@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/dist/shared/fetchChains.js.map

@@ -1 +1 @@
-{"version":3,"file":"fetchChains.js","sourceRoot":"","sources":["../../src/shared/fetchChains.ts"],"names":[],"mappings":";;;AAAA,6CAI2B;AAC3B,qDAAgE;AAiCzD,KAAK,UAAU,WAAW,CAAC,IAAuB;IACvD,IAAI;QACF,MAAM,EAAE,YAAY,EAAE,SAAS,EAAE,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;QAC5D,MAAM,EAAE,UAAU,EAAE,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;QACvC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;QAE3C,IAAI,CAAC,IAAI,CAAC,WAAW,IAAI,IAAI,CAAC,KAAK,EAAE;YACnC,OAAM;SACP;QACD,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QAErB,MAAM,GAAG,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,0BAA0B,EAAE;YACxE,SAAS;YACT,OAAO,EAAE,IAAI,CAAC,YAAY,CAAC,aAAa;YACxC,QAAQ,EAAE,IAAA,6BAAW,EAAC,IAAI,CAAC,QAAQ,CAAC;YACpC,aAAa,EAAE,IAAI,CAAC,aAAa;SAClC,CAAC,CAAc,CAAA;QAEhB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;QACtB,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;KACvB;IAAC,OAAO,CAAC,EAAE;QACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;KACjB;AACH,CAAC;AAxBD,kCAwBC"}
+{"version":3,"file":"fetchChains.js","sourceRoot":"","sources":["../../src/shared/fetchChains.ts"],"names":[],"mappings":";;;AAAA,6CAI2B;AAC3B,qDAA6C;AAmCtC,KAAK,UAAU,WAAW,CAC/B,IAA8D;IAE9D,MAAM,EAAE,YAAY,EAAE,SAAS,EAAE,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;IAC5D,MAAM,EAAE,UAAU,EAAE,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;IACvC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;IAE3C,IAAI,CAAC,IAAI,CAAC,WAAW,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,cAAc,EAAE;QAC1D,OAAM;KACP;IAED,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;IACrB,MAAM,GAAG,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,0BAA0B,EAAE;QACxE,SAAS;QACT,OAAO,EAAE,IAAI,CAAC,YAAY,CAAC,aAAa;QACxC,QAAQ,EAAE,IAAA,6BAAW,EAAC,IAAI,CAAC,QAAQ,CAAC;QACpC,aAAa,EAAE,IAAI,CAAC,aAAa;KAClC,CAAC,CAAc,CAAA;IAEhB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;IACtB,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;AACxB,CAAC;AArBD,kCAqBC"}

package/dist/shared/renderSvg.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+export declare function renderSvg<T extends {
+    id: string;
+    height: number;
+}>(self: T, opts: {
+    rasterizeLayers?: boolean;
+}, cb: (model: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): Promise<React.JSX.Element | undefined>;

package/dist/shared/renderSvg.js

@@ -0,0 +1,69 @@
+"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 (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __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.renderSvg = void 0;
+const react_1 = __importDefault(require("react"));
+const util_1 = require("@jbrowse/core/util");
+// stabilize clipid under test for snapshot
+function getId(id) {
+    const isJest = typeof jest === 'undefined';
+    return `arc-clip-${isJest ? id : 'jest'}`;
+}
+async function renderSvg(self, opts, cb) {
+    const view = (0, util_1.getContainingView)(self);
+    const width = view.dynamicBlocks.totalWidthPx;
+    const height = self.height;
+    if (opts.rasterizeLayers) {
+        const canvas = document.createElement('canvas');
+        canvas.width = width * 2;
+        canvas.height = height * 2;
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        ctx.scale(2, 2);
+        cb(self, ctx, width, height);
+        return (react_1.default.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
+    }
+    else {
+        // @ts-ignore
+        const C2S = await Promise.resolve().then(() => __importStar(require('canvas2svg')));
+        const ctx = new C2S.default(width, height);
+        cb(self, ctx, width, height);
+        const clipid = getId(self.id);
+        return (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement("defs", null,
+                react_1.default.createElement("clipPath", { id: clipid },
+                    react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
+            react_1.default.createElement("g", { 
+                /* eslint-disable-next-line react/no-danger */
+                dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })));
+    }
+}
+exports.renderSvg = renderSvg;
+//# sourceMappingURL=renderSvg.js.map

