@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/dist/PileupRenderer/layoutFeatures.d.ts

@@ -1,5 +0,0 @@
-import type { PreProcessedRenderArgs } from './types';
-export declare function layoutFeats(props: PreProcessedRenderArgs): {
-    layoutRecords: import("./layoutFeature").LayoutRecord[];
-    height: number;
-};

package/dist/PileupRenderer/layoutFeatures.js

@@ -1,29 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.layoutFeats = layoutFeats;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const layoutFeature_1 = require("./layoutFeature");
-const sortUtil_1 = require("./sortUtil");
-function layoutFeats(props) {
-    const { layout, features, sortedBy, config, bpPerPx, showSoftClip, regions } = props;
-    const region = regions[0];
-    const featureMap = (sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type) && region.start === sortedBy.pos
-        ? (0, sortUtil_1.sortFeature)(features, sortedBy)
-        : features;
-    const heightPx = (0, configuration_1.readConfObject)(config, 'height');
-    const displayMode = (0, configuration_1.readConfObject)(config, 'displayMode');
-    const layoutRecords = (0, util_1.iterMap)(featureMap.values(), feature => (0, layoutFeature_1.layoutFeature)({
-        feature,
-        layout,
-        bpPerPx,
-        region,
-        showSoftClip,
-        heightPx,
-        displayMode,
-    }), featureMap.size).filter(util_1.notEmpty);
-    return {
-        layoutRecords,
-        height: Math.max(layout.getTotalHeight(), 1),
-    };
-}

package/dist/PileupRenderer/makeImageData.d.ts

@@ -1,17 +0,0 @@
-import type { FlatbushItem, ProcessedRenderArgs } from './types';
-import type { Feature } from '@jbrowse/core/util';
-interface LayoutFeature {
-    heightPx: number;
-    topPx: number;
-    feature: Feature;
-}
-export declare function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }: {
-    ctx: CanvasRenderingContext2D;
-    canvasWidth: number;
-    layoutRecords: LayoutFeature[];
-    renderArgs: ProcessedRenderArgs;
-}): {
-    flatbush: ArrayBufferLike;
-    items: FlatbushItem[];
-};
-export {};

package/dist/PileupRenderer/makeImageData.js

@@ -1,97 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeImageData = makeImageData;
-const configuration_1 = require("@jbrowse/core/configuration");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const flatbush_1 = __importDefault(require("@jbrowse/core/util/flatbush"));
-const renderAlignment_1 = require("./renderers/renderAlignment");
-const renderMismatches_1 = require("./renderers/renderMismatches");
-const renderSoftClipping_1 = require("./renderers/renderSoftClipping");
-const util_2 = require("./util");
-function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
-    const { stopToken, config, showSoftClip, colorBy, theme: configTheme, } = renderArgs;
-    const mismatchAlpha = (0, configuration_1.readConfObject)(config, 'mismatchAlpha');
-    const minSubfeatureWidth = (0, configuration_1.readConfObject)(config, 'minSubfeatureWidth');
-    const largeInsertionIndicatorScale = (0, configuration_1.readConfObject)(config, 'largeInsertionIndicatorScale');
-    const hideSmallIndels = (0, configuration_1.readConfObject)(config, 'hideSmallIndels');
-    const defaultColor = (0, configuration_1.readConfObject)(config, 'color') === '#f0f';
-    const theme = (0, ui_1.createJBrowseTheme)(configTheme);
-    const colorMap = (0, util_2.getColorBaseMap)(theme);
-    const colorContrastMap = (0, util_2.getContrastBaseMap)(theme);
-    ctx.font = 'bold 10px Courier New,monospace';
-    const { charWidth, charHeight } = (0, util_2.getCharWidthHeight)();
-    const drawSNPsMuted = (0, util_2.shouldDrawSNPsMuted)(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
-    const drawIndels = (0, util_2.shouldDrawIndels)();
-    const coords = [];
-    const items = [];
-    (0, util_1.forEachWithStopTokenCheck)(layoutRecords, stopToken, feat => {
-        const alignmentRet = (0, renderAlignment_1.renderAlignment)({
-            ctx,
-            feat,
-            renderArgs,
-            defaultColor,
-            colorMap,
-            colorContrastMap,
-            charWidth,
-            charHeight,
-            canvasWidth,
-        });
-        for (let i = 0, l = alignmentRet.coords.length; i < l; i++) {
-            coords.push(alignmentRet.coords[i]);
-        }
-        for (let i = 0, l = alignmentRet.items.length; i < l; i++) {
-            items.push(alignmentRet.items[i]);
-        }
-        const ret = (0, renderMismatches_1.renderMismatches)({
-            ctx,
-            feat,
-            renderArgs,
-            hideSmallIndels,
-            mismatchAlpha,
-            drawSNPsMuted,
-            drawIndels,
-            largeInsertionIndicatorScale,
-            minSubfeatureWidth,
-            charWidth,
-            charHeight,
-            colorMap,
-            colorContrastMap,
-            canvasWidth,
-        });
-        for (let i = 0, l = ret.coords.length; i < l; i++) {
-            coords.push(ret.coords[i]);
-        }
-        for (let i = 0, l = ret.items.length; i < l; i++) {
-            items.push(ret.items[i]);
-        }
-        if (showSoftClip) {
-            (0, renderSoftClipping_1.renderSoftClipping)({
-                ctx,
-                feat,
-                renderArgs,
-                colorMap,
-                config,
-                theme,
-                canvasWidth,
-            });
-        }
-    });
-    const flatbush = new flatbush_1.default(Math.max(items.length, 1));
-    if (coords.length) {
-        for (let i = 0; i < coords.length; i += 4) {
-            flatbush.add(coords[i], coords[i + 1], coords[i + 2], coords[i + 3]);
-        }
-    }
-    else {
-        flatbush.add(0, 0);
-    }
-    flatbush.finish();
-    return {
-        flatbush: flatbush.data,
-        items,
-    };
-}

