@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/util.js

@@ -1,125 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.modificationData = exports.pairMap = exports.orientationTypes = void 0;
-exports.getTagAlt = getTagAlt;
-exports.getColorWGBS = getColorWGBS;
-exports.fetchSequence = fetchSequence;
-exports.createAutorun = createAutorun;
-exports.randomColor = randomColor;
-exports.getColorForModification = getColorForModification;
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const rxjs_1 = require("rxjs");
-const operators_1 = require("rxjs/operators");
-function getTagAlt(feature, tag, alt) {
-    var _a;
-    const tags = feature.get('tags');
-    return (_a = tags[tag]) !== null && _a !== void 0 ? _a : tags[alt];
-}
-exports.orientationTypes = {
-    fr: {
-        F1R2: 'LR',
-        F2R1: 'LR',
-        F1F2: 'LL',
-        F2F1: 'LL',
-        R1R2: 'RR',
-        R2R1: 'RR',
-        R1F2: 'RL',
-        R2F1: 'RL',
-    },
-    rf: {
-        R1F2: 'LR',
-        R2F1: 'LR',
-        R1R2: 'LL',
-        R2R1: 'LL',
-        F1F2: 'RR',
-        F2F1: 'RR',
-        F1R2: 'RL',
-        F2R1: 'RL',
-    },
-    ff: {
-        F2F1: 'LR',
-        R1R2: 'LR',
-        F2R1: 'LL',
-        R1F2: 'LL',
-        R2F1: 'RR',
-        F1R2: 'RR',
-        R2R1: 'RL',
-        F1F2: 'RL',
-    },
-};
-exports.pairMap = {
-    LR: 'color_pair_lr',
-    LL: 'color_pair_ll',
-    RR: 'color_pair_rr',
-    RL: 'color_pair_rl',
-};
-function getColorWGBS(strand, base) {
-    if (strand === 1) {
-        if (base === 'C') {
-            return '#f00';
-        }
-        if (base === 'T') {
-            return '#00f';
-        }
-    }
-    else if (strand === -1) {
-        if (base === 'G') {
-            return '#f00';
-        }
-        if (base === 'A') {
-            return '#00f';
-        }
-    }
-    return '#888';
-}
-async function fetchSequence(region, adapter) {
-    var _a;
-    const { start, end, originalRefName, refName } = region;
-    const feats = await (0, rxjs_1.firstValueFrom)(adapter
-        .getFeatures({
-        ...region,
-        refName: originalRefName || refName,
-        end,
-        start,
-    })
-        .pipe((0, operators_1.toArray)()));
-    return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
-}
-exports.modificationData = {
-    m: { color: 'rgb(255,0,0)', name: '5mC' },
-    h: { color: 'rgb(255,0,255)', name: '5hmC' },
-    o: { color: 'rgb(111, 78, 129)', name: '8oxoG' },
-    f: { color: 'rgb(246, 200, 95)', name: '5fC' },
-    c: { color: 'rgb(157, 216, 102)', name: '5cac' },
-    g: { color: 'rgb(255, 160, 86)', name: '5hmu' },
-    e: { color: 'rgb(141, 221, 208)', name: '5fU' },
-    b: { color: 'rgb(0,100,47)', name: '5caU' },
-    a: { color: 'rgb(51,0,111)', name: '6mA' },
-    17082: { color: 'rgb(51,153,255)', name: 'pseU' },
-    17596: { color: 'rgb(102,153,0)', name: 'inosine' },
-    21839: { color: 'rgb(153,0,153)', name: '4mC' },
-};
-function createAutorun(self, cb, opts) {
-    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-        try {
-            await cb();
-        }
-        catch (e) {
-            if ((0, mobx_state_tree_1.isAlive)(self)) {
-                self.setError(e);
-            }
-        }
-    }, opts));
-}
-function randomColor(str) {
-    let sum = 0;
-    for (let i = 0; i < str.length; i++) {
-        sum += str.charCodeAt(i);
-    }
-    return `hsl(${sum * 10}, 20%, 50%)`;
-}
-function getColorForModification(str) {
-    var _a;
-    return ((_a = exports.modificationData[str]) === null || _a === void 0 ? void 0 : _a.color) || randomColor(str);
-}

package/esm/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.d.ts

@@ -1 +0,0 @@
-export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js

@@ -1 +0,0 @@
-export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.d.ts

@@ -1 +0,0 @@
-export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js

@@ -1 +0,0 @@
-export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/CramAdapter/util.d.ts