package/dist/shared/renderSvg.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../src/shared/renderSvg.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kDAAyB;AACzB,6CAAsD;AAGtD,2CAA2C;AAC3C,SAAS,KAAK,CAAC,EAAU;IACvB,MAAM,MAAM,GAAG,OAAO,IAAI,KAAK,WAAW,CAAA;IAC1C,OAAO,YAAY,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,EAAE,CAAA;AAC3C,CAAC;AAIM,KAAK,UAAU,SAAS,CAC7B,IAAO,EACP,IAAmC,EACnC,EAKS;IAET,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;IAC3C,MAAM,KAAK,GAAG,IAAI,CAAC,aAAa,CAAC,YAAY,CAAA;IAC7C,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;IAC1B,IAAI,IAAI,CAAC,eAAe,EAAE;QACxB,MAAM,MAAM,GAAG,QAAQ,CAAC,aAAa,CAAC,QAAQ,CAAC,CAAA;QAC/C,MAAM,CAAC,KAAK,GAAG,KAAK,GAAG,CAAC,CAAA;QACxB,MAAM,CAAC,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QAC1B,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QACnC,IAAI,CAAC,GAAG,EAAE;YACR,OAAM;SACP;QACD,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACf,EAAE,CAAC,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;QAC5B,OAAO,CACL,yCACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,CAAC,SAAS,CAAC,WAAW,CAAC,GACxC,CACH,CAAA;KACF;SAAM;QACL,aAAa;QACb,MAAM,GAAG,GAAG,wDAAa,YAAY,GAAC,CAAA;QACtC,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC1C,EAAE,CAAC,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;QAC5B,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QAC7B,OAAO,CACL;YACE;gBACE,4CAAU,EAAE,EAAE,MAAM;oBAClB,wCAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CACzC,CACN;YACP;gBACE,8CAA8C;gBAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,EAC3D,QAAQ,EAAE,QAAQ,MAAM,GAAG,GAC3B,CACD,CACJ,CAAA;KACF;AACH,CAAC;AAnDD,8BAmDC"}

package/dist/shared/util.d.ts

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

package/dist/shared/util.js

@@ -0,0 +1,13 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.hasPairedReads = void 0;
+function hasPairedReads(features) {
+    for (const f of features.chains.values()) {
+        if (f[0].flags & 1) {
+            return true;
+        }
+    }
+    return false;
+}
+exports.hasPairedReads = hasPairedReads;
+//# sourceMappingURL=util.js.map

package/dist/shared/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/shared/util.ts"],"names":[],"mappings":";;;AAEA,SAAgB,cAAc,CAAC,QAAmB;IAChD,KAAK,MAAM,CAAC,IAAI,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE;QACxC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,EAAE;YAClB,OAAO,IAAI,CAAA;SACZ;KACF;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAPD,wCAOC"}

package/dist/util.d.ts

@@ -1,6 +1,7 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AugmentedRegion } from '@jbrowse/core/util';
+import { Feature, AugmentedRegion } from '@jbrowse/core/util';
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { IAutorunOptions } from 'mobx';
 export declare function getTag(feature: Feature, tag: string): any;
 export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
 export declare const orientationTypes: {
@@ -14,6 +15,19 @@ export declare const orientationTypes: {
         [key: string]: string;
     };
 };
+export declare const pairMap: {
+    readonly LR: "color_pair_lr";
+    readonly LL: "color_pair_ll";
+    readonly RR: "color_pair_rr";
+    readonly RL: "color_pair_rl";
+};
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
 export declare function shouldFetchReferenceSequence(type?: string): boolean;
+export declare const modificationColors: Record<string, string | undefined>;
+type DisplayModel = IAnyStateTreeNode & {
+    setError: (arg: unknown) => void;
+};
+export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
+export declare function randomColor(): string;
+export {};

