand}`;
+            if (skipmap[hash] === undefined) {
+                skipmap[hash] = {
+                    feature: feature,
+                    start: mstart,
+                    end: mend,
+                    strand: fstrand,
+                    effectiveStrand,
+                    score: 0,
+                };
+            }
+            skipmap[hash].score++;
+        }
+    }
+}

package/dist/SNPCoverageAdapter/processModifications.d.ts

@@ -0,0 +1,10 @@
+import type { ColorBy, PreBaseCoverageBin } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
+import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
+export declare function processModifications({ feature, colorBy, region, bins, regionSequence, }: {
+    bins: PreBaseCoverageBin[];
+    feature: Feature;
+    region: Region;
+    colorBy?: ColorBy;
+    regionSequence: string;
+}): void;

package/dist/SNPCoverageAdapter/processModifications.js

@@ -0,0 +1,49 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.processModifications = processModifications;
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("./util");
+const getMaximumModificationAtEachPosition_1 = require("../shared/getMaximumModificationAtEachPosition");
+function processModifications({ feature, colorBy, region, bins, regionSequence, }) {
+    var _a, _b, _c;
+    const fstart = feature.get('start');
+    const fstrand = feature.get('strand');
+    const fend = feature.get('end');
+    const twoColor = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.twoColor;
+    const isolatedModification = (_b = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _b === void 0 ? void 0 : _b.isolatedModification;
+    (_c = (0, getMaximumModificationAtEachPosition_1.getMaxProbModAtEachPosition)(feature)) === null || _c === void 0 ? void 0 : _c.forEach(({ type, prob, allProbs }, pos) => {
+        if (isolatedModification && type !== isolatedModification) {
+            return;
+        }
+        const epos = pos + fstart - region.start;
+        if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+            if (bins[epos] === undefined) {
+                bins[epos] = {
+                    depth: 0,
+                    readsCounted: 0,
+                    snps: {},
+                    ref: {
+                        probabilities: [],
+                        entryDepth: 0,
+                        '-1': 0,
+                        0: 0,
+                        1: 0,
+                    },
+                    mods: {},
+                    nonmods: {},
+                    delskips: {},
+                    noncov: {},
+                };
+            }
+            const s = 1 - (0, util_1.sum)(allProbs);
+            const bin = bins[epos];
+            bin.refbase = regionSequence[epos];
+            if (twoColor && s > (0, util_1.max)(allProbs)) {
+                (0, util_2.incWithProbabilities)(bin, fstrand, 'nonmods', `nonmod_${type}`, s);
+            }
+            else {
+                (0, util_2.incWithProbabilities)(bin, fstrand, 'mods', `mod_${type}`, prob);
+            }
+        }
+    });
+}

package/dist/SNPCoverageAdapter/processReferenceCpGs.d.ts

@@ -0,0 +1,9 @@
+import type { PreBaseCoverageBin } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
+import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
+export declare function processReferenceCpGs({ feature, region, bins, regionSequence, }: {
+    bins: PreBaseCoverageBin[];
+    feature: Feature;
+    region: Region;
+    regionSequence: string;
+}): void;

