@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/dist/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/dist/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/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js

@@ -7,6 +7,7 @@ const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const SimpleField_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField"));
 const useStyles = (0, mui_1.makeStyles)()({
     compact: {
         paddingRight: 0,
@@ -33,7 +34,7 @@ function AlignmentFlags(props) {
     const { feature } = props;
     const { flags } = feature;
     return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Flags" },
-        react_1.default.createElement(BaseFeatureDetail_1.SimpleValue, { name: "Flag", value: flags }),
+        react_1.default.createElement(SimpleField_1.default, { name: "Flag", value: flags }),
         react_1.default.createElement(material_1.FormGroup, null, flagNames.map((name, idx) => {
             const val = flags & (1 << idx);
             const key = `${name}_${val}`;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map

@@ -1 +1 @@
-{"version":3,"file":"AlignmentsFeatureFlags.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAqE;AACrE,uCAA0C;AAC1C,yFAG0D;AAE1D,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,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,SAAwB,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,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,OAAO;QAChC,8BAAC,+BAAW,IAAC,IAAI,EAAC,MAAM,EAAC,KAAK,EAAE,KAAK,GAAI;QACzC,8BAAC,oBAAS,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,8BAAC,2BAAgB,IACf,GAAG,EAAE,GAAG,EACR,OAAO,EACL,8BAAC,mBAAQ,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;AA9BD,iCA8BC"}
+{"version":3,"file":"AlignmentsFeatureFlags.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAqE;AACrE,uCAA0C;AAC1C,yFAA4E;AAC5E,gHAAuF;AAEvF,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,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,SAAwB,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,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,OAAO;QAChC,8BAAC,qBAAW,IAAC,IAAI,EAAC,MAAM,EAAC,KAAK,EAAE,KAAK,GAAI;QACzC,8BAAC,oBAAS,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,8BAAC,2BAAgB,IACf,GAAG,EAAE,GAAG,EACR,OAAO,EACL,8BAAC,mBAAQ,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;AA9BD,iCA8BC"}

package/dist/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/dist/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/dist/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/dist/AlignmentsTrack/configSchemaF.js

@@ -0,0 +1,19 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const pluggableElementTypes_1 = require("@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
+function configSchemaFactory(pluginManager) {
+    return (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
+    });
+}
+exports.default = configSchemaFactory;
+//# sourceMappingURL=configSchemaF.js.map

package/dist/AlignmentsTrack/configSchemaF.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchemaF.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/configSchemaF.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,+EAA2E;AAG3E;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAwB,mBAAmB,CAAC,aAA4B;IACtE,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,6CAAqB,EAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AAXD,sCAWC"}

package/dist/AlignmentsTrack/index.js

@@ -4,24 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@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 (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, {
-        /**
-         * #baseConfiguration
-         */
-        baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager),
-    });
-}
+const configSchemaF_1 = __importDefault(require("./configSchemaF"));
 function register(pm) {
     pm.addTrackType(() => {
-        const configSchema = configSchemaFactory(pm);
+        const configSchema = (0, configSchemaF_1.default)(pm);
         const track = new TrackType_1.default({
             name: 'AlignmentsTrack',
             displayName: 'Alignments track',

package/dist/AlignmentsTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,+DAAiE;AACjE,uEAGmD;AAEnD;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AACD,SAAwB,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,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;AAhBD,2BAgBC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,uEAAiF;AACjF,oEAA2C;AAE3C,SAAwB,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,IAAA,uBAAa,EAAC,EAAE,CAAC,CAAA;QACtC,MAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,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;AAhBD,2BAgBC"}

package/dist/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/dist/BamAdapter/BamAdapter.js

