@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/util.js

@@ -1,135 +1,144 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.fetchSequence = fetchSequence;
-exports.getColorWGBS = getColorWGBS;
-exports.getTag = getTag;
-exports.getTagAlt = getTagAlt;
-exports.orientationTypes = void 0;
-exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _operators = require("rxjs/operators");
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.shouldFetchReferenceSequence = exports.fetchSequence = exports.getColorWGBS = exports.orientationTypes = exports.getTagAlt = exports.getTag = void 0;
+var operators_1 = require("rxjs/operators");
 // get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
 // BAM does not
 function getTag(feature, tag) {
-  var tags = feature.get('tags');
-  return tags ? tags[tag] : feature.get(tag);
-} // use fallback alt tag, used in situations where upper case/lower case tags
+    var tags = feature.get('tags');
+    return tags ? 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);
-} // orientation definitions from igv.js, see also
+    return getTag(feature, tag) || getTag(feature, alt);
+}
+exports.getTagAlt = getTagAlt;
+// orientation definitions from igv.js, see also
 // https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
-
-
-var 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.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.orientationTypes = orientationTypes;
-
 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 (strand === 1) {
+        if (base === 'C') {
+            return '#f00';
+        }
+        if (base === 'T') {
+            return '#00f';
+        }
     }
-
-    if (base === 'A') {
-      return '#00f';
+    else if (strand === -1) {
+        if (base === 'G') {
+            return '#f00';
+        }
+        if (base === 'A') {
+            return '#00f';
+        }
     }
-  }
-
-  return '#888';
+    return '#888';
 }
-
-function fetchSequence(_x, _x2) {
-  return _fetchSequence.apply(this, arguments);
-} // has to check underlying C-G (aka CpG) on the reference sequence
-
-
-function _fetchSequence() {
-  _fetchSequence = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(region, adapter) {
-    var _feats$;
-
-    var end, originalRefName, refName, feats;
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            end = region.end, originalRefName = region.originalRefName, refName = region.refName;
-            _context.next = 3;
-            return adapter.getFeatures(_objectSpread(_objectSpread({}, region), {}, {
-              refName: originalRefName || refName,
-              end: end + 1
-            })).pipe((0, _operators.toArray)()).toPromise();
-
-          case 3:
-            feats = _context.sent;
-            return _context.abrupt("return", (_feats$ = feats[0]) === null || _feats$ === void 0 ? void 0 : _feats$.get('seq'));
-
-          case 5:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  }));
-  return _fetchSequence.apply(this, arguments);
+exports.getColorWGBS = getColorWGBS;
+function fetchSequence(region, adapter) {
+    var _a;
+    return __awaiter(this, void 0, void 0, function () {
+        var end, originalRefName, refName, feats;
+        return __generator(this, function (_b) {
+            switch (_b.label) {
+                case 0:
+                    end = region.end, originalRefName = region.originalRefName, refName = region.refName;
+                    return [4 /*yield*/, adapter
+                            .getFeatures(__assign(__assign({}, region), { refName: originalRefName || refName, end: end + 1 }))
+                            .pipe((0, operators_1.toArray)())
+                            .toPromise()];
+                case 1:
+                    feats = _b.sent();
+                    return [2 /*return*/, (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')];
+            }
+        });
+    });
 }
-
+exports.fetchSequence = fetchSequence;
+// has to check underlying C-G (aka CpG) on the reference sequence
 function shouldFetchReferenceSequence(type) {
-  return type === 'methylation';
-}
+    return type === 'methylation';
+}
+exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
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package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+declare function AlignmentFeatureDetails(props: {
+    model: any;
+}): JSX.Element;
+declare const _default: typeof AlignmentFeatureDetails;
+export default _default;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -0,0 +1,145 @@
+import React, { useState } from 'react';
+import { Typography, Link, Paper, Checkbox, FormControlLabel, FormGroup, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+import copy from 'copy-to-clipboard';
+import { FeatureDetails, BaseCard, SimpleValue, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import { parseCigar } from '../BamAdapter/MismatchParser';
+const useStyles = makeStyles()(() => ({
+    compact: {
+        paddingRight: 0,
+        paddingTop: 0,
+        paddingBottom: 0,
+    },
+}));
+const omit = ['clipPos', 'flags'];
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function AlignmentFlags(props) {
+    const { classes } = useStyles();
+    const { feature } = props;
+    const { flags } = feature;
+    const flagNames = [
+        'read paired',
+        'read mapped in proper pair',
+        'read unmapped',
+        'mate unmapped',
