@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/esm/LinearReadCloudDisplay/drawPairChains.js

@@ -1,90 +0,0 @@
-import { getConf } from '@jbrowse/core/configuration';
-import { max, min } from '@jbrowse/core/util';
-import { fillRectCtx, strokeRectCtx } from './util';
-import { getPairedInsertSizeAndOrientationColor, getPairedInsertSizeColor, getPairedOrientationColor, } from '../shared/color';
-export function drawPairChains({ ctx, self, chainData, view, asm, }) {
-    var _a, _b, _c, _d, _e, _f, _g;
-    const coords = [];
-    const featureHeight = getConf(self, 'featureHeight');
-    const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
-    const { chains, stats } = chainData;
-    for (const chain of chains) {
-        if (chain.length > 1) {
-            const v0 = chain[0];
-            const v1 = chain[1];
-            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
-            const ra2 = asm.getCanonicalRefName(v1.refName) || v1.refName;
-            const r1s = (_b = view.bpToPx({ refName: ra1, coord: v0.start })) === null || _b === void 0 ? void 0 : _b.offsetPx;
-            const r1e = (_c = view.bpToPx({ refName: ra1, coord: v0.end })) === null || _c === void 0 ? void 0 : _c.offsetPx;
-            const r2s = (_d = view.bpToPx({ refName: ra2, coord: v1.start })) === null || _d === void 0 ? void 0 : _d.offsetPx;
-            const r2e = (_e = view.bpToPx({ refName: ra2, coord: v1.end })) === null || _e === void 0 ? void 0 : _e.offsetPx;
-            let distance = 0;
-            if (r1s !== undefined &&
-                r1e !== undefined &&
-                r2s !== undefined &&
-                r2e !== undefined) {
-                if (v0.refName === v1.refName) {
-                    const s = Math.min(v0.start, v1.start);
-                    const e = Math.max(v0.end, v1.end);
-                    distance = Math.abs(e - s);
-                }
-                coords.push({
-                    r1s,
-                    r1e,
-                    r2s,
-                    r2e,
-                    v0,
-                    v1,
-                    distance,
-                });
-            }
-        }
-        else if (self.drawSingletons) {
-            const v0 = chain[0];
-            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
-            const r1s = (_f = view.bpToPx({ refName: ra1, coord: v0.start })) === null || _f === void 0 ? void 0 : _f.offsetPx;
-            const r1e = (_g = view.bpToPx({ refName: ra1, coord: v0.end })) === null || _g === void 0 ? void 0 : _g.offsetPx;
-            if (r1s !== undefined && r1e !== undefined) {
-                const w1 = Math.max(r1e - r1s, 2);
-                fillRectCtx(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#f00');
-                strokeRectCtx(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#a00');
-            }
-        }
-    }
-    const maxD = Math.log(max(coords.map(c => c.distance)));
-    const minD = Math.max(Math.log(min(coords.map(c => c.distance))) - 1, 0);
-    const scaler = (self.height - 20) / (maxD - minD);
-    for (const { r1e, r1s, r2e, r2s, distance, v0, v1 } of coords) {
-        const w1 = Math.max(r1e - r1s, 2);
-        const w2 = Math.max(r2e - r2s, 2);
-        const [fill, stroke] = getPairedColor({ type, v0, v1, stats }) || [];
-        const top = (Math.log(distance) - minD) * scaler;
-        const halfHeight = featureHeight / 2 - 0.5;
-        const w = r2s - r1e;
-        fillRectCtx(r1e - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
-        strokeRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx, stroke);
-        strokeRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx, stroke);
-        fillRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx, fill);
-        fillRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx, fill);
-    }
-}
-export function getPairedColor({ type, v0, v1, stats, }) {
-    if (type === 'insertSizeAndOrientation') {
-        return getPairedInsertSizeAndOrientationColor(v0, v1, stats);
-    }
-    if (type === 'orientation') {
-        return getPairedOrientationColor(v0);
-    }
-    if (type === 'insertSize') {
-        return getPairedInsertSizeColor(v0, v1, stats);
-    }
-    if (type === 'gradient') {
-        const s = Math.min(v0.start, v1.start);
-        const e = Math.max(v0.end, v1.end);
-        return [
-            `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`,
-            `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,30%)`,
-        ];
-    }
-    return undefined;
-}

