@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/dist/index.js

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MismatchParser = void 0;
+exports.MismatchParser = exports.linearPileupDisplayStateModelFactory = exports.linearPileupDisplayConfigSchemaFactory = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const MismatchParser = __importStar(require("./BamAdapter/MismatchParser"));
 exports.MismatchParser = MismatchParser;
@@ -38,7 +38,9 @@ const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
 const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
 const LinearAlignmentsDisplay_1 = __importDefault(require("./LinearAlignmentsDisplay"));
 const LinearSNPCoverageDisplay_1 = __importDefault(require("./LinearSNPCoverageDisplay"));
-const LinearPileupDisplay_1 = __importDefault(require("./LinearPileupDisplay"));
+const LinearPileupDisplay_1 = __importStar(require("./LinearPileupDisplay"));
+Object.defineProperty(exports, "linearPileupDisplayStateModelFactory", { enumerable: true, get: function () { return LinearPileupDisplay_1.linearPileupDisplayStateModelFactory; } });
+Object.defineProperty(exports, "linearPileupDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearPileupDisplay_1.linearPileupDisplayConfigSchemaFactory; } });
 const AlignmentsTrack_1 = __importDefault(require("./AlignmentsTrack"));
 const AlignmentsFeatureDetail_1 = __importDefault(require("./AlignmentsFeatureDetail"));
 const rpcMethods_1 = require("./PileupRPC/rpcMethods");

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kEAAyC;AAEzC,4EAA6D;AAgI3D,wCAAc;AA7HhB,gEAAuC;AACvC,8DAAuC;AACvC,0EAAkD;AAClD,8EAAsD;AACtD,gFAAwD;AACxD,sEAA8C;AAC9C,wFAAgE;AAChE,0FAAkE;AAClE,6EAG8B;AAiH5B,qHAnHA,0DAAoC,OAmHA;AADpC,uHAjHA,4DAAsC,OAiHA;AA/GxC,wEAAgD;AAChD,wFAAgE;AAEhE,uDAG+B;AAC/B,sDAMkC;AAElC,MAAqB,gBAAiB,SAAQ,gBAAM;IAApD;;QACE,SAAI,GAAG,kBAAkB,CAAA;IA4F3B,CAAC;IA1FC,OAAO,CAAC,aAA4B;QAClC,CAAC;QAAA;YACC,oBAAY;YACZ,qBAAW;YACX,6BAAoB;YACpB,kCAAyB;YACzB,yBAAgB;YAChB,4BAAmB;YACnB,0BAAiB;YACjB,wBAAe;YACf,6BAAoB;YACpB,iCAAwB;YACxB,iCAAwB;SACzB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAA;QAE5B,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,UAAU,CAAA;gBAC7B,MAAM,WAAW,GAAG,aAAa,CAAA;gBACjC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,YAAY,EAAE,IAAI;oBAClB,YAAY,EAAE,KAAK,IAAI,IAAA,kBAAS,EAAC,IAAI,EAAE,OAAO,CAAC;iBAChD,CAAA;gBACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,SAAS,CAAA;gBAC5B,MAAM,WAAW,GAAG,YAAY,CAAA;gBAChC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,SAAS,GAAG,KAAK,IAAI,IAAA,oBAAW,EAAC,KAAK,CAAC,CAAA;gBAE7C,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,WAAW,EAAE,IAAI;oBACjB,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK,IAAI,IAAA,kBAAS,EAAC,IAAI,EAAE,MAAM,CAAC;wBAC1C,SAAS,EAAE,IAAA,sBAAa,EAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;qBAClD;iBACF,CAAA;gBACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;YACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;gBAC7B,IAAI,WAAW,KAAK,YAAY,IAAI,WAAW,KAAK,aAAa,EAAE;oBACjE,OAAO,iBAAiB,CAAA;iBACzB;gBACD,OAAO,gBAAgB,CAAC,WAAW,CAAC,CAAA;YACtC,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QAED,aAAa,CAAC,YAAY,CACxB,GAAG,EAAE,CAAC,IAAI,uCAA0B,CAAC,aAAa,CAAC,CACpD,CAAA;QACD,aAAa,CAAC,YAAY,CACxB,GAAG,EAAE,CAAC,IAAI,0CAA6B,CAAC,aAAa,CAAC,CACvD,CAAA;IACH,CAAC;CACF;AA7FD,mCA6FC"}

