@jbrowse/plugin-alignments 2.17.0 → 3.0.0

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 {};

package/esm/SNPCoverageAdapter/generateCoverageBins.js

@@ -1,259 +1,33 @@
-import { doesIntersect2, max, sum } from '@jbrowse/core/util';
-// locals
-import { parseCigar } from '../MismatchParser';
-import { getMethBins } from '../ModificationParser';
-import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
-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 processDepth({ feature, bins, region, regionSequence, }) {
-    const fstart = feature.get('start');
-    const fend = feature.get('end');
-    const fstrand = feature.get('strand');
-    const regionLength = region.end - region.start;
-    for (let j = fstart; j < fend + 1; j++) {
-        const i = j - region.start;
-        if (i >= 0 && i < regionLength) {
-            if (bins[i] === undefined) {
-                bins[i] = {
-                    depth: 0,
-                    readsCounted: 0,
-                    refbase: regionSequence[i],
-                    ref: {
-                        probabilities: [],
-                        entryDepth: 0,
-                        '-1': 0,
-                        0: 0,
-                        1: 0,
-                    },
-                    snps: {},
-                    mods: {},
-                    nonmods: {},
-                    delskips: {},
-                    noncov: {},
-                };
-            }
-            if (j !== fend) {
-                bins[i].depth++;
-                bins[i].readsCounted++;
-                bins[i].ref.entryDepth++;
-                bins[i].ref[fstrand]++;
-            }
-        }
-    }
-}
-function processSNPs({ 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 : [];
-    // normal SNP based coloring
-    for (const mismatch of mismatches) {
-        const mstart = fstart + mismatch.start;
-        const mlen = 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, type } = mismatch;
-                const interbase = isInterbase(type);
-                if (type === 'deletion' || type === 'skip') {
-                    inc(bin, fstrand, 'delskips', type);
-                    bin.depth--;
-                }
-                else if (!interbase) {
-                    inc(bin, fstrand, 'snps', base);
-                    bin.ref.entryDepth--;
-                    bin.ref[fstrand]--;
-                }
-                else {
-                    inc(bin, fstrand, 'noncov', type);
-                }
-            }
-        }
-        if (mismatch.type === 'skip') {
-            // for upper case XS and TS: reports the literal strand of the genomic
-            // transcript
-            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);
-            // for lower case ts from minimap2: genomic transcript flipped by read
-            // strand
-            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++;
-        }
-    }
-}
-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 = parseCigar(feature.get('CIGAR'));
-        const { methBins, methProbs } = getMethBins(feature, cigarOps);
-        const dels = mismatches.filter(f => f.type === 'deletion');
-        // methylation based coloring takes into account both reference sequence
-        // CpG detection and reads
-        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];
-                // color
-                if ((b0 && (p0 !== undefined ? p0 > 0.5 : true)) ||
-                    (b1 && (p1 !== undefined ? p1 > 0.5 : true))) {
-                    if (bin0) {
-                        incWithProbabilities(bin0, fstrand, 'mods', 'cpg_meth', p0 || 0);
-                        bin0.ref.entryDepth--;
-                        bin0.ref[fstrand]--;
-                    }
-                    if (bin1) {
-                        incWithProbabilities(bin1, fstrand, 'mods', 'cpg_meth', p1 || 0);
-                        bin1.ref.entryDepth--;
-                        bin1.ref[fstrand]--;
-                    }
-                }
-                else {
-                    if (bin0) {
-                        if (!dels.some(d => doesIntersect2(j, j + 1, d.start + fstart, d.start + fstart + d.length))) {
-                            incWithProbabilities(bin0, fstrand, 'nonmods', 'cpg_unmeth', 1 - (p0 || 0));
-                            bin0.ref.entryDepth--;
-                            bin0.ref[fstrand]--;
-                        }
-                    }
-                    if (bin1) {
-                        if (!dels.some(d => doesIntersect2(j + 1, j + 2, d.start + fstart, d.start + fstart + d.length))) {
-                            incWithProbabilities(bin1, fstrand, 'nonmods', 'cpg_unmeth', 1 - (p1 || 0));
-                            bin1.ref.entryDepth--;
-                            bin1.ref[fstrand]--;
-                        }
-                    }
-                }
-            }
-        }
-    }
-}
-function processModification({ 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 = 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,
-                    refbase: regionSequence[epos],
-                    snps: {},
-                    ref: {
-                        probabilities: [],
-                        entryDepth: 0,
-                        '-1': 0,
-                        0: 0,
-                        1: 0,
-                    },
-                    mods: {},
-                    nonmods: {},
-                    delskips: {},
-                    noncov: {},
-                };
-            }
-            const s = 1 - sum(allProbs);
-            const bin = bins[epos];
-            if (twoColor && s > max(allProbs)) {
-                incWithProbabilities(bin, fstrand, 'nonmods', `nonmod_${type}`, s);
-            }
-            else {
-                incWithProbabilities(bin, fstrand, 'mods', `mod_${type}`, prob);
-            }
-        }
-    });
-}
-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]++;
-}
+import { sum } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { processDepth } from './processDepth';
+import { processMismatches } from './processMismatches';
+import { processModifications } from './processModifications';
+import { processReferenceCpGs } from './processReferenceCpGs';
 export async function generateCoverageBins({ fetchSequence, features, region, opts, }) {
-    const { colorBy } = opts;
+    const { stopToken, colorBy } = opts;
     const skipmap = {};
     const bins = [];
     const start2 = Math.max(0, region.start - 1);
     const diff = region.start - start2;
-    const regionSequence = (await fetchSequence({
-        ...region,
-        start: start2,
-        end: region.end + 1,
-    })) || '';
+    let start = performance.now();
     for (const feature of features) {
+        if (performance.now() - start > 400) {
+            checkStopToken(stopToken);
+            start = performance.now();
+        }
         processDepth({
             feature,
             bins,
             region,
-            regionSequence: regionSequence.slice(diff),
         });
         if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-            processModification({
+            const regionSequence = (await fetchSequence({
+                ...region,
+                start: start2,
+                end: region.end + 1,
+            })) || '';
+            processModifications({
                 feature,
                 colorBy,
                 bins,
@@ -262,6 +36,11 @@ export async function generateCoverageBins({ fetchSequence, features, region, op
             });
         }
         else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
+            const regionSequence = (await fetchSequence({
+                ...region,
+                start: start2,
+                end: region.end + 1,
+            })) || '';
             processReferenceCpGs({
                 feature,
                 bins,
@@ -269,10 +48,9 @@ export async function generateCoverageBins({ fetchSequence, features, region, op
                 regionSequence,
             });
         }
-        processSNPs({ feature, skipmap, bins, region });
+        processMismatches({ feature, skipmap, bins, region });
     }
     for (const bin of bins) {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (bin) {
             bin.mods = Object.fromEntries(Object.entries(bin.mods).map(([key, val]) => {
                 return [

