@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/dist/PileupRenderer/renderers/renderMismatches.js

@@ -1,148 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderMismatches = renderMismatches;
-const util_1 = require("@jbrowse/core/util");
-const colord_1 = require("@jbrowse/core/util/colord");
-const util_2 = require("../util");
-function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
-    var _a;
-    const items = [];
-    const coords = [];
-    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 = (_a = feature.get('mismatches')) !== null && _a !== void 0 ? _a : [];
-    const heightLim = charHeight - 2;
-    const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx + 1 : -1;
-    for (const mismatch of mismatches) {
-        const mstart = start + mismatch.start;
-        const mlen = mismatch.length;
-        const mbase = mismatch.base;
-        const [leftPx, rightPx] = (0, util_1.bpSpanPx)(mstart, mstart + mlen, region, bpPerPx);
-        const widthPx = Math.max(minSubfeatureWidth, rightPx - leftPx);
-        if (mismatch.type === 'mismatch') {
-            items.push({
-                type: 'mismatch',
-                seq: mismatch.base,
-            });
-            coords.push(leftPx, topPx, rightPx, topPx + heightPx);
-            if (!drawSNPsMuted) {
-                const baseColor = colorMap[mismatch.base] || '#888';
-                const c = mismatchAlpha && mismatch.qual !== undefined
-                    ? (0, colord_1.colord)(baseColor)
-                        .alpha(Math.min(1, mismatch.qual / 50))
-                        .toHslString()
-                    : baseColor;
-                (0, util_2.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
-                        ? (0, colord_1.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) {
-                (0, util_2.fillRect)(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorMap.deletion);
-                items.push({
-                    type: 'deletion',
-                    seq: `${mismatch.length}`,
-                });
-                coords.push(leftPx, topPx, rightPx, topPx + heightPx);
-                const txt = `${mismatch.length}`;
-                const rwidth = (0, util_1.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) {
-                    (0, util_2.fillRect)(ctx, pos, topPx, insW, heightPx, canvasWidth, colorMap.insertion);
-                    if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
-                        items.push({
-                            type: 'insertion',
-                            seq: mismatch.insertedBases || 'unknown',
-                        });
-                        coords.push(leftPx - 2, topPx, leftPx + insW + 2, topPx + heightPx);
-                        const l = Math.round(pos - insW);
-                        (0, util_2.fillRect)(ctx, l, topPx, insW * 3, 1, canvasWidth);
-                        (0, util_2.fillRect)(ctx, l, topPx + heightPx - 1, insW * 3, 1, canvasWidth);
-                        ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx);
-                    }
-                }
-            }
-        }
-        else if (mismatch.type === 'hardclip' || mismatch.type === 'softclip') {
-            const pos = leftPx + extraHorizontallyFlippedOffset;
-            const c = colorMap[mismatch.type];
-            const clipW = Math.max(minSubfeatureWidth, pxPerBp);
-            (0, util_2.fillRect)(ctx, pos, topPx, clipW, heightPx, canvasWidth, c);
-            if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
-                const l = pos - clipW;
-                (0, util_2.fillRect)(ctx, l, topPx, clipW * 3, 1, canvasWidth);
-                (0, util_2.fillRect)(ctx, l, topPx + heightPx - 1, clipW * 3, 1, canvasWidth);
-                ctx.fillText(`(${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;
-                (0, util_2.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] = (0, util_1.bpSpanPx)(mstart, mstart + mlen, region, bpPerPx);
-                const txt = `${len}`;
-                items.push({
-                    type: 'insertion',
-                    seq: mismatch.insertedBases || 'unknown',
-                });
-                coords.push(leftPx - 3, topPx, leftPx + 4, topPx + heightPx);
-                if (bpPerPx > largeInsertionIndicatorScale) {
-                    (0, util_2.fillRect)(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, colorMap.insertion);
-                }
-                else if (heightPx > charHeight) {
-                    const rwidth = (0, util_1.measureText)(txt);
-                    const padding = 5;
-                    (0, util_2.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;
-                    (0, util_2.fillRect)(ctx, leftPx - padding, topPx, 2 * padding, heightPx, canvasWidth, colorMap.insertion);
-                }
-            }
-        }
-    }
-    return {
-        coords,
-        items,
-    };
-}