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -4,15 +4,16 @@ import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
 import { getSession } from '@jbrowse/core/util';
 import copy from 'copy-to-clipboard';
+import clone from 'clone';
 import { FeatureDetails, BaseCard, SimpleValue, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import { parseCigar } from '../BamAdapter/MismatchParser';
-const useStyles = makeStyles()(() => ({
+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) {
@@ -92,12 +93,12 @@ function SupplementaryAlignments(props) {
             const displayEnd = end.toLocaleString('en-US');
             const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand})`;
             return (React.createElement("li", { key: `${locString}-${index}` },
-                React.createElement(Link, { onClick: event => {
+                React.createElement(Link, { onClick: async (event) => {
                         event.preventDefault();
                         const { view } = model;
                         try {
                             if (view) {
-                                view.navToLocString(locString);
+                                await view.navToLocString(locString);
                             }
                             else {
                                 throw new Error('No view associated with this view anymore');
@@ -113,15 +114,13 @@ function SupplementaryAlignments(props) {
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function PairLink({ locString, model }) {
     const session = getSession(model);
-    return (React.createElement(Link, { onClick: () => {
+    return (React.createElement(Link, { onClick: async () => {
             const { view } = model;
+            if (!view) {
+                throw new Error('No view associated with this feature detail panel anymore');
+            }
             try {
-                if (view) {
-                    view.navToLocString(locString);
-                }
-                else {
-                    session.notify('No view associated with this feature detail panel anymore', 'warning');
-                }
+                await view.navToLocString(locString);
             }
             catch (e) {
                 console.error(e);
@@ -132,14 +131,14 @@ function PairLink({ locString, model }) {
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function AlignmentFeatureDetails(props) {
     const { model } = props;
-    const feat = JSON.parse(JSON.stringify(model.featureData));
+    const feat = clone(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 })));
+        feat.flags !== undefined ? (React.createElement(AlignmentFlags, { feature: feat, ...props })) : null));
 }
 export default observer(AlignmentFeatureDetails);
 //# sourceMappingURL=AlignmentsFeatureDetail.js.map

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

@@ -1 +1 @@
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package/esm/AlignmentsTrack/index.d.ts

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

package/esm/AlignmentsTrack/index.js

@@ -1,18 +1,28 @@
 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: createBaseTrackConfig(pluginManager) });
+    return ConfigurationSchema('AlignmentsTrack', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: createBaseTrackConfig(pluginManager),
+    });
 }
-export default function register(pluginManager) {
-    pluginManager.addTrackType(() => {
-        const configSchema = configSchemaFactory(pluginManager);
+export default function register(pm) {
+    pm.addTrackType(() => {
+        const configSchema = configSchemaFactory(pm);
         const track = new TrackType({
             name: 'AlignmentsTrack',
             configSchema,
-            stateModel: createBaseTrackModel(pluginManager, 'AlignmentsTrack', configSchema),
+            stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema),
         });
-        const linearAlignmentsDisplay = pluginManager.getDisplayType('LinearAlignmentsDisplay');
+        const linearAlignmentsDisplay = pm.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).

package/esm/AlignmentsTrack/index.js.map

@@ -1 +1 @@
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+{"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,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

@@ -1,7 +1,7 @@
 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';
+import { Feature } from '@jbrowse/core/util';
 interface Header {
     idToName: string[];
     nameToId: Record<string, number>;
@@ -9,9 +9,13 @@ interface Header {
 export default class BamAdapter extends BaseFeatureDataAdapter {
     private samHeader?;
     private setupP?;
-    protected configured?: Promise<{
+    private configureP?;
+    protected configurePre(): Promise<{
         bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter;
+        sequenceAdapter: BaseFeatureDataAdapter;
+    } | {
+        bam: BamFile;
+        sequenceAdapter?: undefined;
     }>;
     protected configure(): Promise<{
         bam: BamFile;