package/esm/SNPCoverageAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function SNPCoverageAdapterF(pluginManager: PluginManager): void;

package/esm/SNPCoverageAdapter/processDepth.d.ts

@@ -0,0 +1,8 @@
+import type { PreBaseCoverageBin } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
+import type { AugmentedRegion } from '@jbrowse/core/util/types';
+export declare function processDepth({ feature, bins, region, }: {
+    feature: Feature;
+    bins: PreBaseCoverageBin[];
+    region: AugmentedRegion;
+}): void;

package/esm/SNPCoverageAdapter/processDepth.js

@@ -0,0 +1,35 @@
+export function processDepth({ feature, bins, region, }) {
+    const fstart = feature.get('start');
+    const fend = feature.get('end');
+    const fstrand = feature.get('strand');
+    const regionLength = region.end - region.start;
+    for (let j = fstart; j < fend + 1; j++) {
+        const i = j - region.start;
+        if (i >= 0 && i < regionLength) {
+            if (bins[i] === undefined) {
+                bins[i] = {
+                    depth: 0,
+                    readsCounted: 0,
+                    ref: {
+                        probabilities: [],
+                        entryDepth: 0,
+                        '-1': 0,
+                        0: 0,
+                        1: 0,
+                    },
+                    snps: {},
+                    mods: {},
+                    nonmods: {},
+                    delskips: {},
+                    noncov: {},
+                };
+            }
+            if (j !== fend) {
+                bins[i].depth++;
+                bins[i].readsCounted++;
+                bins[i].ref.entryDepth++;
+                bins[i].ref[fstrand]++;
+            }
+        }
+    }
+}

package/esm/SNPCoverageAdapter/processMismatches.d.ts

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

package/esm/SNPCoverageAdapter/processMismatches.js

@@ -0,0 +1,55 @@
+import { inc, isInterbase, mismatchLen } from './util';
+export 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 = 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 = isInterbase(type);
+                if (type === 'deletion' || type === 'skip') {
+                    inc(bin, fstrand, 'delskips', type);
+                    bin.depth--;
+                }
+                else if (!interbase) {
+                    inc(bin, fstrand, 'snps', base);
+                    bin.ref.entryDepth--;
+                    bin.ref[fstrand]--;
+                    bin.refbase = altbase;
+                }
+                else {
+                    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/esm/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/esm/SNPCoverageAdapter/processModifications.js

@@ -0,0 +1,46 @@
+import { max, sum } from '@jbrowse/core/util';
+import { incWithProbabilities } from './util';
+import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
+export 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 = 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 - sum(allProbs);
+            const bin = bins[epos];
+            bin.refbase = regionSequence[epos];
+            if (twoColor && s > max(allProbs)) {
+                incWithProbabilities(bin, fstrand, 'nonmods', `nonmod_${type}`, s);
+            }
+            else {
+                incWithProbabilities(bin, fstrand, 'mods', `mod_${type}`, prob);
+            }
+        }
+    });
+}

package/esm/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;