package/dist/PileupRenderer/renderers/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/dist/PileupRenderer/renderers/getAlignmentShapeColor.js

@@ -1,61 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getAlignmentShapeColor = getAlignmentShapeColor;
-const configuration_1 = require("@jbrowse/core/configuration");
-const color_1 = require("../../shared/color");
-const colorBy_1 = require("../colorBy");
-function getAlignmentShapeColor({ colorType, tag, feature, config, defaultColor, colorTagMap, }) {
-    switch (colorType) {
-        case 'insertSize':
-            return (0, colorBy_1.colorByInsertSize)(feature);
-        case 'strand':
-            return (0, colorBy_1.colorByStrand)(feature);
-        case 'mappingQuality':
-            return (0, colorBy_1.colorByMappingQuality)(feature);
-        case 'pairOrientation':
-            return (0, colorBy_1.colorByOrientation)(feature, config);
-        case 'stranded':
-            return (0, colorBy_1.colorByStrandedRnaSeq)(feature);
-        case 'xs':
-        case 'tag': {
-            const tags = feature.get('tags');
-            const val = tags ? tags[tag] : feature.get(tag);
-            if (tag === 'XS' || tag === 'TS') {
-                if (val === '-') {
-                    return color_1.fillColor.color_rev_strand;
-                }
-                else if (val === '+') {
-                    return color_1.fillColor.color_fwd_strand;
-                }
-                else {
-                    return color_1.fillColor.color_nostrand;
-                }
-            }
-            if (tag === 'ts') {
-                if (val === '-') {
-                    return feature.get('strand') === -1
-                        ? color_1.fillColor.color_fwd_strand
-                        : color_1.fillColor.color_rev_strand;
-                }
-                else if (val === '+') {
-                    return feature.get('strand') === -1
-                        ? color_1.fillColor.color_rev_strand
-                        : color_1.fillColor.color_fwd_strand;
-                }
-                else {
-                    return color_1.fillColor.color_nostrand;
-                }
-            }
-            return colorTagMap[val] || color_1.fillColor.color_nostrand;
-        }
-        case 'insertSizeAndPairOrientation':
-            break;
-        case 'modifications':
-        case 'methylation':
-            return feature.get('flags') & 16 ? '#c8dcc8' : '#c8c8c8';
-        default:
-            return defaultColor
-                ? 'lightgrey'
-                : (0, configuration_1.readConfObject)(config, 'color', { feature });
-    }
-}

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

@@ -1,16 +0,0 @@
-import type { FlatbushItem, ProcessedRenderArgs } from '../types';
-import type { LayoutFeature } from '../util';
-export declare function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, charWidth, charHeight, defaultColor, canvasWidth, }: {
-    ctx: CanvasRenderingContext2D;
-    feat: LayoutFeature;
-    renderArgs: ProcessedRenderArgs;
-    colorMap: Record<string, string>;
-    colorContrastMap: Record<string, string>;
-    charWidth: number;
-    charHeight: number;
-    defaultColor: boolean;
-    canvasWidth: number;
-}): {
-    coords: number[];
-    items: FlatbushItem[];
-};