package/esm/LinearReadCloudDisplay/util.d.ts

@@ -1,2 +0,0 @@
-export declare function fillRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, fillColor?: string): void;
-export declare function strokeRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, strokeColor?: string): void;

package/esm/PileupRPC/methods/GetReducedFeatures.d.ts

@@ -1,37 +0,0 @@
-import PileupBaseRPC from '../base';
-import type { Region } from '@jbrowse/core/util';
-export default class PileupGetReducedFeatures extends PileupBaseRPC {
-    name: string;
-    execute(args: {
-        adapterConfig: Record<string, unknown>;
-        stopToken?: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriver: string): Promise<{
-        chains: {
-            id: string;
-            refName: string;
-            name: any;
-            start: number;
-            strand: any;
-            end: number;
-            flags: any;
-            tlen: any;
-            pair_orientation: any;
-            next_ref: any;
-            next_pos: any;
-            clipPos: number;
-            SA: any;
-        }[][];
-        stats: {
-            upper: number;
-            lower: number;
-            avg: number;
-            sd: number;
-        } | undefined;
-        hasPaired: boolean;
-        containsNoTransferables: boolean;
-    }>;
-}

package/esm/PileupRPC/methods/GetReducedFeatures.js

@@ -1,48 +0,0 @@
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { dedupe, groupBy } from '@jbrowse/core/util';
-import { firstValueFrom } from 'rxjs';
-import { toArray } from 'rxjs/operators';
-import { getClip } from '../../MismatchParser';
-import PileupBaseRPC from '../base';
-import { filterForPairs, getInsertSizeStats } from '../util';
-export default class PileupGetReducedFeatures extends PileupBaseRPC {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetReducedFeatures';
-    }
-    async execute(args, rpcDriver) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriver);
-        const { adapterConfig, sessionId, regions } = deserializedArgs;
-        const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const featuresArray = await firstValueFrom(dataAdapter
-            .getFeaturesInMultipleRegions(regions, deserializedArgs)
-            .pipe(toArray()));
-        const reduced = dedupe(featuresArray.map(f => {
-            var _a;
-            return ({
-                id: f.id(),
-                refName: f.get('refName'),
-                name: f.get('name'),
-                start: f.get('start'),
-                strand: f.get('strand'),
-                end: f.get('end'),
-                flags: f.get('flags'),
-                tlen: f.get('template_length'),
-                pair_orientation: f.get('pair_orientation'),
-                next_ref: f.get('next_ref'),
-                next_pos: f.get('next_pos'),
-                clipPos: getClip(f.get('CIGAR'), f.get('strand')),
-                SA: (_a = f.get('tags')) === null || _a === void 0 ? void 0 : _a.SA,
-            });
-        }), f => f.id);
-        const filtered = filterForPairs(reduced);
-        const stats = filtered.length ? getInsertSizeStats(filtered) : undefined;
-        const chains = groupBy(reduced, f => f.name);
-        return {
-            chains: Object.values(chains),
-            stats,
-            hasPaired: !!stats,
-            containsNoTransferables: true,
-        };
-    }
-}

package/esm/PileupRPC/util.d.ts

@@ -1,8 +0,0 @@
-import type { ReducedFeature } from '../shared/fetchChains';
-export declare function getInsertSizeStats(features: ReducedFeature[]): {
-    upper: number;
-    lower: number;
-    avg: number;
-    sd: number;
-};
-export declare function filterForPairs(features: ReducedFeature[]): ReducedFeature[];