package/dist/SNPCoverageAdapter/processReferenceCpGs.js

@@ -0,0 +1,63 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.processReferenceCpGs = processReferenceCpGs;
+const util_1 = require("@jbrowse/core/util");
+const MismatchParser_1 = require("../MismatchParser");
+const ModificationParser_1 = require("../ModificationParser");
+const util_2 = require("./util");
+function processReferenceCpGs({ feature, region, bins, regionSequence, }) {
+    var _a;
+    const fstart = feature.get('start');
+    const fend = feature.get('end');
+    const fstrand = feature.get('strand');
+    const seq = feature.get('seq');
+    const mismatches = (_a = feature.get('mismatches')) !== null && _a !== void 0 ? _a : [];
+    const r = regionSequence.toLowerCase();
+    if (seq) {
+        const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+        const { methBins, methProbs } = (0, ModificationParser_1.getMethBins)(feature, cigarOps);
+        const dels = mismatches.filter(f => f.type === 'deletion');
+        for (let i = 0; i < fend - fstart; i++) {
+            const j = i + fstart;
+            const l1 = r[j - region.start + 1];
+            const l2 = r[j - region.start + 2];
+            if (l1 === 'c' && l2 === 'g') {
+                const bin0 = bins[j - region.start];
+                const bin1 = bins[j - region.start + 1];
+                const b0 = methBins[i];
+                const b1 = methBins[i + 1];
+                const p0 = methProbs[i];
+                const p1 = methProbs[i + 1];
+                if ((b0 && (p0 !== undefined ? p0 > 0.5 : true)) ||
+                    (b1 && (p1 !== undefined ? p1 > 0.5 : true))) {
+                    if (bin0) {
+                        (0, util_2.incWithProbabilities)(bin0, fstrand, 'mods', 'cpg_meth', p0 || 0);
+                        bin0.ref.entryDepth--;
+                        bin0.ref[fstrand]--;
+                    }
+                    if (bin1) {
+                        (0, util_2.incWithProbabilities)(bin1, fstrand, 'mods', 'cpg_meth', p1 || 0);
+                        bin1.ref.entryDepth--;
+                        bin1.ref[fstrand]--;
+                    }
+                }
+                else {
+                    if (bin0) {
+                        if (!dels.some(d => (0, util_1.doesIntersect2)(j, j + 1, d.start + fstart, d.start + fstart + d.length))) {
+                            (0, util_2.incWithProbabilities)(bin0, fstrand, 'nonmods', 'cpg_unmeth', 1 - (p0 || 0));
+                            bin0.ref.entryDepth--;
+                            bin0.ref[fstrand]--;
+                        }
+                    }
+                    if (bin1) {
+                        if (!dels.some(d => (0, util_1.doesIntersect2)(j + 1, j + 2, d.start + fstart, d.start + fstart + d.length))) {
+                            (0, util_2.incWithProbabilities)(bin1, fstrand, 'nonmods', 'cpg_unmeth', 1 - (p1 || 0));
+                            bin1.ref.entryDepth--;
+                            bin1.ref[fstrand]--;
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

package/dist/SNPCoverageAdapter/util.d.ts

@@ -0,0 +1,10 @@
+import type { ColorBy, Mismatch, PreBaseCoverageBin, PreBaseCoverageBinSubtypes } from '../shared/types';
+export interface Opts {
+    bpPerPx?: number;
+    colorBy?: ColorBy;
+    stopToken?: string;
+}
+export declare function mismatchLen(mismatch: Mismatch): number;
+export declare function isInterbase(type: string): type is "insertion" | "hardclip" | "softclip";
+export declare function inc(bin: PreBaseCoverageBin, strand: -1 | 0 | 1, type: keyof PreBaseCoverageBinSubtypes, field: string): void;
+export declare function incWithProbabilities(bin: PreBaseCoverageBin, strand: -1 | 0 | 1, type: keyof PreBaseCoverageBinSubtypes, field: string, probability: number): void;

package/dist/SNPCoverageAdapter/util.js

@@ -0,0 +1,41 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.mismatchLen = mismatchLen;
+exports.isInterbase = isInterbase;
+exports.inc = inc;
+exports.incWithProbabilities = incWithProbabilities;
+function mismatchLen(mismatch) {
+    return !isInterbase(mismatch.type) ? mismatch.length : 1;
+}
+function isInterbase(type) {
+    return type === 'softclip' || type === 'hardclip' || type === 'insertion';
+}
+function inc(bin, strand, type, field) {
+    let thisBin = bin[type][field];
+    if (thisBin === undefined) {
+        thisBin = bin[type][field] = {
+            entryDepth: 0,
+            probabilities: [],
+            '-1': 0,
+            '0': 0,
+            '1': 0,
+        };
+    }
+    thisBin.entryDepth++;
+    thisBin[strand]++;
+}
+function incWithProbabilities(bin, strand, type, field, probability) {
+    let thisBin = bin[type][field];
+    if (thisBin === undefined) {
+        thisBin = bin[type][field] = {
+            entryDepth: 0,
+            probabilities: [],
+            '-1': 0,
+            '0': 0,
+            '1': 0,
+        };
+    }
+    thisBin.entryDepth++;
+    thisBin.probabilities.push(probability);
+    thisBin[strand]++;
+}