@@ -9,9 +9,9 @@ const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const operators_1 = require("rxjs/operators");
+const rxjs_2 = require("rxjs");
 // locals
 const BamSlightlyLazyFeature_1 = __importDefault(require("./BamSlightlyLazyFeature"));
-const rxjs_2 = require("rxjs");
 class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     // derived classes may not use the same configuration so a custom
     // configure method allows derived classes to override this behavior
@@ -28,8 +28,6 @@ class BamAdapter extends BaseAdapter_1.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');
@@ -66,9 +64,7 @@ class BamAdapter extends BaseAdapter_1.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
@@ -134,44 +130,43 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, rxjs_1.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 (0, util_1.updateStatus)('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end, opts));
+            await (0, util_1.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_1.default(record, this, ref));
                 }
-                if (readName && record.get('name') !== readName) {
-                    continue;
-                }
-                observer.next(new BamSlightlyLazyFeature_1.default(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 (0, util_1.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/dist/BamAdapter/BamAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"BamAdapter.js","sourceRoot":"","sources":["../../src/BamAdapter/BamAdapter.ts"],"names":[],"mappings":";;;;;AAAA,mCAAmC;AACnC,yEAGgD;AAEhD,6CAA2E;AAC3E,8CAAoD;AACpD,kDAA0D;AAC1D,8CAAwC;AAExC,SAAS;AACT,sFAA6D;AAC7D,+BAAqC;AAOrC,MAAqB,UAAW,SAAQ,oCAAsB;IAS5D,iEAAiE;IACjE,oEAAoE;IAC1D,KAAK,CAAC,YAAY;QAC1B,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACtD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,SAAS,KAAK,KAAK,CAAA;QAC/B,MAAM,GAAG,GAAG,IAAI,aAAO,CAAC;YACtB,aAAa,EAAE,IAAA,iBAAY,EAAC,WAAW,EAAE,EAAE,CAAC;YAC5C,aAAa,EAAE,GAAG,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC3D,aAAa,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAE5D,8DAA8D;YAC9D,gEAAgE;YAChE,mEAAmE;YACnE,cAAc,EAAE,QAAQ;YACxB,cAAc,EAAE,QAAQ;YACxB,eAAe,EAAE,QAAQ;SAC1B,CAAC,CAAA;QAEF,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QACrD,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;YACvC,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAA;YAC/D,OAAO;gBACL,GAAG;gBACH,eAAe,EAAE,WAAqC;aACvD,CAAA;SACF;aAAM;YACL,OAAO,EAAE,GAAG,EAAE,CAAA;SACf;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,aAAa,CAAC,IAAI,CAAC,CAAA;IAChC,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,IAAI,CAAC,SAAS,GAAG,MAAM,IAAA,mBAAY,EACjC,mBAAmB,EACnB,cAAc,EACd,KAAK,IAAI,EAAE;YACT,MAAM,SAAS,GAAG,MAAM,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YAE3C,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,QAAQ,GAAa,EAAE,CAAA;YAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;YAC3C,SAAS;iBACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;iBAC3B,OAAO,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;gBACzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACzB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;wBACrB,uBAAuB;wBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;wBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;wBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;qBAC1B;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YAEJ,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,CAAA;QAC/B,CAAC,CACF,CAAA;QACD,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3C,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAe,EAAE,KAAa,EAAE,GAAW;QAChE,