@jbrowse/plugin-alignments 3.6.5 → 3.7.0

package/esm/shared/menuItems.js

@@ -0,0 +1,49 @@
+import { lazy } from 'react';
+import { getSession } from '@jbrowse/core/util';
+import FilterListIcon from '@mui/icons-material/ClearAll';
+import PaletteIcon from '@mui/icons-material/Palette';
+const FilterByTagDialog = lazy(() => import('./components/FilterByTagDialog'));
+export function getColorSchemeMenuItem(model) {
+    return {
+        label: 'Color scheme',
+        icon: PaletteIcon,
+        subMenu: [
+            {
+                label: 'Insert size ± 3σ and orientation',
+                onClick: () => {
+                    model.setColorScheme({ type: 'insertSizeAndOrientation' });
+                },
+            },
+            {
+                label: 'Insert size ± 3σ',
+                onClick: () => {
+                    model.setColorScheme({ type: 'insertSize' });
+                },
+            },
+            {
+                label: 'Orientation',
+                onClick: () => {
+                    model.setColorScheme({ type: 'orientation' });
+                },
+            },
+            {
+                label: 'Insert size gradient',
+                onClick: () => {
+                    model.setColorScheme({ type: 'gradient' });
+                },
+            },
+        ],
+    };
+}
+export function getFilterByMenuItem(model) {
+    return {
+        label: 'Filter by',
+        icon: FilterListIcon,
+        onClick: () => {
+            getSession(model).queueDialog((handleClose) => [
+                FilterByTagDialog,
+                { model, handleClose },
+            ]);
+        },
+    };
+}

package/esm/shared/modificationData.d.ts

@@ -0,0 +1,6 @@
+export interface ModificationData {
+    color: string;
+    name: string;
+}
+export declare const modificationData: Record<string, ModificationData>;
+export declare function getModificationName(type: string): string;

package/esm/shared/modificationData.js

@@ -0,0 +1,18 @@
+export const 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' },
+};
+export function getModificationName(type) {
+    var _a;
+    return ((_a = modificationData[type]) === null || _a === void 0 ? void 0 : _a.name) || type;
+}

package/esm/shared/primaryStrand.d.ts

@@ -0,0 +1,3 @@
+import type { ReducedFeature } from './fetchChains';
+export declare function getPrimaryStrand(feat: ReducedFeature): number;
+export declare function getPrimaryStrandFromFlags(feat: ReducedFeature): 1 | -1;

package/esm/shared/primaryStrand.js

@@ -0,0 +1,20 @@
+export function getPrimaryStrand(feat) {
+    var _a, _b;
+    if (!(feat.flags & 2048)) {
+        return feat.strand;
+    }
+    else {
+        const res = (_b = (_a = feat.SA) === null || _a === void 0 ? void 0 : _a.split(';')[0]) === null || _b === void 0 ? void 0 : _b.split(',')[2];
+        return res === '-' ? -1 : 1;
+    }
+}
+export function getPrimaryStrandFromFlags(feat) {
+    var _a, _b;
+    if (!(feat.flags & 2048)) {
+        return feat.flags & 16 ? -1 : 1;
+    }
+    else {
+        const res = (_b = (_a = feat.SA) === null || _a === void 0 ? void 0 : _a.split(';')[0]) === null || _b === void 0 ? void 0 : _b.split(',')[2];
+        return res === '-' ? -1 : 1;
+    }
+}

package/esm/shared/types.d.ts

@@ -63,6 +63,7 @@ export interface ColorBy {
     modifications?: {
         twoColor?: boolean;
         isolatedModification?: string;
+        threshold?: number;
     };
 }
 export interface FilterBy {
@@ -85,6 +86,7 @@ export interface Mismatch {
     qual?: number;
     start: number;
     length: number;
+    insertedBases?: string;
     type: string;
     base: string;
     altbase?: string;

package/esm/shared/util.d.ts

@@ -18,3 +18,5 @@ export declare function cacheGetter<T>(ctor: {
 }, prop: keyof T): void;
 export declare function filterReadFlag(flags: number, flagInclude: number, flagExclude: number): boolean;
 export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;
+export declare function shouldRenderChevrons(bpPerPx: number, featureHeight: number): boolean;
+export declare const CHEVRON_WIDTH = 5;

package/esm/shared/util.js

@@ -53,3 +53,7 @@ export function filterTagValue(readVal, filterVal) {
         ? readVal === undefined
         : `${readVal}` !== `${filterVal}`;
 }
+export function shouldRenderChevrons(bpPerPx, featureHeight) {
+    return bpPerPx < 50 && featureHeight >= 3;
+}
+export const CHEVRON_WIDTH = 5;

package/esm/util.d.ts

@@ -16,15 +16,10 @@ export declare const pairMap: {
 };
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-interface ModificationData {
-    color: string;
-    name: string;
-}
-export declare const modificationData: Record<string, ModificationData>;
 type DisplayModel = IAnyStateTreeNode & {
     setError: (arg: unknown) => void;
 };
 export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
 export declare function randomColor(str: string): string;
 export declare function getColorForModification(str: string): string;
-export {};
+export { modificationData } from './shared/modificationData';