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts

@@ -1,21 +1,5 @@
-import { Feature } from '@jbrowse/core/util';
-import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
-import { ModificationTypeWithColor } from '../shared/types';
-export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
-    bpPerPx: number;
-    height: number;
-    highResolutionScaling: number;
-    scaleOpts: ScaleOpts;
-}
-export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
-    features: Map<string, Feature>;
-    ticks: {
-        values: number[];
-    };
-    displayCrossHatches: boolean;
-    visibleModifications?: Record<string, ModificationTypeWithColor>;
-}
+import { WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
+import type { RenderArgsDeserializedWithFeatures } from './types';
 export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<undefined>;
 }

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -1,296 +1,43 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const util_2 = require("../shared/util");
-// width/height of the triangle above e.g. insertion indicators
-const INTERBASE_INDICATOR_WIDTH = 7;
-const INTERBASE_INDICATOR_HEIGHT = 4.5;
-// minimum read depth to draw the insertion indicators, below this the
-// 'statistical significance' is low
-const MINIMUM_INTERBASE_INDICATOR_READ_DEPTH = 7;
-const complementBase = {
-    C: 'G',
-    G: 'C',
-    A: 'T',
-    T: 'A',
-};
-const fudgeFactor = 0.6;
 class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
-    // note: the snps are drawn on linear scale even if the data is drawn in log
-    // scape hence the two different scales being used
     async draw(ctx, props) {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k;
-        const { features, regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, } = props;
-        const theme = (0, ui_1.createJBrowseTheme)(configTheme);
-        const region = regions[0];
-        const width = (region.end - region.start) / bpPerPx;
-        // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
-        // wiggle display, and makes the height of the actual drawn area add
-        // "padding" to the top and bottom of the display
-        const offset = plugin_wiggle_1.YSCALEBAR_LABEL_OFFSET;
-        const height = unadjustedHeight - offset * 2;
-        const opts = { ...scaleOpts, range: [0, height] };
-        const viewScale = (0, plugin_wiggle_1.getScale)(opts);
-        // clipping and insertion indicators, uses a smaller height/2 scale
-        const indicatorViewScale = (0, plugin_wiggle_1.getScale)({
-            ...opts,
-            range: [0, height / 2],
-            scaleType: 'linear',
-        });
-        const originY = (0, plugin_wiggle_1.getOrigin)(scaleOpts.scaleType);
-        const originLinear = (0, plugin_wiggle_1.getOrigin)('linear');
-        const indicatorThreshold = (0, configuration_1.readConfObject)(cfg, 'indicatorThreshold');
-        const drawInterbaseCounts = (0, configuration_1.readConfObject)(cfg, 'drawInterbaseCounts');
-        const drawArcs = (0, configuration_1.readConfObject)(cfg, 'drawArcs');
-        const drawIndicators = (0, configuration_1.readConfObject)(cfg, 'drawIndicators');
-        // get the y coordinate that we are plotting at, this can be log scale
-        const toY = (n) => height - (viewScale(n) || 0) + offset;
-        const toHeight = (n) => toY(originY) - toY(n);
-        // used specifically for indicator
-        const toY2 = (n) => height - (indicatorViewScale(n) || 0) + offset;
-        const toHeight2 = (n) => toY2(originLinear) - toY2(n);
-        const { bases } = theme.palette;
-        const colorForBase = {
-            A: bases.A.main,
-            C: bases.C.main,
-            G: bases.G.main,
-            T: bases.T.main,
-            insertion: 'purple',
-            softclip: 'blue',
-            hardclip: 'red',
-            total: (0, configuration_1.readConfObject)(cfg, 'color'),
-            mod_NONE: 'blue',
-            cpg_meth: 'red',
-            cpg_unmeth: 'blue',
-        };
-        const feats = [...features.values()];
-        // Use two pass rendering, which helps in visualizing the SNPs at higher
-        // bpPerPx First pass: draw the gray background