package/dist/PileupRenderer/renderers/renderAlignment.js

@@ -1,90 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderAlignment = renderAlignment;
-const getAlignmentShapeColor_1 = require("./getAlignmentShapeColor");
-const renderAlignmentShape_1 = require("./renderAlignmentShape");
-const renderMethylation_1 = require("./renderMethylation");
-const renderModifications_1 = require("./renderModifications");
-const renderPerBaseLettering_1 = require("./renderPerBaseLettering");
-const renderPerBaseQuality_1 = require("./renderPerBaseQuality");
-const MismatchParser_1 = require("../../MismatchParser");
-function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, charWidth, charHeight, defaultColor, canvasWidth, }) {
-    const items = [];
-    const coords = [];
-    const { config, bpPerPx, regions, colorBy, colorTagMap = {} } = renderArgs;
-    const { tag = '', type: colorType = '' } = colorBy || {};
-    const { feature } = feat;
-    const region = regions[0];
-    ctx.fillStyle = (0, getAlignmentShapeColor_1.getAlignmentShapeColor)({
-        feature,
-        config,
-        tag,
-        defaultColor,
-        colorType,
-        colorTagMap,
-    });
-    (0, renderAlignmentShape_1.renderAlignmentShape)({ ctx, feat, renderArgs });
-    switch (colorType) {
-        case 'perBaseQuality': {
-            const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-            (0, renderPerBaseQuality_1.renderPerBaseQuality)({
-                ctx,
-                feat,
-                region,
-                bpPerPx,
-                canvasWidth,
-                cigarOps,
-            });
-            break;
-        }
-        case 'perBaseLettering': {
-            const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-            (0, renderPerBaseLettering_1.renderPerBaseLettering)({
-                ctx,
-                feat,
-                region,
-                bpPerPx,
-                colorMap,
-                colorContrastMap,
-                charWidth,
-                charHeight,
-                canvasWidth,
-                cigarOps,
-            });
-            break;
-        }
-        case 'modifications': {
-            const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-            const ret = (0, renderModifications_1.renderModifications)({
-                ctx,
-                feat,
-                region,
-                bpPerPx,
-                renderArgs,
-                canvasWidth,
-                cigarOps,
-            });
-            for (let i = 0, l = ret.coords.length; i < l; i++) {
-                coords.push(ret.coords[i]);
-            }
-            for (let i = 0, l = ret.items.length; i < l; i++) {
-                items.push(ret.items[i]);
-            }
-            break;
-        }
-        case 'methylation': {
-            const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-            (0, renderMethylation_1.renderMethylation)({
-                ctx,
-                feat,
-                region,
-                bpPerPx,
-                renderArgs,
-                canvasWidth,
-                cigarOps,
-            });
-            break;
-        }
-    }
-    return { coords, items };
-}

package/dist/PileupRenderer/renderers/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/dist/PileupRenderer/renderers/renderAlignmentShape.js

@@ -1,120 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderAlignmentShape = renderAlignmentShape;
-const util_1 = require("@jbrowse/core/util");
-const MismatchParser_1 = require("../../MismatchParser");
-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 = (0, MismatchParser_1.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] = (0, util_1.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] = (0, util_1.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] = (0, util_1.bpSpanPx)(drawStart - drawLen, drawStart, region, bpPerPx);
-                        ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx);
-                    }
-                    drawStart -= drawLen + opLen;
-                    drawLen = 0;
-                }
-            }
-            if (drawLen !== 0) {
-                const [leftPx, rightPx] = (0, util_1.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] = (0, util_1.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/dist/PileupRenderer/renderers/renderMethylation.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 renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }: {
-    ctx: CanvasRenderingContext2D;
-    feat: LayoutFeature;
-    region: Region;
-    bpPerPx: number;
-    renderArgs: ProcessedRenderArgs;
-    canvasWidth: number;
-    cigarOps: string[];
-}): void;

package/dist/PileupRenderer/renderers/renderMethylation.js

@@ -1,60 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderMethylation = renderMethylation;
-const util_1 = require("@jbrowse/core/util");
-const colord_1 = require("@jbrowse/core/util/colord");
-const getMethBins_1 = require("../../ModificationParser/getMethBins");
-const util_2 = require("../util");
-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 } = (0, getMethBins_1.getMethBins)(feature, cigarOps);
-    function getCol(k) {
-        if (methBins[k]) {
-            const p = methProbs[k] || 0;
-            return (p > 0.5
-                ? (0, colord_1.colord)('red').alpha((p - 0.5) * 2)
-                : (0, colord_1.colord)('blue').alpha(1 - p * 2)).toHslString();
-        }
-        if (hydroxyMethBins[k]) {
-            const p = hydroxyMethProbs[k] || 0;
-            return (p > 0.5
-                ? (0, colord_1.colord)('pink').alpha((p - 0.5) * 2)
-                : (0, colord_1.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] = (0, util_1.bpSpanPx)(j, j + 2, region, bpPerPx);
-                const w = rightPx - leftPx + 0.5;
-                const c = getCol(i) || getCol(i + 1) || 'blue';
-                (0, util_2.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-            }
-            else {
-                const [leftPx, rightPx] = (0, util_1.bpSpanPx)(j, j + 1, region, bpPerPx);
-                const w = rightPx - leftPx + 0.5;
-                const c = getCol(i) || 'blue';
-                (0, util_2.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-                const [leftPx2, rightPx2] = (0, util_1.bpSpanPx)(j + 1, j + 2, region, bpPerPx);
-                const w2 = rightPx2 - leftPx2 + 0.5;
-                const c2 = getCol(i + 1) || 'blue';
-                (0, util_2.fillRect)(ctx, leftPx2, topPx, w2, heightPx, canvasWidth, c2);
-            }
-        }
-    }
-}

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

@@ -1,21 +0,0 @@
-import type { FlatbushItem, 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;
-}): {
-    coords: number[];
-    items: FlatbushItem[];
-};