@jbrowse/plugin-alignments 3.6.5 → 3.7.0

package/dist/shared/drawLongReadChains.js

@@ -0,0 +1,104 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.drawLongReadChains = drawLongReadChains;
+const canvasUtils_1 = require("./canvasUtils");
+const chevron_1 = require("./chevron");
+const color_1 = require("./color");
+const primaryStrand_1 = require("./primaryStrand");
+const util_1 = require("./util");
+function drawLongReadChains({ ctx, chainData, view, asm, chainYOffsets, renderChevrons, featureHeight, featuresForFlatbush, computedChains, flipStrandLongReadChains, }) {
+    var _a, _b;
+    const getStrandColorKey = (strand) => strand === -1 ? 'color_rev_strand' : 'color_fwd_strand';
+    for (const computedChain of computedChains) {
+        const { id, chain, minX, maxX } = computedChain;
+        let isPairedEnd = false;
+        for (const element of chain) {
+            if (element.flags & 1) {
+                isPairedEnd = true;
+                break;
+            }
+        }
+        if (isPairedEnd) {
+            continue;
+        }
+        const chainY = chainYOffsets.get(id);
+        if (chainY === undefined) {
+            continue;
+        }
+        const nonSupplementary = [];
+        for (const element of chain) {
+            if (!(element.flags & 2048)) {
+                nonSupplementary.push(element);
+            }
+        }
+        const isSingleton = chain.length === 1;
+        const c1 = nonSupplementary[0] || chain[0];
+        const primaryStrand = (0, primaryStrand_1.getPrimaryStrandFromFlags)(c1);
+        if (!isSingleton) {
+            const firstFeat = chain[0];
+            const lastFeat = chain[chain.length - 1];
+            const firstPx = (_a = view.bpToPx({
+                refName: asm.getCanonicalRefName2(firstFeat.refName),
+                coord: firstFeat.start,
+            })) === null || _a === void 0 ? void 0 : _a.offsetPx;
+            const lastPx = (_b = view.bpToPx({
+                refName: asm.getCanonicalRefName2(lastFeat.refName),
+                coord: lastFeat.end,
+            })) === null || _b === void 0 ? void 0 : _b.offsetPx;
+            if (firstPx !== undefined && lastPx !== undefined) {
+                const lineY = chainY + featureHeight / 2 - 0.5;
+                ctx.beginPath();
+                ctx.strokeStyle = '#666';
+                ctx.moveTo(firstPx - view.offsetPx, lineY);
+                ctx.lineTo(lastPx - view.offsetPx, lineY);
+                ctx.stroke();
+            }
+        }
+        const viewOffsetPx = view.offsetPx;
+        const chainMinXPx = minX - viewOffsetPx;
+        const chainMaxXPx = maxX - viewOffsetPx;
+        for (let i = 0, l = chain.length; i < l; i++) {
+            const feat = chain[i];
+            const s = view.bpToPx({
+                refName: asm.getCanonicalRefName2(feat.refName),
+                coord: feat.start,
+            });
+            const e = view.bpToPx({
+                refName: asm.getCanonicalRefName2(feat.refName),
+                coord: feat.end,
+            });
+            if (!s || !e) {
+                continue;
+            }
+            const effectiveStrand = isSingleton || !flipStrandLongReadChains
+                ? feat.strand
+                : feat.strand * primaryStrand;
+            const [featureFill, featureStroke] = isSingleton
+                ? (0, color_1.getSingletonColor)(feat, chainData.stats)
+                : [
+                    color_1.fillColor[getStrandColorKey(effectiveStrand)],
+                    color_1.strokeColor[getStrandColorKey(effectiveStrand)],
+                ];
+            const xPos = s.offsetPx - viewOffsetPx;
+            const width = Math.max(e.offsetPx - s.offsetPx, 3);
+            if (renderChevrons) {
+                (0, chevron_1.drawChevron)(ctx, xPos, chainY, width, featureHeight, effectiveStrand, featureFill, util_1.CHEVRON_WIDTH, featureStroke);
+            }
+            else {
+                (0, canvasUtils_1.fillRectCtx)(xPos, chainY, width, featureHeight, ctx, featureFill);
+                (0, canvasUtils_1.strokeRectCtx)(xPos, chainY, width, featureHeight, ctx, featureStroke);
+            }
+            featuresForFlatbush.push({
+                x1: xPos,
+                y1: chainY,
+                x2: xPos + width,
+                y2: chainY + featureHeight,
+                data: feat,
+                chainId: id,
+                chainMinX: chainMinXPx,
+                chainMaxX: chainMaxXPx,
+                chain,
+            });
+        }
+    }
+}