package/esm/PileupRPC/util.js

@@ -1,14 +0,0 @@
-export function getInsertSizeStats(features) {
-    const filtered = features.map(f => Math.abs(f.tlen));
-    const sum = filtered.reduce((a, b) => a + b, 0);
-    const sum2 = filtered.map(a => a * a).reduce((a, b) => a + b, 0);
-    const total = filtered.length;
-    const avg = sum / total;
-    const sd = Math.sqrt((total * sum2 - sum * sum) / (total * total));
-    const upper = avg + 4 * sd;
-    const lower = avg - 3 * sd;
-    return { upper, lower, avg, sd };
-}
-export function filterForPairs(features) {
-    return features.filter(f => f.flags & 2 && !(f.flags & 256) && !(f.flags & 2048));
-}

package/esm/PileupRenderer/getAlignmentShapeColor.d.ts

@@ -1,10 +0,0 @@
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Feature } from '@jbrowse/core/util';
-export declare function getAlignmentShapeColor({ colorType, tag, feature, config, defaultColor, colorTagMap, }: {
-    colorType: string;
-    tag: string;
-    feature: Feature;
-    defaultColor: boolean;
-    config: AnyConfigurationModel;
-    colorTagMap: Record<string, string>;
-}): any;

package/esm/PileupRenderer/renderAlignmentShape.d.ts

@@ -1,7 +0,0 @@
-import type { ProcessedRenderArgs } from './types';
-import type { LayoutFeature } from './util';
-export declare function renderAlignmentShape({ ctx, feat, renderArgs, }: {
-    ctx: CanvasRenderingContext2D;
-    feat: LayoutFeature;
-    renderArgs: ProcessedRenderArgs;
-}): void;