+        'read reverse strand',
+        'mate reverse strand',
+        'first in pair',
+        'second in pair',
+        'not primary alignment',
+        'read fails platform/vendor quality checks',
+        'read is PCR or optical duplicate',
+        'supplementary alignment',
+    ];
+    return (React.createElement(BaseCard, { ...props, title: "Flags" },
+        React.createElement(SimpleValue, { name: 'Flag', value: flags }),
+        React.createElement(FormGroup, null, flagNames.map((name, index) => {
+            const val = flags & (1 << index);
+            const key = `${name}_${val}`;
+            return (React.createElement(FormControlLabel, { key: key, control: React.createElement(Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }));
+        }))));
+}
+function Formatter({ value }) {
+    const [show, setShow] = useState(false);
+    const [copied, setCopied] = useState(false);
+    const display = String(value);
+    if (display.length > 100) {
+        return (React.createElement(React.Fragment, null,
+            React.createElement("button", { type: "button", onClick: () => {
+                    copy(display);
+                    setCopied(true);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 700);
+                } }, copied ? 'Copied to clipboard' : 'Copy'),
+            React.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
+            React.createElement("div", null, show ? display : `${display.slice(0, 100)}...`)));
+    }
+    return React.createElement("div", null, display);
+}
+// utility function to get length of alignment from cigar
+function getLengthOnRef(cigar) {
+    const cigarOps = parseCigar(cigar);
+    let lengthOnRef = 0;
+    for (let i = 0; i < cigarOps.length; i += 2) {
+        const len = +cigarOps[i];
+        const op = cigarOps[i + 1];
+        if (op !== 'H' && op !== 'S' && op !== 'I') {
+            lengthOnRef += len;
+        }
+    }
+    return lengthOnRef;
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function SupplementaryAlignments(props) {
+    const { tag, model } = props;
+    const session = getSession(model);
+    return (React.createElement(BaseCard, { ...props, title: "Supplementary alignments" },
+        React.createElement(Typography, null, "List of supplementary alignment locations"),
+        React.createElement("ul", null, tag
+            .split(';')
+            .filter(SA => !!SA)
+            .map((SA, index) => {
+            const [saRef, saStart, saStrand, saCigar] = SA.split(',');
+            const saLength = getLengthOnRef(saCigar);
+            const extra = Math.floor(saLength / 5);
+            const start = +saStart;
+            const end = +saStart + saLength;
+            const locString = `${saRef}:${Math.max(1, start - extra)}-${end + extra}`;
+            const displayStart = start.toLocaleString('en-US');
+            const displayEnd = end.toLocaleString('en-US');
+            const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand})`;
+            return (React.createElement("li", { key: `${locString}-${index}` },
+                React.createElement(Link, { onClick: event => {
+                        event.preventDefault();
+                        const { view } = model;
+                        try {
+                            if (view) {
+                                view.navToLocString(locString);
+                            }
+                            else {
+                                throw new Error('No view associated with this view anymore');
+                            }
+                        }
+                        catch (e) {
+                            console.error(e);
+                            session.notify(`${e}`);
+                        }
+                    }, href: "#" }, displayString)));
+        }))));
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function PairLink({ locString, model }) {
+    const session = getSession(model);
+    return (React.createElement(Link, { onClick: () => {
+            const { view } = model;
+            try {
+                if (view) {
+                    view.navToLocString(locString);
+                }
+                else {
+                    session.notify('No view associated with this feature detail panel anymore', 'warning');
+                }
+            }
+            catch (e) {
+                console.error(e);
+                session.notify(`${e}`);
+            }
+        }, href: "#" }, locString));
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function AlignmentFeatureDetails(props) {
+    const { model } = props;
+    const feat = JSON.parse(JSON.stringify(model.featureData));
+    const SA = (feat.tags && feat.tags.SA) || feat.SA;
+    return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
+        React.createElement(FeatureDetails, { ...props, omit: omit, feature: feat, formatter: (value, key) => {
+                return key === 'next_segment_position' ? (React.createElement(PairLink, { model: model, locString: value })) : (React.createElement(Formatter, { value: value }));
+            } }),
+        SA ? React.createElement(SupplementaryAlignments, { model: model, tag: SA }) : null,
+        React.createElement(AlignmentFlags, { feature: feat, ...props })));
+}
+export default observer(AlignmentFeatureDetails);
+//# sourceMappingURL=AlignmentsFeatureDetail.js.map