package/dist/util.js

@@ -1,19 +1,22 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.shouldFetchReferenceSequence = exports.fetchSequence = exports.getColorWGBS = exports.orientationTypes = exports.getTagAlt = exports.getTag = void 0;
+exports.randomColor = exports.createAutorun = exports.modificationColors = exports.shouldFetchReferenceSequence = exports.fetchSequence = exports.getColorWGBS = exports.pairMap = exports.orientationTypes = exports.getTagAlt = exports.getTag = void 0;
 const operators_1 = require("rxjs/operators");
 const rxjs_1 = require("rxjs");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mobx_1 = require("mobx");
 // get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
 // BAM does not
 function getTag(feature, tag) {
     const tags = feature.get('tags');
-    return tags ? tags[tag] : feature.get(tag);
+    return tags !== undefined ? tags[tag] : feature.get(tag);
 }
 exports.getTag = getTag;
 // use fallback alt tag, used in situations where upper case/lower case tags
 // exist e.g. Mm/MM for base modifications
 function getTagAlt(feature, tag, alt) {
-    return getTag(feature, tag) || getTag(feature, alt);
+    var _a;
+    return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
 }
 exports.getTagAlt = getTagAlt;
 // orientation definitions from igv.js, see also
@@ -50,6 +53,12 @@ exports.orientationTypes = {
         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') {
@@ -70,14 +79,17 @@ function getColorWGBS(strand, base) {
     return '#888';
 }
 exports.getColorWGBS = getColorWGBS;
+// fetches region sequence augmenting by +/- 1bp for CpG on either side of
+// requested region
 async function fetchSequence(region, adapter) {
     var _a;
-    const { end, originalRefName, refName } = region;
+    const { start, end, originalRefName, refName } = region;
     const feats = await (0, rxjs_1.firstValueFrom)(adapter
         .getFeatures({
         ...region,
         refName: originalRefName || refName,
         end: end + 1,
+        start: Math.max(0, start - 1),
     })
         .pipe((0, operators_1.toArray)()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
@@ -88,4 +100,33 @@ function shouldFetchReferenceSequence(type) {
     return type === 'methylation';
 }
 exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
+// adapted from IGV
+// https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
+exports.modificationColors = {
+    m: 'rgb(255,0,0)',
+    h: 'rgb(11, 132, 165)',
+    o: 'rgb(111, 78, 129)',
+    f: 'rgb(246, 200, 95)',
+    c: 'rgb(157, 216, 102)',
+    g: 'rgb(255, 160, 86)',
+    e: 'rgb(141, 221, 208)',
+    b: 'rgb(202, 71, 47)',
+};
+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));
+}
+exports.createAutorun = createAutorun;
+function randomColor() {
+    return `hsl(${Math.random() * 200}, 50%, 50%)`;
+}
+exports.randomColor = randomColor;
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AAEA,8CAAwC;AACxC,+BAAqC;AACrC,qDAAyE;AACzE,+BAA+C;AAE/C,4EAA4E;AAC5E,eAAe;AACf,SAAgB,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC1D,CAAC;AAHD,wBAGC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,SAAgB,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;;IAClE,OAAO,MAAA,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,mCAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAFD,8BAEC;AAED,gDAAgD;AAChD,kFAAkF;AACrE,QAAA,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAEY,QAAA,OAAO,GAAG;IACrB,EAAE,EAAE,eAAe;IACnB,EAAE,EAAE,eAAe;IACnB,EAAE,EAAE,eAAe;IACnB,EAAE,EAAE,eAAe;CACX,CAAA;AAEV,SAAgB,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAjBD,oCAiBC;AAED,0EAA0E;AAC1E,mBAAmB;AACZ,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEvD,MAAM,KAAK,GAAG,MAAM,IAAA,qBAAc,EAChC,OAAO;SACJ,WAAW,CAAC;QACX,GAAG,MAAM;QACT,OAAO,EAAE,eAAe,IAAI,OAAO;QACnC,GAAG,EAAE,GAAG,GAAG,CAAC;QACZ,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,CAAC,CAAC;KAC9B,CAAC;SACD,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACnB,CAAA;IACD,OAAO,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,CAAA;AAC7B,CAAC;AAjBD,sCAiBC;AAED,kEAAkE;AAClE,SAAgB,4BAA4B,CAAC,IAAa;IACxD,OAAO,IAAI,KAAK,aAAa,CAAA;AAC/B,CAAC;AAFD,oEAEC;AAED,mBAAmB;AACnB,oJAAoJ;AACvI,QAAA,kBAAkB,GAAG;IAChC,CAAC,EAAE,cAAc;IACjB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,oBAAoB;IACvB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,oBAAoB;IACvB,CAAC,EAAE,kBAAkB;CACgB,CAAA;AAIvC,SAAgB,aAAa,CAC3B,IAAkB,EAClB,EAAuB,EACvB,IAAsB;IAEtB,IAAA,6BAAW,EACT,IAAI,EACJ,IAAA,cAAO,EAAC,KAAK,IAAI,EAAE;QACjB,IAAI;YACF,MAAM,EAAE,EAAE,CAAA;SACX;QAAC,OAAO,CAAC,EAAE;YACV,IAAI,IAAA,yBAAO,EAAC,IAAI,CAAC,EAAE;gBACjB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;aACjB;SACF;IACH,CAAC,EAAE,IAAI,CAAC,CACT,CAAA;AACH,CAAC;AAjBD,sCAiBC;AACD,SAAgB,WAAW;IACzB,OAAO,OAAO,IAAI,CAAC,MAAM,EAAE,GAAG,GAAG,aAAa,CAAA;AAChD,CAAC;AAFD,kCAEC"}