@@ -1,9 +0,0 @@
-import type { Mismatch } from '../shared/types';
-import type { CramRecord } from '@gmod/cram';
-type ReadFeatures = CramRecord['readFeatures'];
-export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
-export declare function readFeaturesToCIGAR(readFeatures: ReadFeatures, alignmentStart: number, readLen: number, refRegion?: {
-    seq: string;
-    start: number;
-}): string;
-export {};

package/esm/CramAdapter/util.js

@@ -1,209 +0,0 @@
-export function readFeaturesToMismatches(readFeatures, start, qual) {
-    if (!readFeatures) {
-        return [];
-    }
-    const mismatches = new Array(readFeatures.length);
-    let j = 0;
-    let insLen = 0;
-    let refPos = 0;
-    let sublen = 0;
-    let lastPos = start;
-    for (const { refPos: p, code, pos, data, sub, ref } of readFeatures) {
-        sublen = refPos - lastPos;
-        lastPos = refPos;
-        if (sublen && insLen > 0) {
-            mismatches[j++] = {
-                start: refPos,
-                type: 'insertion',
-                base: `${insLen}`,
-                length: 0,
-            };
-            insLen = 0;
-        }
-        refPos = p - 1 - start;
-        if (code === 'X') {
-            mismatches[j++] = {
-                start: refPos,
-                length: 1,
-                base: sub,
-                qual: qual === null || qual === void 0 ? void 0 : qual[pos - 1],
-                altbase: ref === null || ref === void 0 ? void 0 : ref.toUpperCase(),
-                type: 'mismatch',
-            };
-        }
-        else if (code === 'I') {
-            mismatches[j++] = {
-                start: refPos,
-                type: 'insertion',
-                base: `${data.length}`,
-                length: 0,
-            };
-        }
-        else if (code === 'N') {
-            mismatches[j++] = {
-                type: 'skip',
-                length: data,
-                start: refPos,
-                base: 'N',
-            };
-        }
-        else if (code === 'S') {
-            const len = data.length;
-            mismatches[j++] = {
-                start: refPos,
-                type: 'softclip',
-                base: `S${len}`,
-                cliplen: len,
-                length: 1,
-            };
-        }
-        else if (code === 'P') {
-        }
-        else if (code === 'H') {
-            const len = data;
-            mismatches[j++] = {
-                start: refPos,
-                type: 'hardclip',
-                base: `H${len}`,
-                cliplen: len,
-                length: 1,
-            };
-        }
-        else if (code === 'D') {
-            mismatches[j++] = {
-                type: 'deletion',
-                length: data,
-                start: refPos,
-                base: '*',
-            };
-        }
-        else if (code === 'b') {
-        }
-        else if (code === 'q') {
-        }
-        else if (code === 'B') {
-        }
-        else if (code === 'i') {
-            insLen++;
-        }
-        else if (code === 'Q') {
-        }
-    }
-    if (sublen && insLen > 0) {
-        mismatches[j++] = {
-            start: refPos,
-            type: 'insertion',
-            base: `${insLen}`,
-            length: 0,
-        };
-        insLen = 0;
-    }
-    return mismatches.slice(0, j);
-}
-export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
-    let seq = '';
-    let cigar = '';
-    let op = 'M';
-    let oplen = 0;
-    if (!refRegion) {
-        return '';
-    }
-    const ref = refRegion.seq;
-    const refStart = refRegion.start;
-    let lastPos = alignmentStart;
-    let sublen = 0;
-    let insLen = 0;
-    if (readFeatures !== undefined) {
-        for (const { code, refPos, sub, data } of readFeatures) {
-            sublen = refPos - lastPos;
-            seq += ref.slice(lastPos - refStart, refPos - refStart);
-            lastPos = refPos;
-            if (insLen > 0 && sublen) {
-                cigar += `${insLen}I`;
-                insLen = 0;
-            }
-            if (oplen && op !== 'M') {
-                cigar += `${oplen}${op}`;
-                oplen = 0;
-            }
-            if (sublen) {
-                op = 'M';
-                oplen += sublen;
-            }
-            if (code === 'b') {
-                const ret = data.split(',');
-                const added = String.fromCharCode(...ret);
-                seq += added;
-                lastPos += added.length;
-                oplen += added.length;
-            }
-            else if (code === 'B') {
-                seq += sub;
-                lastPos++;
-                oplen++;
-            }
-            else if (code === 'X') {
-                seq += sub;
-                lastPos++;
-                oplen++;
-            }
-            else if (code === 'D' || code === 'N') {
-                lastPos += data;
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += data + code;
-                oplen = 0;
-            }
-            else if (code === 'I' || code === 'S') {
-                seq += data;
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += data.length + code;
-                oplen = 0;
-            }
-            else if (code === 'i') {
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                insLen++;
-                seq += data;
-                oplen = 0;
-            }
-            else if (code === 'P') {
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += `${data}P`;
-            }
-            else if (code === 'H') {
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += `${data}H`;
-                oplen = 0;
-            }
-        }
-    }
-    else {
-        sublen = readLen - seq.length;
-    }
-    if (seq.length !== readLen) {
-        sublen = readLen - seq.length;
-        seq += ref.slice(lastPos - refStart, lastPos - refStart + sublen);
-        if (oplen && op !== 'M') {
-            cigar += `${oplen}${op}`;
-            oplen = 0;
-        }
-        op = 'M';
-        oplen += sublen;
-    }
-    if (sublen && insLen > 0) {
-        cigar += `${insLen}I`;
-    }
-    if (oplen) {
-        cigar += `${oplen}${op}`;
-    }
-    return cigar;
-}