package/dist/PileupRenderer/renderers/renderModifications.d.ts

@@ -1,15 +0,0 @@
-import type { FlatbushItem, 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[];
-}): {
-    coords: number[];
-    items: FlatbushItem[];
-};

package/dist/PileupRenderer/renderers/renderModifications.js

@@ -1,84 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderModifications = renderModifications;
-const util_1 = require("@jbrowse/core/util");
-const MismatchParser_1 = require("../../MismatchParser");
-const getModPositions_1 = require("../../ModificationParser/getModPositions");
-const getModProbabilities_1 = require("../../ModificationParser/getModProbabilities");
-const getMaximumModificationAtEachPosition_1 = require("../../shared/getMaximumModificationAtEachPosition");
-const modificationData_1 = require("../../shared/modificationData");
-const util_2 = require("../../shared/util");
-const util_3 = require("../../util");
-const util_4 = require("../util");
-function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
-    var _a, _b, _c, _d, _e;
-    const items = [];
-    const coords = [];
-    const { feature, topPx, heightPx } = feat;
-    const { colorBy, visibleModifications = {} } = renderArgs;
-    const seq = feature.get('seq');
-    if (!seq) {
-        return { coords, items };
-    }
-    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;
-    const modificationThreshold = (_d = (_c = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _c === void 0 ? void 0 : _c.threshold) !== null && _d !== void 0 ? _d : 10;
-    const thresholdFraction = modificationThreshold / 100;
-    const fstrand = feature.get('strand');
-    const mm = (0, util_3.getTagAlt)(feature, 'MM', 'Mm') || '';
-    const modifications = (0, getModPositions_1.getModPositions)(mm, seq, fstrand);
-    const probabilities = (0, getModProbabilities_1.getModProbabilities)(feature);
-    const modsByPosition = new Map();
-    let probIndex = 0;
-    for (const { type, base, strand, positions } of modifications) {
-        for (const { ref, idx } of (0, MismatchParser_1.getNextRefPos)(cigarOps, positions)) {
-            const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[probIndex + (fstrand === -1 ? positions.length - 1 - idx : idx)]) || 0;
-            if (!modsByPosition.has(ref)) {
-                modsByPosition.set(ref, []);
-            }
-            modsByPosition.get(ref).push({ type, base, strand, prob });
-        }
-        probIndex += positions.length;
-    }
-    (_e = (0, getMaximumModificationAtEachPosition_1.getMaxProbModAtEachPosition)(feature, cigarOps)) === null || _e === void 0 ? void 0 : _e.forEach(({ allProbs, prob, type }, pos) => {
-        const r = start + pos;
-        const [leftPx, rightPx] = (0, util_1.bpSpanPx)(r, r + 1, region, bpPerPx);
-        const mod = visibleModifications[type];
-        if (!mod) {
-            console.warn(`${type} not known yet`);
-            return;
-        }
-        if (isolatedModification && mod.type !== isolatedModification) {
-            return;
-        }
-        if (prob < thresholdFraction) {
-            return;
-        }
-        const col = mod.color || 'black';
-        const s = 1 - (0, util_1.sum)(allProbs);
-        if (twoColor && s > (0, util_1.max)(allProbs)) {
-            const c = (0, util_2.alphaColor)('blue', s);
-            const w = rightPx - leftPx + 0.5;
-            (0, util_4.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-        }
-        else {
-            const c = (0, util_2.alphaColor)(col, prob);
-            const w = rightPx - leftPx + 0.5;
-            (0, util_4.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-        }
-        const modsAtPos = modsByPosition.get(pos) || [];
-        const strandInfo = modsAtPos
-            .map(m => `${m.base}${m.strand}${m.type} ${(0, modificationData_1.getModificationName)(m.type)} (${(m.prob * 100).toFixed(1)}%)`)
-            .join('<br/>');
-        items.push({
-            type: 'modification',
-            seq: strandInfo || mod.base,
-            modType: type,
-            probability: prob,
-        });
-        coords.push(leftPx, topPx, rightPx, topPx + heightPx);
-        pos++;
-    });
-    return { coords, items };
-}

package/dist/PileupRenderer/renderers/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/dist/PileupRenderer/renderers/renderPerBaseLettering.js