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,6 +1,6 @@
-/// <reference types="react" />
+import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 declare const _default: (props: {
     model: IAnyStateTreeNode;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts

@@ -1,6 +1,6 @@
-/// <reference types="react" />
+import React from 'react';
 export default function AlignmentFlags(props: {
     feature: {
         flags: number;
     };
-}): JSX.Element;
+}): React.JSX.Element;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js

@@ -1,7 +1,8 @@
 import React from 'react';
 import { Checkbox, FormControlLabel, FormGroup } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import { BaseCard, SimpleValue, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField';
 const useStyles = makeStyles()({
     compact: {
         paddingRight: 0,
@@ -28,7 +29,7 @@ export default function AlignmentFlags(props) {
     const { feature } = props;
     const { flags } = feature;
     return (React.createElement(BaseCard, { ...props, title: "Flags" },
-        React.createElement(SimpleValue, { name: "Flag", value: flags }),
+        React.createElement(SimpleField, { name: "Flag", value: flags }),
         React.createElement(FormGroup, null, flagNames.map((name, idx) => {
             const val = flags & (1 << idx);
             const key = `${name}_${val}`;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map

@@ -1 +1 @@
-{"version":3,"file":"AlignmentsFeatureFlags.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACrE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EACL,QAAQ,EACR,WAAW,GACZ,MAAM,mDAAmD,CAAA;AAE1D,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,OAAO,EAAE;QACP,YAAY,EAAE,CAAC;QACf,UAAU,EAAE,CAAC;QACb,aAAa,EAAE,CAAC;KACjB;CACF,CAAC,CAAA;AAEF,MAAM,SAAS,GAAG;IAChB,aAAa;IACb,4BAA4B;IAC5B,eAAe;IACf,eAAe;IACf,qBAAqB;IACrB,qBAAqB;IACrB,eAAe;IACf,gBAAgB;IAChB,uBAAuB;IACvB,2CAA2C;IAC3C,kCAAkC;IAClC,yBAAyB;CAC1B,CAAA;AAED,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,KAAqC;IAC1E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAA;IAEzB,OAAO,CACL,oBAAC,QAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,OAAO;QAChC,oBAAC,WAAW,IAAC,IAAI,EAAC,MAAM,EAAC,KAAK,EAAE,KAAK,GAAI;QACzC,oBAAC,SAAS,QACP,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,GAAG,EAAE,EAAE;YAC3B,MAAM,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,IAAI,GAAG,CAAC,CAAA;YAC9B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,oBAAC,gBAAgB,IACf,GAAG,EAAE,GAAG,EACR,OAAO,EACL,oBAAC,QAAQ,IACP,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,IAAI,EAAE,IAAI,EACV,QAAQ,SACR,EAEJ,KAAK,EAAE,IAAI,GACX,CACH,CAAA;QACH,CAAC,CAAC,CACQ,CACH,CACZ,CAAA;AACH,CAAC"}
+{"version":3,"file":"AlignmentsFeatureFlags.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACrE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,mDAAmD,CAAA;AAC5E,OAAO,WAAW,MAAM,+DAA+D,CAAA;AAEvF,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,OAAO,EAAE;QACP,YAAY,EAAE,CAAC;QACf,UAAU,EAAE,CAAC;QACb,aAAa,EAAE,CAAC;KACjB;CACF,CAAC,CAAA;AAEF,MAAM,SAAS,GAAG;IAChB,aAAa;IACb,4BAA4B;IAC5B,eAAe;IACf,eAAe;IACf,qBAAqB;IACrB,qBAAqB;IACrB,eAAe;IACf,gBAAgB;IAChB,uBAAuB;IACvB,2CAA2C;IAC3C,kCAAkC;IAClC,yBAAyB;CAC1B,CAAA;AAED,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,KAAqC;IAC1E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAA;IAEzB,OAAO,CACL,oBAAC,QAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,OAAO;QAChC,oBAAC,WAAW,IAAC,IAAI,EAAC,MAAM,EAAC,KAAK,EAAE,KAAK,GAAI;QACzC,oBAAC,SAAS,QACP,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,GAAG,EAAE,EAAE;YAC3B,MAAM,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,IAAI,GAAG,CAAC,CAAA;YAC9B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,oBAAC,gBAAgB,IACf,GAAG,EAAE,GAAG,EACR,OAAO,EACL,oBAAC,QAAQ,IACP,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,IAAI,EAAE,IAAI,EACV,QAAQ,SACR,EAEJ,KAAK,EAAE,IAAI,GACX,CACH,CAAA;QACH,CAAC,CAAC,CACQ,CACH,CACZ,CAAA;AACH,CAAC"}