package/esm/LinearPileupDisplay/components/SetMaxHeightDialog.d.ts

@@ -1,8 +0,0 @@
-declare const SetMaxHeightDialog: (props: {
-    model: {
-        maxHeight?: number;
-        setMaxHeight: (arg?: number) => void;
-    };
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default SetMaxHeightDialog;

package/esm/LinearReadArcsDisplay/drawFeats.d.ts

@@ -1,2 +0,0 @@
-import type { LinearReadArcsDisplayModel } from './model';
-export declare function drawFeats(self: LinearReadArcsDisplayModel, ctx: CanvasRenderingContext2D, width: number, height: number): void;

package/esm/LinearReadArcsDisplay/drawFeats.js

@@ -1,149 +0,0 @@
-import { getContainingView, getSession } from '@jbrowse/core/util';
-import { featurizeSA } from '../MismatchParser';
-import { getPairedInsertSizeAndOrientationColor, getPairedInsertSizeColor, getPairedOrientationColor, } from '../shared/color';
-import { hasPairedReads } from '../shared/util';
-function jitter(n) {
-    return Math.random() * 2 * n - n;
-}
-function drawLineAtOffset(ctx, offset, height, color) {
-    ctx.strokeStyle = color;
-    ctx.beginPath();
-    ctx.moveTo(offset, 0);
-    ctx.lineTo(offset, height);
-    ctx.stroke();
-}
-export function drawFeats(self, ctx, width, height) {
-    const { chainData, colorBy, drawInter, drawLongRange, lineWidthSetting, jitterVal, } = self;
-    if (!chainData) {
-        return;
-    }
-    const view = getContainingView(self);
-    const { assemblyManager } = getSession(self);
-    const { chains, stats } = chainData;
-    const hasPaired = hasPairedReads(chainData);
-    const asm = assemblyManager.get(view.assemblyNames[0]);
-    const type = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) || 'insertSizeAndOrientation';
-    if (!asm) {
-        return;
-    }
-    ctx.lineWidth = lineWidthSetting;
-    function draw(k1, k2, assembly, longRange) {
-        var _a, _b, _c;
-        const s1 = k1.strand;
-        const s2 = k2.strand;
-        const f1 = s1 === -1;
-        const f2 = s2 === -1;
-        const p1 = f1 ? k1.start : k1.end;
-        const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start;
-        const ra1 = assembly.getCanonicalRefName(k1.refName) || k1.refName;
-        const ra2 = assembly.getCanonicalRefName(k2.refName) || k2.refName;
-        const r1 = (_a = view.bpToPx({ refName: ra1, coord: p1 })) === null || _a === void 0 ? void 0 : _a.offsetPx;
-        const r2 = (_b = view.bpToPx({ refName: ra2, coord: p2 })) === null || _b === void 0 ? void 0 : _b.offsetPx;
-        if (r1 !== undefined && r2 !== undefined) {
-            const radius = (r2 - r1) / 2;
-            const absrad = Math.abs(radius);
-            const p = r1 - view.offsetPx;
-            const p2 = r2 - view.offsetPx;
-            const drawArcInsteadOfBezier = absrad > 10000;
-            if (longRange && drawArcInsteadOfBezier) {
-                ctx.moveTo(p, 0);
-                ctx.beginPath();
-            }
-            else {
-                ctx.beginPath();
-                ctx.moveTo(p, 0);
-            }
-            if (longRange && drawArcInsteadOfBezier) {
-                ctx.strokeStyle = 'red';
-            }
-            else {
-                if (hasPaired) {
-                    if (type === 'insertSizeAndOrientation') {
-                        ctx.strokeStyle = getPairedInsertSizeAndOrientationColor(k1, k2, stats)[0];
-                    }
-                    else if (type === 'orientation') {
-                        ctx.strokeStyle = getPairedOrientationColor(k1)[0];