package/dist/shared/drawPairChains.d.ts

@@ -0,0 +1,24 @@
+import type { ChainData, ReducedFeature } from './fetchChains';
+import type { FlatbushEntry } from './flatbushType';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+type LGV = LinearGenomeViewModel;
+export declare function drawPairChains({ ctx, type, chainData, view, asm, chainYOffsets, renderChevrons, featureHeight, featuresForFlatbush, computedChains, }: {
+    ctx: CanvasRenderingContext2D;
+    type: string;
+    chainData: ChainData;
+    view: LGV;
+    asm: Assembly;
+    chainYOffsets: Map<string, number>;
+    renderChevrons: boolean;
+    featureHeight: number;
+    featuresForFlatbush: FlatbushEntry[];
+    computedChains: {
+        distance: number;
+        minX: number;
+        maxX: number;
+        chain: ReducedFeature[];
+        id: string;
+    }[];
+}): void;
+export {};

package/dist/shared/drawPairChains.js

@@ -0,0 +1,94 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.drawPairChains = drawPairChains;
+const canvasUtils_1 = require("./canvasUtils");
+const chevron_1 = require("./chevron");
+const color_1 = require("./color");
+const util_1 = require("./util");
+function drawPairChains({ ctx, type, chainData, view, asm, chainYOffsets, renderChevrons, featureHeight, featuresForFlatbush, computedChains, }) {
+    var _a, _b;
+    for (const computedChain of computedChains) {
+        const { id, chain, minX, maxX } = computedChain;
+        let isPairedEnd = false;
+        for (const element of chain) {
+            if (element.flags & 1) {
+                isPairedEnd = true;
+                break;
+            }
+        }
+        if (!isPairedEnd) {
+            continue;
+        }
+        const chainY = chainYOffsets.get(id);
+        if (chainY === undefined) {
+            continue;
+        }
+        const nonSupplementary = [];
+        for (const element of chain) {
+            if (!(element.flags & 2048)) {
+                nonSupplementary.push(element);
+            }
+        }
+        const hasBothMates = nonSupplementary.length === 2;
+        const [pairedFill, pairedStroke] = hasBothMates
+            ? (0, color_1.getPairedColor)({
+                type,
+                v0: nonSupplementary[0],
+                v1: nonSupplementary[1],
+                stats: chainData.stats,
+            }) || ['#888', '#888']
+            : (0, color_1.getSingletonColor)(nonSupplementary[0] || chain[0], chainData.stats);
+        if (hasBothMates) {
+            const v0 = nonSupplementary[0];
+            const v1 = nonSupplementary[1];
+            const r1s = (_a = view.bpToPx({
+                refName: asm.getCanonicalRefName2(v0.refName),
+                coord: v0.start,
+            })) === null || _a === void 0 ? void 0 : _a.offsetPx;
+            const r2s = (_b = view.bpToPx({
+                refName: asm.getCanonicalRefName2(v1.refName),
+                coord: v1.start,
+            })) === null || _b === void 0 ? void 0 : _b.offsetPx;
+            if (r1s !== undefined && r2s !== undefined) {
+                (0, canvasUtils_1.fillRectCtx)(r1s - view.offsetPx, chainY + featureHeight / 2 - 0.5, r2s - r1s, 1, ctx, '#666');
+            }
+        }
+        const viewOffsetPx = view.offsetPx;
+        const chainMinXPx = minX - viewOffsetPx;
+        const chainMaxXPx = maxX - viewOffsetPx;
+        for (let i = 0, l = chain.length; i < l; i++) {
+            const feat = chain[i];
+            const s = view.bpToPx({
+                refName: asm.getCanonicalRefName2(feat.refName),
+                coord: feat.start,
+            });
+            const e = view.bpToPx({
+                refName: asm.getCanonicalRefName2(feat.refName),
+                coord: feat.end,
+            });
+            if (!s || !e) {
+                continue;
+            }
+            const xPos = s.offsetPx - viewOffsetPx;
+            const width = Math.max(e.offsetPx - s.offsetPx, 3);
+            if (renderChevrons) {
+                (0, chevron_1.drawChevron)(ctx, xPos, chainY, width, featureHeight, feat.strand, pairedFill, util_1.CHEVRON_WIDTH, pairedStroke);
+            }
+            else {
+                (0, canvasUtils_1.fillRectCtx)(xPos, chainY, width, featureHeight, ctx, pairedFill);
+                (0, canvasUtils_1.strokeRectCtx)(xPos, chainY, width, featureHeight, ctx, pairedStroke);
+            }
+            featuresForFlatbush.push({
+                x1: xPos,
+                y1: chainY,
+                x2: xPos + width,
+                y2: chainY + featureHeight,
+                data: feat,
+                chainId: id,
+                chainMinX: chainMinXPx,
+                chainMaxX: chainMaxXPx,
+                chain,
+            });
+        }
+    }
+}