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,MAAM,WAAW,GAAG,eAAe,CAAA;QACnC,IAAI,CAAC,WAAW,EAAE;YAChB,OAAO,SAAS,CAAA;SACjB;QACD,IAAI,CAAC,OAAO,EAAE;YACZ,OAAO,SAAS,CAAA;SACjB;QAED,MAAM,QAAQ,GAAG,WAAW,CAAC,WAAW,CAAC;YACvC,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC,CAAA;QAEF,MAAM,SAAS,GAAG,MAAM,IAAA,qBAAc,EAAC,QAAQ,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,CAAA;QAEhE,IAAI,QAAQ,GAAG,EAAE,CAAA;QACjB,SAAS;aACN,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;aAC/C,OAAO,CAAC,KAAK,CAAC,EAAE;YACf,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;YACjD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;YACjE,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;YACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;YAC1D,QAAQ,IAAI,QAAQ,CAAC,KAAK,CAAC,SAAS,EAAE,SAAS,GAAG,UAAU,CAAC,CAAA;QAC/D,CAAC,CAAC,CAAA;QAEJ,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;YACnC,MAAM,IAAI,KAAK,CACb,mCAAmC,OAAO,IAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,IAAI,GAAG,CAAC,cAAc,EAAE,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;SACF;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAED,WAAW,CACT,MAA6C,EAC7C,IAOC;QAED,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,eAAe,EAAE,GAAG,MAAM,CAAA;QACvD,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAClE,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YACtC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACtB,cAAc,CAAC,wBAAwB,CAAC,CAAA;YACxC,MAAM,OAAO,GAAG,MAAM,GAAG,CAAC,kBAAkB,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;YAEvE,MAAM,EACJ,WAAW,GAAG,CAAC,EACf,WAAW,GAAG,CAAC,EACf,SAAS,EACT,QAAQ,GACT,GAAG,QAAQ,IAAI,EAAE,CAAA;YAElB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;gBAC5B,IAAI,GAAuB,CAAA;gBAC3B,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;oBACrB,GAAG,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvB,eAAe,IAAI,OAAO,EAC1B,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,EACnB,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAClB,CAAA;iBACF;gBAED,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAA;gBAC1B,IACE,CAAC,CAAC,CAAC,KAAK,GAAG,WAAW,CAAC,KAAK,WAAW,IAAI,CAAC,CAAC,KAAK,GAAG,WAAW,CAAC,CAAC,EAClE;oBACA,SAAQ;iBACT;gBAED,IAAI,SAAS,EAAE;oBACb,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAA;oBACrC,IAAI,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,CAAC,KAAK,CAAC,EAAE;wBAChE,SAAQ;qBACT;iBACF;gBAED,IAAI,QAAQ,IAAI,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,QAAQ,EAAE;oBAC/C,SAAQ;iBACT;gBAED,QAAQ,CAAC,IAAI,CAAC,IAAI,gCAAsB,CAAC,MAAM,EAAE,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;aAC7D;YACD,cAAc,CAAC,EAAE,CAAC,CAAA;YAClB,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,MAAM,CAAC,CAAA;IACZ,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,uDAAuD;QACvD,mBAAmB;QACnB,IAAI,GAAG,CAAC,KAAK,CAAC,UAAU,KAAK,GAAG,EAAE;YAChC,MAAM,KAAK,GAAG,MAAM,IAAA,sBAAe,EAAC,OAAO,EAAE,GAAG,CAAC,CAAA;YACjD,MAAM,cAAc,GAAG,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAA;YACrD,OAAO,EAAE,KAAK,EAAE,cAAc,EAAE,CAAA;SACjC;aAAM;YACL,OAAO,KAAK,CAAC,oBAAoB,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;SACjD;IACH,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;IAExC,2DAA2D;IAC3D,WAAW,CAAC,KAAa;;QACvB,OAAO,MAAA,IAAI,CAAC,SAAS,0CAAE,QAAQ,CAAC,KAAK,CAAC,CAAA;IACxC,CAAC;CACF;AApOD,6BAoOC"}