-        ctx.fillStyle = colorForBase.total;
-        for (const feature of feats) {
-            if (feature.get('type') === 'skip') {
-                continue;
-            }
-            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-            const w = rightPx - leftPx + fudgeFactor;
-            const score = feature.get('score');
-            ctx.fillRect(leftPx, toY(score), w, toHeight(score));
-        }
-        // Keep track of previous total which we will use it to draw the interbase
-        // indicator (if there is a sudden clip, there will be no read coverage but
-        // there will be "clip" coverage) at that position beyond the read.
-        //
-        // if the clip is right at a block boundary then prevTotal will not be
-        // available, so this is a best attempt to plot interbase indicator at the
-        // "cliffs"
-        let prevTotal = 0;
-        // 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 : 0;
-        // @ts-expect-error
-        const drawingModifications = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications';
-        // @ts-expect-error
-        const drawingMethylation = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation';
-        const isolatedModification = 
-        // @ts-expect-error
-        (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
-        // Second pass: draw the SNP data, and add a minimum feature width of 1px
-        // which can be wider than the actual bpPerPx This reduces overdrawing of
-        // the grey background over the SNPs
-        for (const feature of feats) {
-            if (feature.get('type') === 'skip') {
-                continue;
-            }
-            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-            const snpinfo = feature.get('snpinfo');
-            const w = Math.max(rightPx - leftPx, 1);
-            const score0 = feature.get('score');
-            if (drawingModifications) {
-                let curr = 0;
-                const refbase = (_b = snpinfo.refbase) === null || _b === void 0 ? void 0 : _b.toUpperCase();
-                const { nonmods, mods, snps, ref } = snpinfo;
-                for (const m of Object.keys(nonmods).sort().reverse()) {
-                    const mod = visibleModifications[m.replace('nonmod_', '')] ||
-                        visibleModifications[m.replace('mod_', '')];
-                    if (!mod) {
-                        console.warn(`${m} not known yet`);
-                        continue;
-                    }
-                    if (isolatedModification && mod.type !== isolatedModification) {
-                        continue;
-                    }
-                    const cmp = complementBase[mod.base];
-                    // this approach is inspired from the 'simplex' approach in igv
-                    // https://github.com/igvteam/igv/blob/af07c3b1be8806cfd77343ee04982aeff17d2beb/src/main/java/org/broad/igv/sam/mods/BaseModificationCoverageRenderer.java#L51
-                    const detectable = mod.base === 'N'
-                        ? score0
-                        : (((_c = snps[mod.base]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
-                            (((_d = snps[cmp]) === null || _d === void 0 ? void 0 : _d.entryDepth) || 0) +
-                            (refbase === mod.base ? ref['1'] : 0) +
-                            (refbase === cmp ? ref['-1'] : 0);
-                    const modifiable = mod.base === 'N'
-                        ? score0
-                        : (((_e = snps[mod.base]) === null || _e === void 0 ? void 0 : _e.entryDepth) || 0) +
-                            (((_f = snps[cmp]) === null || _f === void 0 ? void 0 : _f.entryDepth) || 0) +
-                            (refbase === mod.base ? ref.entryDepth : 0) +
-                            (refbase === cmp ? ref.entryDepth : 0);
-                    const { entryDepth, avgProbability = 0 } = snpinfo.nonmods[m];
-                    const modFraction = (modifiable / score0) * (entryDepth / detectable);
-                    const nonModColor = 'blue';
-                    const c = (0, util_2.alphaColor)(nonModColor, avgProbability);
-                    const height = toHeight(score0);