package/esm/util.js

@@ -2,6 +2,7 @@ import { autorun } from 'mobx';
 import { addDisposer, isAlive } from 'mobx-state-tree';
 import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
+import { modificationData } from './shared/modificationData';
 export function getTagAlt(feature, tag, alt) {
     var _a;
     const tags = feature.get('tags');
@@ -77,20 +78,6 @@ export async function fetchSequence(region, adapter) {
         .pipe(toArray()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
 }
-export const 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' },
-};
 export function createAutorun(self, cb, opts) {
     addDisposer(self, autorun(async () => {
         try {
@@ -114,3 +101,4 @@ export function getColorForModification(str) {
     var _a;
     return ((_a = modificationData[str]) === null || _a === void 0 ? void 0 : _a.color) || randomColor(str);
 }
+export { modificationData } from './shared/modificationData';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "3.6.5",
+  "version": "3.7.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,10 +38,10 @@
   "dependencies": {
     "@gmod/bam": "^6.0.1",
     "@gmod/cram": "^5.0.4",
-    "@jbrowse/core": "^3.6.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.5",
-    "@jbrowse/plugin-wiggle": "^3.6.5",
-    "@jbrowse/sv-core": "^3.6.5",
+    "@jbrowse/core": "^3.7.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.7.0",
+    "@jbrowse/plugin-wiggle": "^3.7.0",
+    "@jbrowse/sv-core": "^3.7.0",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "canvas2svg": "^1.0.16",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
+  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
 }

package/dist/LinearReadCloudDisplay/drawFeats.js

@@ -1,27 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawFeats = drawFeats;
-const util_1 = require("@jbrowse/core/util");
-const drawLongReadChains_1 = require("./drawLongReadChains");
-const drawPairChains_1 = require("./drawPairChains");
-const util_2 = require("../shared/util");
-function drawFeats(self, ctx) {
-    const { chainData } = self;
-    if (!chainData) {
-        return;
-    }
-    const { assemblyManager } = (0, util_1.getSession)(self);
-    const view = (0, util_1.getContainingView)(self);
-    const assemblyName = view.assemblyNames[0];
-    const asm = assemblyManager.get(assemblyName);
-    if (!asm) {
-        return;
-    }
-    const hasPaired = (0, util_2.hasPairedReads)(chainData);
-    if (hasPaired) {
-        (0, drawPairChains_1.drawPairChains)({ self, view, asm, ctx, chainData });
-    }
-    else {
-        (0, drawLongReadChains_1.drawLongReadChains)({ self, view, asm, ctx, chainData });
-    }
-}

package/dist/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/dist/LinearReadCloudDisplay/drawLongReadChains.js

@@ -1,64 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawLongReadChains = drawLongReadChains;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
-const color_1 = require("../shared/color");
-function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
-    var _a, _b, _c, _d, _e;
-    const computedChains = [];
-    const { chains } = chainData;
-    const { height } = self;
-    const featureHeight = (0, configuration_1.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((0, util_1.max)(distances));
-    const minD = Math.max(Math.log((0, util_1.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;
-        (0, util_2.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';
-                (0, util_2.strokeRectCtx)(l, top, w, featureHeight, ctx, color_1.strokeColor[c]);
-                (0, util_2.fillRectCtx)(l, top, w, featureHeight, ctx, color_1.fillColor[c]);
-            }
-        }
-    }
-}

package/dist/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;

package/dist/LinearReadCloudDisplay/drawPairChains.js

@@ -1,94 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawPairChains = drawPairChains;
-exports.getPairedColor = getPairedColor;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
-const color_1 = require("../shared/color");
-function drawPairChains({ ctx, self, chainData, view, asm, }) {
-    var _a, _b, _c, _d, _e, _f, _g;
-    const coords = [];
-    const featureHeight = (0, configuration_1.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);
-                (0, util_2.fillRectCtx)(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#f00');
-                (0, util_2.strokeRectCtx)(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#a00');
-            }
-        }
-    }
-    const maxD = Math.log((0, util_1.max)(coords.map(c => c.distance)));
-    const minD = Math.max(Math.log((0, util_1.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;
-        (0, util_2.fillRectCtx)(r1e - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
-        (0, util_2.strokeRectCtx)(r1s - view.offsetPx, top, w1, featureHeight, ctx, stroke);
-        (0, util_2.strokeRectCtx)(r2s - view.offsetPx, top, w2, featureHeight, ctx, stroke);
-        (0, util_2.fillRectCtx)(r1s - view.offsetPx, top, w1, featureHeight, ctx, fill);
-        (0, util_2.fillRectCtx)(r2s - view.offsetPx, top, w2, featureHeight, ctx, fill);
-    }
-}
-function getPairedColor({ type, v0, v1, stats, }) {
-    if (type === 'insertSizeAndOrientation') {
-        return (0, color_1.getPairedInsertSizeAndOrientationColor)(v0, v1, stats);
-    }
-    if (type === 'orientation') {
-        return (0, color_1.getPairedOrientationColor)(v0);
-    }
-    if (type === 'insertSize') {
-        return (0, color_1.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/dist/PileupRenderer/renderModifications.js

@@ -1,44 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderModifications = renderModifications;
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
-const getMaximumModificationAtEachPosition_1 = require("../shared/getMaximumModificationAtEachPosition");
-const util_3 = require("../shared/util");
-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 = (0, getMaximumModificationAtEachPosition_1.getMaxProbModAtEachPosition)(feature, cigarOps)) === null || _c === void 0 ? void 0 : _c.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;
-        }
-        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_3.alphaColor)('blue', s);
-            const w = rightPx - leftPx + 0.5;
-            (0, util_2.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-        }
-        else {
-            const c = (0, util_3.alphaColor)(col, prob);
-            const w = rightPx - leftPx + 0.5;
-            (0, util_2.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-        }
-        pos++;
-    });
-}

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;