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts

@@ -1,6 +1,6 @@
-/// <reference types="react" />
+import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 export default function SupplementaryAlignments(props: {
     tag: string;
     model: IAnyStateTreeNode;
-}): JSX.Element;
+}): React.JSX.Element;

package/esm/AlignmentsFeatureDetail/index.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
@@ -13,10 +13,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
+    error: unknown;
+} & {
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
     setExtra(type?: string | undefined, trackId?: string | undefined): void;
+    setError(e: unknown): void;
 } & {
     afterCreate(): void;
 }, {

package/esm/AlignmentsTrack/configSchemaF.d.ts

@@ -0,0 +1,74 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;

package/esm/AlignmentsTrack/configSchemaF.js

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+/**
+ * #config AlignmentsTrack
+ * has very little config; most config and state logic is on the display
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+export default function configSchemaFactory(pluginManager) {
+    return ConfigurationSchema('AlignmentsTrack', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: createBaseTrackConfig(pluginManager),
+    });
+}
+//# sourceMappingURL=configSchemaF.js.map

package/esm/AlignmentsTrack/configSchemaF.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchemaF.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/configSchemaF.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAG3E;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,CAAC,OAAO,UAAU,mBAAmB,CAAC,aAA4B;IACtE,OAAO,mBAAmB,CACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC"}

package/esm/AlignmentsTrack/index.js

@@ -1,22 +1,9 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { createBaseTrackConfig, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes/models';
-/**
- * #config AlignmentsTrack
- * has very little config; most config and state logic is on the display
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-function configSchemaFactory(pluginManager) {
-    return ConfigurationSchema('AlignmentsTrack', {}, {
-        /**
-         * #baseConfiguration
-         */
-        baseConfiguration: createBaseTrackConfig(pluginManager),
-    });
-}
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
+import configSchemaF from './configSchemaF';
 export default function register(pm) {
     pm.addTrackType(() => {
-        const configSchema = configSchemaFactory(pm);
+        const configSchema = configSchemaF(pm);
         const track = new TrackType({
             name: 'AlignmentsTrack',
             displayName: 'Alignments track',

package/esm/AlignmentsTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EACL,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,4CAA4C,CAAA;AAEnD;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,mBAAmB,CACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AACD,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,oBAAoB,EAAE,MAAM,4CAA4C,CAAA;AACjF,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAE3C,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,aAAa,CAAC,EAAE,CAAC,CAAA;QACtC,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/BamAdapter/BamAdapter.d.ts