-                    }
-                    else if (type === 'insertSize') {
-                        ctx.strokeStyle =
-                            ((_c = getPairedInsertSizeColor(k1, k2, stats)) === null || _c === void 0 ? void 0 : _c[0]) || 'grey';
-                    }
-                    else if (type === 'gradient') {
-                        ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`;
-                    }
-                }
-                else {
-                    if (type === 'orientation' || type === 'insertSizeAndOrientation') {
-                        if (s1 === -1 && s2 === 1) {
-                            ctx.strokeStyle = 'navy';
-                        }
-                        else if (s1 === 1 && s2 === -1) {
-                            ctx.strokeStyle = 'green';
-                        }
-                        else {
-                            ctx.strokeStyle = 'grey';
-                        }
-                    }
-                    else if (type === 'gradient') {
-                        ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`;
-                    }
-                }
-            }
-            const destX = p + radius * 2;
-            const destY = Math.min(height + jitter(jitterVal), absrad);
-            if (longRange) {
-                if (absrad > 100000) {
-                    drawLineAtOffset(ctx, p + jitter(jitterVal), height, 'red');
-                    drawLineAtOffset(ctx, p2 + jitter(jitterVal), height, 'red');
-                }
-                else if (drawArcInsteadOfBezier) {
-                    ctx.arc(p + radius + jitter(jitterVal), 0, absrad, 0, Math.PI);
-                    ctx.stroke();
-                }
-                else {
-                    ctx.bezierCurveTo(p + jitter(jitterVal), destY, destX, destY, destX + jitter(jitterVal), 0);
-                    ctx.stroke();
-                }
-            }
-            else {
-                ctx.bezierCurveTo(p + jitter(jitterVal), destY, destX, destY, destX + jitter(jitterVal), 0);
-                ctx.stroke();
-            }
-        }
-        else if (r1 && drawInter) {
-            drawLineAtOffset(ctx, r1 - view.offsetPx, height, 'purple');
-        }
-    }
-    for (const chain of chains) {
-        if (chain.length === 1 && drawLongRange) {
-            const f = chain[0];
-            if (hasPaired && !(f.flags & 8)) {
-                const mate = {
-                    refName: f.next_ref || '',
-                    start: f.next_pos || 0,
-                    end: f.next_pos || 0,
-                    strand: f.strand,
-                };
-                draw(f, mate, asm, true);
-            }
-            else {
-                const features = [f, ...featurizeSA(f.SA, f.id, f.strand, f.name)].sort((a, b) => a.clipPos - b.clipPos);
-                for (let i = 0; i < features.length - 1; i++) {
-                    const f = features[i];
-                    const v1 = features[i + 1];
-                    draw(f, v1, asm, true);
-                }
-            }
-        }
-        else {
-            const res = hasPaired
-                ? chain.filter(f => !(f.flags & 2048) && !(f.flags & 8))
-                : chain
-                    .sort((a, b) => a.clipPos - b.clipPos)
-                    .filter(f => !(f.flags & 256));
-            for (let i = 0; i < res.length - 1; i++) {
-                draw(res[i], res[i + 1], asm, false);
-            }
-        }
-    }
-}