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

@@ -0,0 +1 @@
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package/esm/AlignmentsFeatureDetail/index.d.ts

@@ -0,0 +1,38 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+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">;
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
+}, {
+    setFeatureData(featureData: Record<string, unknown>): void;
+    clearFeatureData(): void;
+    setFormattedData(feat: Record<string, unknown>): void;
+} & {
+    afterCreate(): void;
+}, {
+    type: "BaseFeatureWidget";
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
+    id: string;
+    type: "BaseFeatureWidget";
+    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    formattedFields: any;
+    finalizedFeatureData: any;
+} & import("mobx-state-tree")._NotCustomized>;
+export default function register(pluginManager: PluginManager): void;
+export { configSchema };

package/esm/AlignmentsFeatureDetail/index.js

@@ -0,0 +1,23 @@
+import { lazy } from 'react';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
+import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
+const configSchema = ConfigurationSchema('AlignmentsFeatureWidget', {});
+export function stateModelFactory(pluginManager) {
+    const baseModel = baseModelFactory(pluginManager);
+    return types.compose(baseModel, types.model('AlignmentsFeatureWidget', {
+        type: types.literal('AlignmentsFeatureWidget'),
+    }));
+}
+export default function register(pluginManager) {
+    pluginManager.addWidgetType(() => new WidgetType({
+        name: 'AlignmentsFeatureWidget',
+        heading: 'Feature details',
+        configSchema,
+        stateModel: stateModelFactory(pluginManager),
+        ReactComponent: lazy(() => import('./AlignmentsFeatureDetail')),
+    }));
+}
+export { configSchema };
+//# sourceMappingURL=index.js.map

package/esm/AlignmentsFeatureDetail/index.js.map

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package/esm/AlignmentsTrack/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

package/esm/AlignmentsTrack/index.js

@@ -0,0 +1,23 @@
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes/models';
+function configSchemaFactory(pluginManager) {
+    return ConfigurationSchema('AlignmentsTrack', {}, { baseConfiguration: createBaseTrackConfig(pluginManager) });
+}
+export default function register(pluginManager) {
+    pluginManager.addTrackType(() => {
+        const configSchema = configSchemaFactory(pluginManager);
+        const track = new TrackType({
+            name: 'AlignmentsTrack',
+            configSchema,
+            stateModel: createBaseTrackModel(pluginManager, 'AlignmentsTrack', configSchema),
+        });
+        const linearAlignmentsDisplay = pluginManager.getDisplayType('LinearAlignmentsDisplay');
+        // Add LinearAlignmentsDisplay here so that it has priority over the other
+        // linear displays (defaults to order the displays are added, but we have
+        // to add the Pileup and SNPCoverage displays first).
+        track.addDisplayType(linearAlignmentsDisplay);
+        return track;
+    });
+}
+//# sourceMappingURL=index.js.map

package/esm/AlignmentsTrack/index.js.map

@@ -0,0 +1 @@
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package/esm/BamAdapter/BamAdapter.d.ts

@@ -0,0 +1,40 @@
+import { BamFile } from '@gmod/bam';
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export default class BamAdapter extends BaseFeatureDataAdapter {
+    private samHeader?;
+    private setupP?;
+    protected configured?: Promise<{
+        bam: BamFile;
+        sequenceAdapter?: BaseFeatureDataAdapter;
+    }>;
+    protected configure(): Promise<{
+        bam: BamFile;
+        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
+    }>;
+    getHeader(opts?: BaseOptions): Promise<any>;
+    private setupPre;
+    private setup;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    private seqFetch;
+    getFeatures(region: Region & {
+        originalRefName?: string;
+    }, opts?: BaseOptions & {
+        filterBy: {
+            flagInclude: number;
+            flagExclude: number;
+            tagFilter: {
+                tag: string;
+                value: unknown;
+            };
+            readName: string;
+        };
+    }): import("rxjs").Observable<Feature>;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats | {
+        bytes: number;
+        fetchSizeLimit: any;
+    }>;
+    freeResources(): void;
+    refIdToName(refId: number): string | undefined;
+}