package/esm/BamAdapter/BamAdapter.js

@@ -4,43 +4,48 @@ 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 { readConfObject } from '@jbrowse/core/configuration';
+// locals
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature';
 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
+    async configurePre() {
+        const bamLocation = this.getConf('bamLocation');
+        const location = this.getConf(['index', 'location']);
+        const indexType = this.getConf(['index', 'indexType']);
+        const pm = this.pluginManager;
+        const csi = indexType === 'CSI';
+        const bam = new BamFile({
+            bamFilehandle: openLocation(bamLocation, pm),
+            csiFilehandle: csi ? openLocation(location, pm) : undefined,
+            baiFilehandle: !csi ? openLocation(location, pm) : undefined,
+            // 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');
+        if (adapterConfig && this.getSubAdapter) {
+            const { dataAdapter } = await this.getSubAdapter(adapterConfig);
+            return {
+                bam,
+                sequenceAdapter: dataAdapter,
+            };
+        }
+        else {
+            return { bam };
+        }
+    }
     async configure() {
-        if (!this.configured) {
-            const bamLocation = readConfObject(this.config, 'bamLocation');
-            const location = readConfObject(this.config, ['index', 'location']);
-            const indexType = readConfObject(this.config, ['index', 'indexType']);
-            const bam = new BamFile({
-                bamFilehandle: openLocation(bamLocation, this.pluginManager),
-                csiFilehandle: indexType === 'CSI'
-                    ? openLocation(location, this.pluginManager)
-                    : undefined,
-                baiFilehandle: indexType !== 'CSI'
-                    ? openLocation(location, this.pluginManager)
-                    : undefined,
-                // 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,
+        if (!this.configureP) {
+            this.configureP = this.configurePre().catch(e => {
+                this.configureP = undefined;
+                throw e;
             });
-            const adapterConfig = readConfObject(this.config, 'sequenceAdapter');
-            if (adapterConfig && this.getSubAdapter) {
-                this.configured = this.getSubAdapter(adapterConfig).then(({ dataAdapter }) => ({
-                    bam,
-                    sequenceAdapter: dataAdapter,
-                }));
-            }
-            else {
-                this.configured = Promise.resolve({ bam });
-            }
         }
-        return this.configured;
+        return this.configureP;
     }
     async getHeader(opts) {
         const { bam } = await this.configure();
@@ -156,7 +161,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         // @ts-ignore
         if (bam.index.filehandle !== '?') {
             const bytes = await bytesForRegions(regions, bam);
-            const fetchSizeLimit = readConfObject(this.config, 'fetchSizeLimit');
+            const fetchSizeLimit = this.getConf('fetchSizeLimit');
             return { bytes, fetchSizeLimit };
         }
         else {

package/esm/BamAdapter/BamAdapter.js.map

@@ -1 +1 @@
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package/esm/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,3 +1,4 @@
+// locals
 import { getMismatches } from './MismatchParser';
 export default class BamSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class

package/esm/BamAdapter/BamSlightlyLazyFeature.js.map

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

@@ -10,13 +10,13 @@ export interface Mismatch {
     cliplen?: number;
 }
 export declare function parseCigar(cigar?: string): string[];
-export declare function cigarToMismatches(ops: string[], seq: string, ref?: string, qual?: Buffer): Mismatch[];
+export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 /**
  * parse a SAM MD tag to find mismatching bases of the template versus the reference
  * @returns array of mismatches and their positions
  */
 export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
-export declare function getMismatches(cigar: string, md: string, seq: string, ref?: string, qual?: Buffer): Mismatch[];
+export declare function getMismatches(cigar: string, md?: string, seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 export declare function getNextRefPos(cigarOps: string[], positions: number[]): Generator<number, void, unknown>;
 export declare function getModificationPositions(mm: string, fseq: string, fstrand: number): {
     type: string;

package/esm/BamAdapter/MismatchParser.js

@@ -56,7 +56,7 @@ export function cigarToMismatches(ops, seq, ref, qual) {
             });
         }
         else if (op === 'X') {
-            const r = seq.slice(soffset, soffset + len);
+            const r = (seq === null || seq === void 0 ? void 0 : seq.slice(soffset, soffset + len)) || [];
             const q = (qual === null || qual === void 0 ? void 0 : qual.slice(soffset, soffset + len)) || [];
             for (let j = 0; j < len; j++) {
                 mismatches.push({
@@ -167,10 +167,7 @@ export function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
                 }
                 const s = getTemplateCoordLocal(curr.start);
                 curr.base = seq[s] || 'X';
-                const qualScore = qual === null || qual === void 0 ? void 0 : qual[s];
-                if (qualScore) {
-                    curr.qual = qualScore;
-                }
+                curr.qual = qual === null || qual === void 0 ? void 0 : qual[s];
                 curr.altbase = token;
                 nextRecord();
             }
@@ -186,7 +183,7 @@ export function getMismatches(cigar, md, seq, ref, qual) {
         mismatches = mismatches.concat(cigarToMismatches(ops, seq, ref, qual));
     }
     // now let's look for CRAM or MD mismatches
-    if (md) {
+    if (md && seq) {
         mismatches = mismatches.concat(mdToMismatches(md, ops, mismatches, seq, qual));
     }
     return mismatches;
@@ -282,7 +279,7 @@ export function getModificationTypes(mm) {
         const [basemod] = mod.split(',');
         const matches = basemod.match(modificationRegex);
         if (!matches) {
-            throw new Error('bad format for MM tag');
+            throw new Error(`bad format for MM tag: ${mm}`);
         }
         const [, , , typestr] = matches;
         // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so