package/esm/LinearReadArcsDisplay/util.d.ts

@@ -1,2 +0,0 @@
-import type { ChainData } from '../shared/fetchChains';
-export declare function hasPairedReads(features: ChainData): boolean;

package/esm/LinearReadArcsDisplay/util.js

@@ -1,8 +0,0 @@
-export function hasPairedReads(features) {
-    for (const f of features.chains.values()) {
-        if (f[0].flags & 1) {
-            return true;
-        }
-    }
-    return false;
-}

package/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts

@@ -1,5 +0,0 @@
-import type { LinearReadCloudDisplayModel } from '../model';
-declare const LinearReadCloudReactComponent: ({ model, }: {
-    model: LinearReadCloudDisplayModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default LinearReadCloudReactComponent;

package/esm/LinearReadCloudDisplay/components/ReactComponent.js

@@ -1,18 +0,0 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import { useCallback } from 'react';
-import { getContainingView } from '@jbrowse/core/util';
-import { observer } from 'mobx-react';
-import BaseDisplayComponent from '../../shared/components/BaseDisplayComponent';
-const Cloud = observer(function ({ model, }) {
-    const view = getContainingView(model);
-    const width = Math.round(view.dynamicBlocks.totalWidthPx);
-    const height = model.height;
-    const cb = useCallback((ref) => {
-        model.setRef(ref);
-    }, [model, width, height]);
-    return (_jsx("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
-});
-const LinearReadCloudReactComponent = observer(function ({ model, }) {
-    return (_jsx(BaseDisplayComponent, { model: model, children: _jsx(Cloud, { model: model }) }));
-});
-export default LinearReadCloudReactComponent;

package/esm/LinearReadCloudDisplay/drawFeats.d.ts

@@ -1,2 +0,0 @@
-import type { LinearReadCloudDisplayModel } from './model';
-export declare function drawFeats(self: LinearReadCloudDisplayModel, ctx: CanvasRenderingContext2D): void;

package/esm/LinearReadCloudDisplay/drawFeats.js

@@ -1,24 +0,0 @@
-import { getContainingView, getSession } from '@jbrowse/core/util';
-import { drawLongReadChains } from './drawLongReadChains';
-import { drawPairChains } from './drawPairChains';
-import { hasPairedReads } from '../shared/util';
-export function drawFeats(self, ctx) {
-    const { chainData } = self;
-    if (!chainData) {
-        return;
-    }
-    const { assemblyManager } = getSession(self);
-    const view = getContainingView(self);
-    const assemblyName = view.assemblyNames[0];
-    const asm = assemblyManager.get(assemblyName);
-    if (!asm) {
-        return;
-    }
-    const hasPaired = hasPairedReads(chainData);
-    if (hasPaired) {
-        drawPairChains({ self, view, asm, ctx, chainData });
-    }
-    else {
-        drawLongReadChains({ self, view, asm, ctx, chainData });
-    }
-}

package/esm/LinearReadCloudDisplay/drawLongReadChains.d.ts

@@ -1,11 +0,0 @@
-import type { LinearReadCloudDisplayModel } from './model';
-import type { ChainData } from '../shared/fetchChains';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function drawLongReadChains({ ctx, self, chainData, view, asm, }: {
-    ctx: CanvasRenderingContext2D;
-    self: LinearReadCloudDisplayModel;
-    chainData: ChainData;
-    view: LinearGenomeViewModel;
-    asm: Assembly;
-}): void;