package/esm/PileupRenderer/renderAlignmentShape.js

@@ -1,117 +0,0 @@
-import { bpSpanPx } from '@jbrowse/core/util';
-import { parseCigar } from '../MismatchParser';
-export function renderAlignmentShape({ ctx, feat, renderArgs, }) {
-    const { regions, bpPerPx } = renderArgs;
-    const { heightPx, topPx, feature } = feat;
-    const region = regions[0];
-    const s = feature.get('start');
-    const e = feature.get('end');
-    const CIGAR = feature.get('CIGAR');
-    const flip = region.reversed ? -1 : 1;
-    const strand = feature.get('strand') * flip;
-    const renderChevrons = bpPerPx < 10 && heightPx > 5;
-    if (CIGAR === null || CIGAR === void 0 ? void 0 : CIGAR.includes('N')) {
-        const cigarOps = parseCigar(CIGAR);
-        if (strand === 1) {
-            let drawLen = 0;
-            let drawStart = s;
-            for (let i = 0; i < cigarOps.length; i += 2) {
-                const opLen = +cigarOps[i];
-                const op = cigarOps[i + 1];
-                if (op === 'M' || op === 'X' || op === '=' || op === 'D') {
-                    drawLen += opLen;
-                }
-                else if (op === 'N') {
-                    if (drawStart !== drawLen) {
-                        const [leftPx, rightPx] = bpSpanPx(drawStart, drawStart + drawLen, region, bpPerPx);
-                        const w = rightPx - leftPx;
-                        ctx.fillRect(leftPx, topPx, w, heightPx);
-                    }
-                    drawStart += drawLen + opLen;
-                    drawLen = 0;
-                }
-            }
-            if (drawStart !== drawLen) {
-                const [leftPx, rightPx] = bpSpanPx(drawStart, drawStart + drawLen, region, bpPerPx);
-                const w = rightPx - leftPx;
-                if (renderChevrons) {
-                    ctx.beginPath();
-                    ctx.moveTo(leftPx, topPx);
-                    ctx.lineTo(leftPx, topPx + heightPx);
-                    ctx.lineTo(rightPx, topPx + heightPx);
-                    ctx.lineTo(rightPx + 5, topPx + heightPx / 2);
-                    ctx.lineTo(rightPx, topPx);
-                    ctx.closePath();
-                    ctx.fill();
-                }
-                else {
-                    ctx.fillRect(leftPx, topPx, w, heightPx);
-                }
-            }
-        }
-        else if (strand === -1) {
-            let drawLen = 0;
-            let drawStart = e;
-            for (let i = cigarOps.length - 2; i >= 0; i -= 2) {
-                const opLen = +cigarOps[i];
-                const op = cigarOps[i + 1];
-                if (op === 'M' || op === 'X' || op === '=' || op === 'D') {
-                    drawLen += opLen;
-                }
-                else if (op === 'N') {
-                    if (drawLen !== 0) {
-                        const [leftPx, rightPx] = bpSpanPx(drawStart - drawLen, drawStart, region, bpPerPx);
-                        ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx);
-                    }
-                    drawStart -= drawLen + opLen;
-                    drawLen = 0;
-                }
-            }
-            if (drawLen !== 0) {
-                const [leftPx, rightPx] = bpSpanPx(drawStart - drawLen, drawStart, region, bpPerPx);
-                const w = rightPx - leftPx;
-                if (renderChevrons) {
-                    ctx.beginPath();
-                    ctx.moveTo(leftPx - 5, topPx + heightPx / 2);
-                    ctx.lineTo(leftPx, topPx + heightPx);
-                    ctx.lineTo(rightPx, topPx + heightPx);
-                    ctx.lineTo(rightPx, topPx);