-                    const bottom = toY(score0) + height;
-                    ctx.fillStyle = c;
-                    ctx.fillRect(Math.round(leftPx), bottom - (curr + modFraction * height), w, modFraction * height);
-                    curr += modFraction * height;
-                }
-                for (const m of Object.keys(mods).sort().reverse()) {
-                    const mod = visibleModifications[m.replace('mod_', '')];
-                    if (!mod) {
-                        console.warn(`${m} not known yet`);
-                        continue;
-                    }
-                    if (isolatedModification && mod.type !== isolatedModification) {
-                        continue;
-                    }
-                    const cmp = complementBase[mod.base];
-                    // this approach is inspired from the 'simplex' approach in igv
-                    // https://github.com/igvteam/igv/blob/af07c3b1be8806cfd77343ee04982aeff17d2beb/src/main/java/org/broad/igv/sam/mods/BaseModificationCoverageRenderer.java#L51
-                    const detectable = mod.base === 'N'
-                        ? score0
-                        : (((_g = snps[mod.base]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
-                            (((_h = snps[cmp]) === null || _h === void 0 ? void 0 : _h.entryDepth) || 0) +
-                            (refbase === mod.base ? ref['1'] : 0) +
-                            (refbase === cmp ? ref['-1'] : 0);
-                    const modifiable = mod.base === 'N'
-                        ? score0
-                        : (((_j = snps[mod.base]) === null || _j === void 0 ? void 0 : _j.entryDepth) || 0) +
-                            (((_k = snps[cmp]) === null || _k === void 0 ? void 0 : _k.entryDepth) || 0) +
-                            (refbase === mod.base ? ref.entryDepth : 0) +
-                            (refbase === cmp ? ref.entryDepth : 0);
-                    const { entryDepth, avgProbability = 0 } = mods[m];
-                    const modFraction = (modifiable / score0) * (entryDepth / detectable);
-                    const baseColor = mod.color || 'black';
-                    const c = (0, util_2.alphaColor)(baseColor, avgProbability);
-                    const height = toHeight(score0);
-                    const bottom = toY(score0) + height;
-                    ctx.fillStyle = c;
-                    ctx.fillRect(Math.round(leftPx), bottom - (curr + modFraction * height), w, modFraction * height);
-                    curr += modFraction * height;
-                }
-            }
-            else if (drawingMethylation) {
-                const { depth, nonmods, mods } = snpinfo;
-                let curr = 0;
-                for (const base of Object.keys(mods).sort().reverse()) {
-                    const { entryDepth } = mods[base];
-                    const height = toHeight(score0);
-                    const bottom = toY(score0) + height;
-                    ctx.fillStyle = colorForBase[base] || 'black';
-                    ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
-                    curr += entryDepth;
-                }
-                for (const base of Object.keys(nonmods).sort().reverse()) {
-                    const { entryDepth } = nonmods[base];
-                    const height = toHeight(score0);
-                    const bottom = toY(score0) + height;
-                    ctx.fillStyle = colorForBase[base] || 'black';
-                    ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
-                    curr += entryDepth;
-                }
-            }
-            else {
-                const { depth, snps } = snpinfo;
-                let curr = 0;
-                for (const base of Object.keys(snps).sort().reverse()) {
-                    const { entryDepth } = snps[base];
-                    const height = toHeight(score0);
-                    const bottom = toY(score0) + height;
-                    ctx.fillStyle = colorForBase[base] || 'black';
-                    ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
-                    curr += entryDepth;
-                }
-            }