@@ -1,42 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderPerBaseLettering = renderPerBaseLettering;
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("../util");
-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] = (0, util_1.bpSpanPx)(r, r + 1, region, bpPerPx);
-                const c = colorMap[letter];
-                (0, util_2.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/dist/PileupRenderer/renderers/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;

package/dist/PileupRenderer/renderers/renderPerBaseQuality.js

@@ -1,35 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderPerBaseQuality = renderPerBaseQuality;
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("../util");
-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 w = 1 / bpPerPx;
-    const start = feature.get('start');
-    let soffset = 0;
-    let roffset = 0;
-    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 score = scores[soffset + m];
-                const start0 = start + roffset + m;
-                const leftPx = (0, util_1.bpSpanPx)(start0, start0 + 1, region, bpPerPx)[0];
-                const c = `hsl(${score === 255 ? 150 : score * 1.5},55%,50%)`;
-                (0, util_2.fillRect)(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c);
-            }
-            soffset += len;
-            roffset += len;
-        }
-    }
-}

package/dist/PileupRenderer/renderers/renderSoftClipping.d.ts

@@ -1,13 +0,0 @@
-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, colorMap, canvasWidth, }: {
-    ctx: CanvasRenderingContext2D;
-    feat: LayoutFeature;
-    renderArgs: ProcessedRenderArgs;
-    config: AnyConfigurationModel;
-    colorMap: Record<string, string>;
-    theme: Theme;
-    canvasWidth: number;
-}): void;

package/dist/PileupRenderer/renderers/renderSoftClipping.js

@@ -1,59 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderSoftClipping = renderSoftClipping;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const MismatchParser_1 = require("../../MismatchParser");
-const util_2 = require("../util");
-function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorMap, canvasWidth, }) {
-    const { feature, topPx, heightPx } = feat;
-    const { regions, bpPerPx } = renderArgs;
-    const region = regions[0];
-    const minFeatWidth = (0, configuration_1.readConfObject)(config, 'minSubfeatureWidth');
-    const mismatches = feature.get('mismatches');
-    const seq = feature.get('seq');
-    const { charWidth, charHeight } = (0, util_2.getCharWidthHeight)();
-    if (!(seq && mismatches)) {
-        return;
-    }
-    const heightLim = charHeight - 2;
-    let seqOffset = 0;
-    let refOffset = 0;
-    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);
-                const baseColor = colorMap[base] || '#000000';
-                ctx.fillStyle = baseColor;
-                (0, util_2.fillRect)(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth);
-                if (widthPx >= charWidth && heightPx >= heightLim) {
-                    ctx.fillStyle = theme.palette.getContrastText(baseColor);
-                    ctx.fillText(base, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
-                }
-            }
-            seqOffset += len;
-        }
-        if (op === 'N') {
-            refOffset += len;
-        }
-        if (op === 'M' || op === '=' || op === 'X') {
-            refOffset += len;
-            seqOffset += len;
-        }
-        if (op === 'H') {
-        }
-        if (op === 'D') {
-            refOffset += len;
-        }
-        if (op === 'I') {
-            seqOffset += len;
-        }
-    }
-}

package/dist/PileupRenderer/sortUtil.d.ts

@@ -1,3 +0,0 @@
-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

@@ -1,80 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.sortFeature = void 0;
-const util_1 = require("@jbrowse/core/util");
-const sortFeature = (features, sortedBy) => {
-    const featureArray = Array.from(features.values());
-    const featuresInCenterLine = [];
-    const featuresOutsideCenter = [];
-    const { pos, type } = sortedBy;
-    for (const innerArray of featureArray) {
-        const feature = innerArray;
-        const start = feature.get('start');
-        const end = feature.get('end');
-        if ((0, util_1.doesIntersect2)(pos - 1, pos, start, end)) {
-            featuresInCenterLine.push(innerArray);
-        }
-        else {
-            featuresOutsideCenter.push(innerArray);
-        }
-    }
-    const isCram = featureArray.length ? featureArray[0].get('tags') : false;
-    switch (type) {
-        case 'Start location': {
-            featuresInCenterLine.sort((a, b) => a.get('start') - b.get('start'));
-            break;
-        }
-        case 'tag': {
-            const tag = sortedBy.tag;
-            const getTag = (f, t) => {
-                return isCram ? f.get('tags')[t] : f.get(t);
-            };
-            const isString = featuresInCenterLine[0] &&
-                typeof getTag(featuresInCenterLine[0], tag) === 'string';
-            if (isString) {
-                featuresInCenterLine.sort((a, b) => getTag(b, tag).localeCompare(getTag(a, tag)));
-            }
-            else {
-                featuresInCenterLine.sort((a, b) => (getTag(b, tag) || 0) - (getTag(a, tag) || 0));
-            }
-            break;
-        }
-        case 'Base pair': {
-            const baseSortArray = [];
-            for (const feature of featuresInCenterLine) {
-                const mismatches = feature.get('mismatches');
-                for (const m of mismatches) {
-                    const start = feature.get('start');
-                    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(), 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();
-                return acode === bcode && acode === '*'
-                    ?
-                        aMismatch.length - bMismatch.length
-                    : (acode ? acode.charCodeAt(0) : 0) -
-                        (bcode ? bcode.charCodeAt(0) : 0);
-            });
-            break;
-        }
-        case 'Read strand': {
-            featuresInCenterLine.sort((a, b) => a.get('strand') <= b.get('strand') ? 1 : -1);
-            break;
-        }
-    }
-    return new Map([...featuresInCenterLine, ...featuresOutsideCenter].map(feature => [
-        feature.id(),
-        feature,
-    ]));
-};
-exports.sortFeature = sortFeature;