package/esm/LinearReadCloudDisplay/drawLongReadChains.js

@@ -1,61 +0,0 @@
-import { getConf } from '@jbrowse/core/configuration';
-import { max, min } from '@jbrowse/core/util';
-import { fillRectCtx, strokeRectCtx } from './util';
-import { fillColor, strokeColor } from '../shared/color';
-export function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
-    var _a, _b, _c, _d, _e;
-    const computedChains = [];
-    const { chains } = chainData;
-    const { height } = self;
-    const featureHeight = getConf(self, 'featureHeight');
-    for (const chain of chains) {
-        let minX = Number.MAX_VALUE;
-        let maxX = Number.MIN_VALUE;
-        for (const elt of chain) {
-            const refName = asm.getCanonicalRefName(elt.refName) || elt.refName;
-            const rs = (_a = view.bpToPx({ refName, coord: elt.start })) === null || _a === void 0 ? void 0 : _a.offsetPx;
-            const re = (_b = view.bpToPx({ refName, coord: elt.end })) === null || _b === void 0 ? void 0 : _b.offsetPx;
-            if (rs !== undefined && re !== undefined) {
-                minX = Math.min(minX, rs);
-                maxX = Math.max(maxX, re);
-            }
-        }
-        computedChains.push({
-            distance: Math.abs(maxX - minX),
-            minX,
-            chain,
-        });
-    }
-    const distances = computedChains.map(d => d.distance);
-    const maxD = Math.log(max(distances));
-    const minD = Math.max(Math.log(min(distances)) - 1, 0);
-    const scaler = (height - 20) / (maxD - minD);
-    const halfHeight = featureHeight / 2 - 0.5;
-    for (const { minX, distance, chain } of computedChains) {
-        const w = distance;
-        const top = (Math.log(w) - minD) * scaler;
-        fillRectCtx(minX - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
-        const c1 = chain[0];
-        let primaryStrand;
-        if (!(c1.flags & 2048)) {
-            primaryStrand = c1.strand;
-        }
-        else {
-            const res = (_c = c1.SA) === null || _c === void 0 ? void 0 : _c.split(';')[0].split(',')[2];
-            primaryStrand = res === '-' ? -1 : 1;
-        }
-        for (const v0 of chain) {
-            const ra = asm.getCanonicalRefName(v0.refName) || v0.refName;
-            const rs = (_d = view.bpToPx({ refName: ra, coord: v0.start })) === null || _d === void 0 ? void 0 : _d.offsetPx;
-            const re = (_e = view.bpToPx({ refName: ra, coord: v0.end })) === null || _e === void 0 ? void 0 : _e.offsetPx;
-            if (rs !== undefined && re !== undefined) {
-                const w = Math.max(re - rs, 2);
-                const l = rs - view.offsetPx;
-                const effectiveStrand = v0.strand * primaryStrand;
-                const c = effectiveStrand === -1 ? 'color_rev_strand' : 'color_fwd_strand';
-                strokeRectCtx(l, top, w, featureHeight, ctx, strokeColor[c]);
-                fillRectCtx(l, top, w, featureHeight, ctx, fillColor[c]);
-            }
-        }
-    }
-}

package/esm/LinearReadCloudDisplay/drawPairChains.d.ts

@@ -1,17 +0,0 @@
-import type { LinearReadCloudDisplayModel } from './model';
-import type { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function drawPairChains({ ctx, self, chainData, view, asm, }: {
-    ctx: CanvasRenderingContext2D;
-    self: LinearReadCloudDisplayModel;
-    chainData: ChainData;
-    view: LinearGenomeViewModel;
-    asm: Assembly;
-}): void;
-export declare function getPairedColor({ type, v0, v1, stats, }: {
-    type: string;
-    v0: ReducedFeature;
-    v1: ReducedFeature;
-    stats?: ChainStats;
-}): readonly [string, string] | undefined;