package/dist/shared/flatbushType.d.ts

@@ -0,0 +1,12 @@
+import type { ReducedFeature } from './fetchChains';
+export interface FlatbushEntry {
+    x1: number;
+    y1: number;
+    x2: number;
+    y2: number;
+    data: ReducedFeature;
+    chainId: string;
+    chainMinX: number;
+    chainMaxX: number;
+    chain: ReducedFeature[];
+}

package/dist/shared/flatbushType.js

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

package/dist/shared/getUniqueModifications.d.ts

@@ -12,4 +12,7 @@ export declare function getUniqueModifications({ model, adapterConfig, blocks, o
     adapterConfig: AnyConfigurationModel;
     blocks: BlockSet;
     opts?: ModificationOpts;
-}): Promise<ModificationType[]>;
+}): Promise<{
+    modifications: ModificationType[];
+    simplexModifications: string[];
+}>;

package/dist/shared/menuItems.d.ts

@@ -0,0 +1,23 @@
+interface LinearReadDisplayModel {
+    setColorScheme: (colorBy: {
+        type: string;
+    }) => void;
+}
+export declare function getColorSchemeMenuItem(model: LinearReadDisplayModel): {
+    label: string;
+    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+        muiName: string;
+    };
+    subMenu: {
+        label: string;
+        onClick: () => void;
+    }[];
+};
+export declare function getFilterByMenuItem(model: unknown): {
+    label: string;
+    icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+        muiName: string;
+    };
+    onClick: () => void;
+};
+export {};

package/dist/shared/menuItems.js

@@ -0,0 +1,89 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getColorSchemeMenuItem = getColorSchemeMenuItem;
+exports.getFilterByMenuItem = getFilterByMenuItem;
+const react_1 = require("react");
+const util_1 = require("@jbrowse/core/util");
+const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
+const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
+const FilterByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/FilterByTagDialog'))));
+function getColorSchemeMenuItem(model) {
+    return {
+        label: 'Color scheme',
+        icon: Palette_1.default,
+        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' });
+                },
+            },
+        ],
+    };
+}
+function getFilterByMenuItem(model) {
+    return {
+        label: 'Filter by',
+        icon: ClearAll_1.default,
+        onClick: () => {
+            (0, util_1.getSession)(model).queueDialog((handleClose) => [
+                FilterByTagDialog,
+                { model, handleClose },
+            ]);
+        },
+    };
+}

package/dist/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/dist/shared/modificationData.js

@@ -0,0 +1,22 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.modificationData = void 0;
+exports.getModificationName = getModificationName;
+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 getModificationName(type) {
+    var _a;
+    return ((_a = exports.modificationData[type]) === null || _a === void 0 ? void 0 : _a.name) || type;
+}

package/dist/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/dist/shared/primaryStrand.js

@@ -0,0 +1,24 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getPrimaryStrand = getPrimaryStrand;
+exports.getPrimaryStrandFromFlags = getPrimaryStrandFromFlags;
+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;
+    }
+}
+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/dist/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/dist/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/dist/shared/util.js