-                    ctx.lineTo(leftPx, topPx);
-                    ctx.closePath();
-                    ctx.fill();
-                }
-                else {
-                    ctx.fillRect(leftPx, topPx, w, heightPx);
-                }
-            }
-        }
-    }
-    else {
-        const [leftPx, rightPx] = bpSpanPx(s, e, region, bpPerPx);
-        if (bpPerPx < 10 && heightPx > 5) {
-            if (strand === -1) {
-                ctx.beginPath();
-                ctx.moveTo(leftPx - 5, topPx + heightPx / 2);
-                ctx.lineTo(leftPx, topPx + heightPx);
-                ctx.lineTo(rightPx, topPx + heightPx);
-                ctx.lineTo(rightPx, topPx);
-                ctx.lineTo(leftPx, topPx);
-                ctx.closePath();
-                ctx.fill();
-            }
-            else {
-                ctx.beginPath();
-                ctx.moveTo(leftPx, topPx);
-                ctx.lineTo(leftPx, topPx + heightPx);
-                ctx.lineTo(rightPx, topPx + heightPx);
-                ctx.lineTo(rightPx + 5, topPx + heightPx / 2);
-                ctx.lineTo(rightPx, topPx);
-                ctx.closePath();
-                ctx.fill();
-            }
-        }
-        else {
-            ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx);
-        }
-    }
-}

package/esm/PileupRenderer/renderMethylation.js

@@ -1,57 +0,0 @@
-import { bpSpanPx } from '@jbrowse/core/util';
-import { colord } from '@jbrowse/core/util/colord';
-import { fillRect } from './util';
-import { getMethBins } from '../ModificationParser/getMethBins';
-export function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
-    const { regionSequence } = renderArgs;
-    const { feature, topPx, heightPx } = feat;
-    if (!regionSequence) {
-        throw new Error('region sequence required for methylation');
-    }
-    const seq = feature.get('seq');
-    if (!seq) {
-        return;
-    }
-    const fstart = feature.get('start');
-    const fend = feature.get('end');
-    const { methBins, methProbs, hydroxyMethBins, hydroxyMethProbs } = getMethBins(feature, cigarOps);
-    function getCol(k) {
-        if (methBins[k]) {
-            const p = methProbs[k] || 0;
-            return (p > 0.5
-                ? colord('red').alpha((p - 0.5) * 2)
-                : colord('blue').alpha(1 - p * 2)).toHslString();
-        }
-        if (hydroxyMethBins[k]) {
-            const p = hydroxyMethProbs[k] || 0;
-            return (p > 0.5
-                ? colord('pink').alpha((p - 0.5) * 2)
-                : colord('purple').alpha(1 - p * 2)).toHslString();
-        }
-        return undefined;
-    }
-    const r = regionSequence.toLowerCase();
-    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') {
-            if (bpPerPx > 2) {
-                const [leftPx, rightPx] = bpSpanPx(j, j + 2, region, bpPerPx);
-                const w = rightPx - leftPx + 0.5;
-                const c = getCol(i) || getCol(i + 1) || 'blue';
-                fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-            }
-            else {
-                const [leftPx, rightPx] = bpSpanPx(j, j + 1, region, bpPerPx);
-                const w = rightPx - leftPx + 0.5;
-                const c = getCol(i) || 'blue';
-                fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-                const [leftPx2, rightPx2] = bpSpanPx(j + 1, j + 2, region, bpPerPx);
-                const w2 = rightPx2 - leftPx2 + 0.5;
-                const c2 = getCol(i + 1) || 'blue';
-                fillRect(ctx, leftPx2, topPx, w2, heightPx, canvasWidth, c2);
-            }
-        }
-    }
-}