package/esm/BamAdapter/MismatchParser.js.map

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

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/esm/BamAdapter/configSchema.js

@@ -1,16 +1,30 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-export default types.late(() => ConfigurationSchema('BamAdapter', {
+/**
+ * #config BamAdapter
+ * used to configure BAM adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = ConfigurationSchema('BamAdapter', {
+    /**
+     * #slot
+     */
     bamLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
     },
     index: ConfigurationSchema('BamIndex', {
+        /**
+         * #slot index.indexType
+         */
         indexType: {
             model: types.enumeration('IndexType', ['BAI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'BAI',
         },
+        /**
+         * #slot index.location
+         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -19,13 +33,24 @@ export default types.late(() => ConfigurationSchema('BamAdapter', {
             },
         },
     }),
+    /**
+     * #slot
+     */
     fetchSizeLimit: {
         type: 'number',
+        description: 'size to fetch in bytes over which to display a warning to the user that too much data will be fetched',
         defaultValue: 5000000,
     },
+    /**
+     * #slot
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
     sequenceAdapter: {
         type: 'frozen',
+        description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
         defaultValue: null,
     },
-}, { explicitlyTyped: true }));
+}, { explicitlyTyped: true });
+export default configSchema;
 //# sourceMappingURL=configSchema.js.map

package/esm/BamAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BamAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,YAAY,EACZ;IACE;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;IAED,KAAK,EAAE,mBAAmB,CAAC,UAAU,EAAE;QACrC;;WAEG;QACH,SAAS,EAAE;YACT,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,qBAAqB;gBAC1B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IACF;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,uGAAuG;QACzG,YAAY,EAAE,OAAS;KACxB;IACD;;;;OAIG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8EAA8E;QAChF,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}

package/esm/BamAdapter/index.js

@@ -1,10 +1,12 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
 export default (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType({
-        name: 'BamAdapter',
-        configSchema,
-        getAdapterClass: () => import('./BamAdapter').then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'BamAdapter',
+            configSchema,
+            getAdapterClass: () => import('./BamAdapter').then(r => r.default),
+        });
+    });
 };
 //# sourceMappingURL=index.js.map

package/esm/BamAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BamAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,YAAY;QAClB,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACnE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BamAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,YAAY;YAClB,YAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/CramAdapter/CramAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { IndexedCramFile, CramRecord } from '@gmod/cram';
+import { BaseFeatureDataAdapter, BaseOptions, BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region, Feature } from '@jbrowse/core/util';
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
 interface Header {
     idToName?: string[];
     nameToId?: Record<string, number>;
-    readGroups?: number[];
+    readGroups?: (string | undefined)[];
 }
 interface FilterBy {
     flagInclude: number;
@@ -18,13 +19,18 @@ interface FilterBy {
 export default class CramAdapter extends BaseFeatureDataAdapter {
     samHeader: Header;
     private setupP?;
+    private configureP?;
     private seqIdToRefName;
     private seqIdToOriginalRefName;
+    configurePre(): Promise<{
+        cram: IndexedCramFile;
+        sequenceAdapter: BaseSequenceAdapter;
+    }>;
     configure(): Promise<{
-        cram: any;
-        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
+        cram: IndexedCramFile;
+        sequenceAdapter: BaseSequenceAdapter;
     }>;
-    getHeader(opts?: BaseOptions): Promise<any>;
+    getHeader(opts?: BaseOptions): Promise<string | undefined>;
     private seqFetch;
     private setupPre;
     private setup;
@@ -38,9 +44,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         filterBy: FilterBy;
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
-    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
+    cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
     estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
-        bytes: any;
+        bytes: number;
         fetchSizeLimit: any;
     }>;
     /**