@@ -21,7 +21,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         bam: BamFile;
         sequenceAdapter?: BaseFeatureDataAdapter | undefined;
     }>;
-    getHeader(opts?: BaseOptions): Promise<any>;
+    getHeader(opts?: BaseOptions): Promise<string | undefined>;
     private setupPre;
     setup(opts?: BaseOptions): Promise<Header>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
@@ -39,7 +39,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             readName: string;
         };
     }): import("rxjs").Observable<Feature>;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats | {
+    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
         bytes: number;
         fetchSizeLimit: any;
     }>;

package/esm/BamAdapter/BamAdapter.js

@@ -4,9 +4,9 @@ import { bytesForRegions, updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { toArray } from 'rxjs/operators';
+import { firstValueFrom } from 'rxjs';
 // locals
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature';
-import { firstValueFrom } from 'rxjs';
 export default class BamAdapter extends BaseFeatureDataAdapter {
     // derived classes may not use the same configuration so a custom
     // configure method allows derived classes to override this behavior
@@ -23,8 +23,6 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             // chunkSizeLimit and fetchSizeLimit are more troublesome than
             // helpful, and have given overly large values on the ultra long
             // nanopore reads even with 500MB limits, so disabled with infinity
-            chunkSizeLimit: Infinity,
-            fetchSizeLimit: Infinity,
             yieldThreadTime: Infinity,
         });
         const adapterConfig = this.getConf('sequenceAdapter');
@@ -61,9 +59,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             // mapping between ref ref ID numbers and names
             const idToName = [];
             const nameToId = {};
-            samHeader
-                .filter(l => l.tag === 'SQ')
-                .forEach((sqLine, refId) => {
+            samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
                 sqLine.data.forEach(item => {
                     if (item.tag === 'SN') {
                         // this is the ref name
@@ -129,44 +125,43 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             const { bam } = await this.configure();
             await this.setup(opts);
-            statusCallback('Downloading alignments');
-            const records = await bam.getRecordsForRange(refName, start, end, opts);
-            const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
-            for (const record of records) {
-                let ref;
-                if (!record.get('MD')) {
-                    ref = await this.seqFetch(originalRefName || refName, record.get('start'), record.get('end'));
-                }
-                const flags = record.flags;
-                if (!((flags & flagInclude) === flagInclude && !(flags & flagExclude))) {
-                    continue;
-                }
-                if (tagFilter) {
-                    const val = record.get(tagFilter.tag);
-                    if (!(val === '*' ? val !== undefined : val === tagFilter.value)) {
+            const records = await updateStatus('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end, opts));
+            await updateStatus('Processing alignments', statusCallback, async () => {
+                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
+                for (const record of records) {
+                    let ref;
+                    if (!record.get('MD')) {
+                        ref = await this.seqFetch(originalRefName || refName, record.get('start'), record.get('end'));
+                    }
+                    const flags = record.flags;
+                    if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
                         continue;
                     }
+                    if (tagFilter) {
+                        const v = record.get(tagFilter.tag);
+                        if (!(v === '*' ? v !== undefined : `${v}` === tagFilter.value)) {
+                            continue;
+                        }
+                    }
+                    if (readName && record.get('name') !== readName) {
+                        continue;
+                    }
+                    observer.next(new BamSlightlyLazyFeature(record, this, ref));
                 }
-                if (readName && record.get('name') !== readName) {
-                    continue;
-                }
-                observer.next(new BamSlightlyLazyFeature(record, this, ref));
-            }
-            statusCallback('');
-            observer.complete();
+                observer.complete();
+            });
         }, signal);
     }
-    async estimateRegionsStats(regions, opts) {
+    async getMultiRegionFeatureDensityStats(regions, opts) {
         const { bam } = await this.configure();
         // this is a method to avoid calling on htsget adapters
-        // @ts-expect-error
-        if (bam.index.filehandle !== '?') {
+        if (bam.index) {
             const bytes = await bytesForRegions(regions, bam);
             const fetchSizeLimit = this.getConf('fetchSizeLimit');
             return { bytes, fetchSizeLimit };
         }
         else {
-            return super.estimateRegionsStats(regions, opts);
+            return super.getMultiRegionFeatureDensityStats(regions, opts);
         }
     }
     freeResources( /* { region } */) { }

package/esm/BamAdapter/BamAdapter.js.map

@@ -1 +1 @@
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package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -12,7 +12,7 @@ export default class BamSlightlyLazyFeature implements Feature {
     _get_score(): number;
     _get_flags(): string;
     _get_strand(): number;
-    _get_pair_orientation(): string | null | undefined;
+    _get_pair_orientation(): string | undefined;
     _get_next_ref(): string | undefined;
     _get_next_pos(): number | undefined;
     _get_next_segment_position(): string | undefined;