package/esm/PileupRenderer/renderMismatches.d.ts

@@ -1,18 +0,0 @@
-import type { ProcessedRenderArgs } from './types';
-import type { LayoutFeature } from './util';
-export declare function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels, }: {
-    ctx: CanvasRenderingContext2D;
-    feat: LayoutFeature;
-    renderArgs: ProcessedRenderArgs;
-    colorMap: Record<string, string>;
-    colorContrastMap: Record<string, string>;
-    mismatchAlpha?: boolean;
-    drawIndels?: boolean;
-    drawSNPsMuted?: boolean;
-    minSubfeatureWidth: number;
-    largeInsertionIndicatorScale: number;
-    hideSmallIndels: boolean;
-    charWidth: number;
-    charHeight: number;
-    canvasWidth: number;
-}): void;

package/esm/PileupRenderer/renderMismatches.js

@@ -1,121 +0,0 @@
-import { bpSpanPx, measureText } from '@jbrowse/core/util';
-import { colord } from '@jbrowse/core/util/colord';
-import { fillRect } from './util';
-export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
-    const { bpPerPx, regions } = renderArgs;
-    const { heightPx, topPx, feature } = feat;
-    const region = regions[0];
-    const start = feature.get('start');
-    const pxPerBp = Math.min(1 / bpPerPx, 2);
-    const mismatches = feature.get('mismatches');
-    const heightLim = charHeight - 2;
-    const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx + 1 : -1;
-    if (!mismatches) {
-        return;
-    }
-    for (const mismatch of mismatches) {
-        const mstart = start + mismatch.start;
-        const mlen = mismatch.length;
-        const mbase = mismatch.base;
-        const [leftPx, rightPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx);
-        const widthPx = Math.max(minSubfeatureWidth, rightPx - leftPx);
-        if (mismatch.type === 'mismatch') {
-            if (!drawSNPsMuted) {
-                const baseColor = colorMap[mismatch.base] || '#888';
-                const c = mismatchAlpha && mismatch.qual !== undefined
-                    ? colord(baseColor)
-                        .alpha(Math.min(1, mismatch.qual / 50))
-                        .toHslString()
-                    : baseColor;
-                fillRect(ctx, Math.round(leftPx), topPx, widthPx, heightPx, canvasWidth, c);
-            }
-            if (widthPx >= charWidth && heightPx >= heightLim) {
-                const contrastColor = drawSNPsMuted
-                    ? 'black'
-                    : colorContrastMap[mismatch.base] || 'black';
-                ctx.fillStyle =
-                    mismatchAlpha && mismatch.qual !== undefined
-                        ? colord(contrastColor)
-                            .alpha(Math.min(1, mismatch.qual / 50))
-                            .toHslString()
-                        : contrastColor;
-                ctx.fillText(mbase, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
-            }
-        }
-        else if (mismatch.type === 'deletion' && drawIndels) {
-            const len = mismatch.length;
-            if (!hideSmallIndels || len >= 10) {
-                fillRect(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorMap.deletion);
-                const txt = `${mismatch.length}`;
-                const rwidth = measureText(txt, 10);
-                if (widthPx >= rwidth && heightPx >= heightLim) {
-                    ctx.fillStyle = colorContrastMap.deletion;
-                    ctx.fillText(txt, (leftPx + rightPx) / 2 - rwidth / 2, topPx + heightPx);
-                }
-            }
-        }
-        else if (mismatch.type === 'insertion' && drawIndels) {
-            const pos = leftPx + extraHorizontallyFlippedOffset;
-            const len = +mismatch.base || mismatch.length;
-            const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx));
-            if (len < 10) {
-                if (!hideSmallIndels) {
-                    fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, colorMap.insertion);
-                    if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
-                        const l = Math.round(pos - insW);
-                        fillRect(ctx, l, topPx, insW * 3, 1, canvasWidth);
-                        fillRect(ctx, l, topPx + heightPx - 1, insW * 3, 1, canvasWidth);
-                        ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx);
-                    }
-                }
-            }
-        }
-        else if (mismatch.type === 'hardclip' || mismatch.type === 'softclip') {
-            const pos = leftPx + extraHorizontallyFlippedOffset;
-            const c = colorMap[mismatch.type];
-            const clipW = Math.max(minSubfeatureWidth, pxPerBp);
-            fillRect(ctx, pos, topPx, clipW, heightPx, canvasWidth, c);
-            if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
-                const l = pos - clipW;
-                fillRect(ctx, l, topPx, clipW * 3, 1, canvasWidth);
-                fillRect(ctx, l, topPx + heightPx - 1, clipW * 3, 1, canvasWidth);
-                ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx);
-            }
-        }
-        else if (mismatch.type === 'skip') {
-            if (leftPx + widthPx > 0) {
-                const adjustPx = widthPx - (bpPerPx > 10 ? 1.5 : 0);
-                const l = Math.max(0, leftPx);
-                const t = topPx + heightPx / 2 - 1;
-                const w = adjustPx + Math.min(leftPx, 0);
-                const h = 1;
-                fillRect(ctx, l, t, w, h, canvasWidth, colorMap.skip);
-            }
-        }
-    }
-    if (drawIndels) {
-        for (const mismatch of mismatches) {
-            const mstart = start + mismatch.start;
-            const mlen = mismatch.length;
-            const len = +mismatch.base || mismatch.length;
-            if (mismatch.type === 'insertion' && len >= 10) {
-                const [leftPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx);
-                const txt = `${len}`;
-                if (bpPerPx > largeInsertionIndicatorScale) {
-                    fillRect(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, colorMap.insertion);
-                }
-                else if (heightPx > charHeight) {
-                    const rwidth = measureText(txt);
-                    const padding = 5;
-                    fillRect(ctx, leftPx - rwidth / 2 - padding, topPx, rwidth + 2 * padding, heightPx, canvasWidth, 'purple');
-                    ctx.fillStyle = colorContrastMap.insertion;
-                    ctx.fillText(txt, leftPx - rwidth / 2, topPx + heightPx);
-                }
-                else {
-                    const padding = 2;
-                    fillRect(ctx, leftPx - padding, topPx, 2 * padding, heightPx, canvasWidth, colorMap.insertion);
-                }
-            }
-        }
-    }
-}

package/esm/PileupRenderer/renderModifications.d.ts

@@ -1,12 +0,0 @@
-import type { ProcessedRenderArgs } from './types';
-import type { LayoutFeature } from './util';
-import type { Region } from '@jbrowse/core/util';
-export declare function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }: {
-    ctx: CanvasRenderingContext2D;
-    feat: LayoutFeature;
-    region: Region;
-    bpPerPx: number;
-    renderArgs: ProcessedRenderArgs;
-    canvasWidth: number;
-    cigarOps: string[];
-}): void;