@@ -1,11 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.posFlags = exports.negFlags = exports.defaultFilterFlags = void 0;
+exports.CHEVRON_WIDTH = exports.posFlags = exports.negFlags = exports.defaultFilterFlags = void 0;
 exports.hasPairedReads = hasPairedReads;
 exports.alphaColor = alphaColor;
 exports.cacheGetter = cacheGetter;
 exports.filterReadFlag = filterReadFlag;
 exports.filterTagValue = filterTagValue;
+exports.shouldRenderChevrons = shouldRenderChevrons;
 const colord_1 = require("@jbrowse/core/util/colord");
 function hasPairedReads(features) {
     for (const f of features.chains.values()) {
@@ -61,3 +62,7 @@ function filterTagValue(readVal, filterVal) {
         ? readVal === undefined
         : `${readVal}` !== `${filterVal}`;
 }
+function shouldRenderChevrons(bpPerPx, featureHeight) {
+    return bpPerPx < 50 && featureHeight >= 3;
+}
+exports.CHEVRON_WIDTH = 5;

package/dist/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/dist/util.js

@@ -11,6 +11,7 @@ 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");
+const modificationData_1 = require("./shared/modificationData");
 function getTagAlt(feature, tag, alt) {
     var _a;
     const tags = feature.get('tags');
@@ -86,20 +87,6 @@ async function fetchSequence(region, adapter) {
         .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 {
@@ -121,5 +108,7 @@ function randomColor(str) {
 }
 function getColorForModification(str) {
     var _a;
-    return ((_a = exports.modificationData[str]) === null || _a === void 0 ? void 0 : _a.color) || randomColor(str);
+    return ((_a = modificationData_1.modificationData[str]) === null || _a === void 0 ? void 0 : _a.color) || randomColor(str);
 }
+var modificationData_2 = require("./shared/modificationData");
+Object.defineProperty(exports, "modificationData", { enumerable: true, get: function () { return modificationData_2.modificationData; } });

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -18,14 +18,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         upperCaseCDS: boolean;
         charactersPerRow: number;
         feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
-        mode: string;
+        mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein";
     } & {
         setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
         setShowCoordinates(f: "none" | "relative" | "genomic"): void;
-        setMode(mode: string): void;
+        setMode(mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein"): void;
     } & {
         readonly showCoordinates: boolean;
         readonly showGenomicCoordsOption: boolean;
@@ -68,14 +68,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         upperCaseCDS: boolean;
         charactersPerRow: number;
         feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
-        mode: string;
+        mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein";
     } & {
         setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
         setShowCoordinates(f: "none" | "relative" | "genomic"): void;
-        setMode(mode: string): void;
+        setMode(mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein"): void;
     } & {
         readonly showCoordinates: boolean;
         readonly showGenomicCoordsOption: boolean;

package/esm/CramAdapter/CramAdapter.js

@@ -215,7 +215,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
             const chrId = this.refNameToId(refName);
             return chrId !== undefined
                 ? cram.index.getEntriesForRange(chrId, start, end)
-                : [{ sliceBytes: 0 }];
+                : Promise.resolve([{ sliceBytes: 0 }]);
         }));
         return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0);
     }

package/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -1,4 +1,5 @@
-import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util';
+import { readFeaturesToCIGAR } from './readFeaturesToCIGAR';
+import { readFeaturesToMismatches } from './readFeaturesToMismatches';
 import { cacheGetter } from '../shared/util';
 export default class CramSlightlyLazyFeature {
     constructor(record, _store) {

package/esm/CramAdapter/{util.js → readFeaturesToCIGAR.js}

@@ -1,14 +1,12 @@
-export function readFeaturesToMismatches(readFeatures, start, qual) {
-    if (!readFeatures) {
-        return [];
-    }
+export function readFeaturesToMismatches(readFeatures = [], start, qual) {
     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) {
+    for (const ret of readFeatures) {
+        const { refPos: p, code, pos, data, sub, ref } = ret;
         sublen = refPos - lastPos;
         lastPos = refPos;
         if (sublen && insLen > 0) {
@@ -16,6 +14,7 @@ export function readFeaturesToMismatches(readFeatures, start, qual) {
                 start: refPos,
                 type: 'insertion',
                 base: `${insLen}`,
+                insertedBases: data,
                 length: 0,
             };
             insLen = 0;

package/esm/CramAdapter/readFeaturesToMismatches.d.ts

@@ -0,0 +1,5 @@
+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 {};