package/dist/PileupRenderer/types.d.ts

@@ -1,33 +0,0 @@
-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 FlatbushItem {
-    type: 'insertion' | 'deletion' | 'mismatch' | 'modification';
-    seq: string;
-    modType?: string;
-    probability?: number;
-}
-export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
-    colorBy?: ColorBy;
-    colorTagMap?: Record<string, string>;
-    visibleModifications?: Record<string, ModificationTypeWithColor>;
-    sortedBy?: SortedBy;
-    showSoftClip: boolean;
-    highResolutionScaling: number;
-    statusCallback?: (arg: string) => void;
-}
-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

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

package/dist/PileupRenderer/util.d.ts

@@ -1,28 +0,0 @@
-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;
-    C: string;
-    G: string;
-    T: string;
-    deletion: string;
-    insertion: string;
-    hardclip: string;
-    softclip: string;
-    skip: string;
-};
-export declare function getContrastBaseMap(theme: Theme): {
-    [k: string]: string;
-};
-export declare function shouldDrawSNPsMuted(type?: string): boolean;
-export declare function shouldDrawIndels(): boolean;
-export interface LayoutFeature {
-    heightPx: number;
-    topPx: number;
-    feature: Feature;
-}
-export declare function getCharWidthHeight(): {
-    charWidth: number;
-    charHeight: number;
-};

package/dist/PileupRenderer/util.js

@@ -1,49 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fillRect = fillRect;
-exports.getColorBaseMap = getColorBaseMap;
-exports.getContrastBaseMap = getContrastBaseMap;
-exports.shouldDrawSNPsMuted = shouldDrawSNPsMuted;
-exports.shouldDrawIndels = shouldDrawIndels;
-exports.getCharWidthHeight = getCharWidthHeight;
-const util_1 = require("@jbrowse/core/util");
-function fillRect(ctx, l, t, w, h, cw, color) {
-    if (l + w < 0 || l > cw) {
-        return;
-    }
-    if (color) {
-        ctx.fillStyle = color;
-    }
-    ctx.fillRect(l, t, w, h);
-}
-function getColorBaseMap(theme) {
-    const { skip, deletion, insertion, hardclip, softclip, bases } = theme.palette;
-    return {
-        A: bases.A.main,
-        C: bases.C.main,
-        G: bases.G.main,
-        T: bases.T.main,
-        deletion,
-        insertion,
-        hardclip,
-        softclip,
-        skip,
-    };
-}
-function getContrastBaseMap(theme) {
-    return Object.fromEntries(Object.entries(getColorBaseMap(theme)).map(([key, value]) => [
-        key,
-        theme.palette.getContrastText(value),
-    ]));
-}
-function shouldDrawSNPsMuted(type) {
-    return ['methylation', 'modifications'].includes(type || '');
-}
-function shouldDrawIndels() {
-    return true;
-}
-function getCharWidthHeight() {
-    const charWidth = (0, util_1.measureText)('A');
-    const charHeight = (0, util_1.measureText)('M') - 2;
-    return { charWidth, charHeight };
-}

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -1,14 +0,0 @@
-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;
-        sequenceAdapter: BaseFeatureDataAdapter | undefined;
-    }>;
-    fetchSequence(region: Region): Promise<any>;
-    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-}