-            const interbaseEvents = Object.keys(snpinfo.noncov);
-            if (drawInterbaseCounts) {
-                let curr = 0;
-                for (const base of interbaseEvents) {
-                    const { entryDepth } = snpinfo.noncov[base];
-                    const r = 0.6;
-                    ctx.fillStyle = colorForBase[base];
-                    ctx.fillRect(leftPx - r + extraHorizontallyFlippedOffset, INTERBASE_INDICATOR_HEIGHT + toHeight2(curr), r * 2, toHeight2(entryDepth));
-                    curr += entryDepth;
-                }
-            }
-            if (drawIndicators) {
-                let accum = 0;
-                let max = 0;
-                let maxBase = '';
-                for (const base of interbaseEvents) {
-                    const { entryDepth } = snpinfo.noncov[base];
-                    accum += entryDepth;
-                    if (entryDepth > max) {
-                        max = entryDepth;
-                        maxBase = base;
-                    }
-                }
-                // avoid drawing a bunch of indicators if coverage is very low. note:
-                // also uses the prev total in the case of the "cliff"
-                const indicatorComparatorScore = Math.max(score0, prevTotal);
-                if (accum > indicatorComparatorScore * indicatorThreshold &&
-                    indicatorComparatorScore > MINIMUM_INTERBASE_INDICATOR_READ_DEPTH) {
-                    ctx.fillStyle = colorForBase[maxBase];
-                    ctx.beginPath();
-                    const l = leftPx + extraHorizontallyFlippedOffset;
-                    ctx.moveTo(l - INTERBASE_INDICATOR_WIDTH / 2, 0);
-                    ctx.lineTo(l + INTERBASE_INDICATOR_WIDTH / 2, 0);
-                    ctx.lineTo(l, INTERBASE_INDICATOR_HEIGHT);
-                    ctx.fill();
-                }
-            }
-            prevTotal = score0;
-        }
-        if (drawArcs) {
-            for (const f of feats) {
-                if (f.get('type') !== 'skip') {
-                    continue;
-                }
-                const s = f.get('start');
-                const e = f.get('end');
-                const [left, right] = (0, util_1.bpSpanPx)(s, e, region, bpPerPx);
-                ctx.beginPath();
-                const effectiveStrand = f.get('effectiveStrand');
-                const pos = 'rgba(255,200,200,0.7)';
-                const neg = 'rgba(200,200,255,0.7)';
-                const neutral = 'rgba(200,200,200,0.7)';
-                if (effectiveStrand === 1) {
-                    ctx.strokeStyle = pos;
-                }
-                else if (effectiveStrand === -1) {
-                    ctx.strokeStyle = neg;
-                }
-                else {
-                    ctx.strokeStyle = neutral;
-                }
-                ctx.lineWidth = Math.log(f.get('score') + 1);
-                ctx.moveTo(left, height - offset * 2);
-                ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2);
-                ctx.stroke();
-            }
-        }
-        if (displayCrossHatches) {
-            ctx.lineWidth = 1;
-            ctx.strokeStyle = 'rgba(140,140,140,0.8)';
-            for (const tick of ticks.values) {
-                ctx.beginPath();
-                ctx.moveTo(0, Math.round(toY(tick)));
-                ctx.lineTo(width, Math.round(toY(tick)));
-                ctx.stroke();
-            }
-        }
+        const { makeImage } = await Promise.resolve().then(() => __importStar(require('./makeImage')));
+        await makeImage(ctx, props);
         return undefined;
     }
 }

package/dist/SNPCoverageRenderer/configSchema.d.ts

@@ -1,40 +1,25 @@
 declare const SNPCoverageRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     clipColor: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     indicatorThreshold: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
-    drawArcs: {
+    showArcs: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
-    drawInterbaseCounts: {
+    showInterbaseCounts: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
-    drawIndicators: {
+    showInterbaseIndicators: {
         type: string;
         description: string;
         defaultValue: boolean;