package/esm/PileupRenderer/renderModifications.js

@@ -1,41 +0,0 @@
-import { bpSpanPx, max, sum } from '@jbrowse/core/util';
-import { fillRect } from './util';
-import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
-import { alphaColor } from '../shared/util';
-export function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
-    var _a, _b, _c;
-    const { feature, topPx, heightPx } = feat;
-    const { colorBy, visibleModifications = {} } = renderArgs;
-    const seq = feature.get('seq');
-    if (!seq) {
-        return;
-    }
-    const start = feature.get('start');
-    const isolatedModification = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
-    const twoColor = (_b = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _b === void 0 ? void 0 : _b.twoColor;
-    (_c = getMaxProbModAtEachPosition(feature, cigarOps)) === null || _c === void 0 ? void 0 : _c.forEach(({ allProbs, prob, type }, pos) => {
-        const r = start + pos;
-        const [leftPx, rightPx] = bpSpanPx(r, r + 1, region, bpPerPx);
-        const mod = visibleModifications[type];
-        if (!mod) {
-            console.warn(`${type} not known yet`);
-            return;
-        }
-        if (isolatedModification && mod.type !== isolatedModification) {
-            return;
-        }
-        const col = mod.color || 'black';
-        const s = 1 - sum(allProbs);
-        if (twoColor && s > max(allProbs)) {
-            const c = alphaColor('blue', s);
-            const w = rightPx - leftPx + 0.5;
-            fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-        }
-        else {
-            const c = alphaColor(col, prob);
-            const w = rightPx - leftPx + 0.5;
-            fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-        }
-        pos++;
-    });
-}

package/esm/PileupRenderer/renderPerBaseLettering.d.ts

@@ -1,14 +0,0 @@
-import type { LayoutFeature } from './util';
-import type { Region } from '@jbrowse/core/util';
-export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorMap, colorContrastMap, charWidth, charHeight, canvasWidth, cigarOps, }: {
-    ctx: CanvasRenderingContext2D;
-    feat: LayoutFeature;
-    region: Region;
-    bpPerPx: number;
-    colorMap: Record<string, string>;
-    colorContrastMap: Record<string, string>;
-    charWidth: number;
-    charHeight: number;
-    canvasWidth: number;
-    cigarOps: string[];
-}): void;

package/esm/PileupRenderer/renderPerBaseLettering.js

@@ -1,39 +0,0 @@
-import { bpSpanPx } from '@jbrowse/core/util';
-import { fillRect } from './util';
-export function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorMap, colorContrastMap, charWidth, charHeight, canvasWidth, cigarOps, }) {
-    const heightLim = charHeight - 2;
-    const { feature, topPx, heightPx } = feat;
-    const seq = feature.get('seq');
-    const w = 1 / bpPerPx;
-    const start = feature.get('start');
-    let soffset = 0;
-    let roffset = 0;
-    if (!seq) {
-        return;
-    }
-    for (let i = 0; i < cigarOps.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op === 'S' || op === 'I') {
-            soffset += len;
-        }
-        else if (op === 'D' || op === 'N') {
-            roffset += len;
-        }
-        else if (op === 'M' || op === 'X' || op === '=') {
-            for (let m = 0; m < len; m++) {
-                const letter = seq[soffset + m];
-                const r = start + roffset + m;
-                const [leftPx] = bpSpanPx(r, r + 1, region, bpPerPx);
-                const c = colorMap[letter];
-                fillRect(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c);
-                if (w >= charWidth && heightPx >= heightLim) {
-                    ctx.fillStyle = colorContrastMap[letter];
-                    ctx.fillText(letter, leftPx + (w - charWidth) / 2 + 1, topPx + heightPx);
-                }
-            }
-            soffset += len;
-            roffset += len;
-        }
-    }
-}

package/esm/PileupRenderer/renderPerBaseQuality.d.ts

@@ -1,10 +0,0 @@
-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;