+{"version":3,"file":"BamAdapter.js","sourceRoot":"","sources":["../../src/BamAdapter/BamAdapter.ts"],"names":[],"mappings":";;;;;AAAA,mCAAmC;AACnC,yEAGgD;AAEhD,6CAA2E;AAC3E,8CAAoD;AACpD,kDAA0D;AAC1D,8CAAwC;AACxC,+BAAqC;AAErC,SAAS;AACT,sFAA6D;AAO7D,MAAqB,UAAW,SAAQ,oCAAsB;IAS5D,iEAAiE;IACjE,oEAAoE;IAC1D,KAAK,CAAC,YAAY;QAC1B,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACtD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,SAAS,KAAK,KAAK,CAAA;QAC/B,MAAM,GAAG,GAAG,IAAI,aAAO,CAAC;YACtB,aAAa,EAAE,IAAA,iBAAY,EAAC,WAAW,EAAE,EAAE,CAAC;YAC5C,aAAa,EAAE,GAAG,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC3D,aAAa,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAE5D,8DAA8D;YAC9D,gEAAgE;YAChE,mEAAmE;YACnE,eAAe,EAAE,QAAQ;SAC1B,CAAC,CAAA;QAEF,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QACrD,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;YACvC,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAA;YAC/D,OAAO;gBACL,GAAG;gBACH,eAAe,EAAE,WAAqC;aACvD,CAAA;SACF;aAAM;YACL,OAAO,EAAE,GAAG,EAAE,CAAA;SACf;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,aAAa,CAAC,IAAI,CAAC,CAAA;IAChC,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,IAAI,CAAC,SAAS,GAAG,MAAM,IAAA,mBAAY,EACjC,mBAAmB,EACnB,cAAc,EACd,KAAK,IAAI,EAAE;YACT,MAAM,SAAS,GAAG,MAAM,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YAE3C,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,QAAQ,GAAa,EAAE,CAAA;YAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;YAC3C,SAAS,aAAT,SAAS,uBAAT,SAAS,CACL,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,EAC3B,OAAO,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;gBACzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACzB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;wBACrB,uBAAuB;wBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;wBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;wBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;qBAC1B;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YAEJ,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,CAAA;QAC/B,CAAC,CACF,CAAA;QACD,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3C,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAe,EAAE,KAAa,EAAE,GAAW;QAChE,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,MAAM,WAAW,GAAG,eAAe,CAAA;QACnC,IAAI,CAAC,WAAW,EAAE;YAChB,OAAO,SAAS,CAAA;SACjB;QACD,IAAI,CAAC,OAAO,EAAE;YACZ,OAAO,SAAS,CAAA;SACjB;QAED,MAAM,QAAQ,GAAG,WAAW,CAAC,WAAW,CAAC;YACvC,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC,CAAA;QAEF,MAAM,SAAS,GAAG,MAAM,IAAA,qBAAc,EAAC,QAAQ,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,CAAA;QAEhE,IAAI,QAAQ,GAAG,EAAE,CAAA;QACjB,SAAS;aACN,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;aAC/C,OAAO,CAAC,KAAK,CAAC,EAAE;YACf,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;YACjD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;YACjE,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;YACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;YAC1D,QAAQ,IAAI,QAAQ,CAAC,KAAK,CAAC,SAAS,EAAE,SAAS,GAAG,UAAU,CAAC,CAAA;QAC/D,CAAC,CAAC,CAAA;QAEJ,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;YACnC,MAAM,IAAI,KAAK,CACb,mCAAmC,OAAO,IAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,IAAI,GAAG,CAAC,cAAc,EAAE,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;SACF;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAED,WAAW,CACT,MAA6C,EAC7C,IAOC;QAED,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,eAAe,EAAE,GAAG,MAAM,CAAA;QACvD,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAClE,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YACtC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACtB,MAAM,OAAO,GAAG,MAAM,IAAA,mBAAY,EAChC,wBAAwB,EACxB,cAAc,EACd,GAAG,EAAE,CAAC,GAAG,CAAC,kBAAkB,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CACxD,CAAA;YAED,MAAM,IAAA,mBAAY,EAAC,uBAAuB,EAAE,cAAc,EAAE,KAAK,IAAI,EAAE;gBACrE,MAAM,EACJ,WAAW,GAAG,CAAC,EACf,WAAW,GAAG,CAAC,EACf,SAAS,EACT,QAAQ,GACT,GAAG,QAAQ,IAAI,EAAE,CAAA;gBAElB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;oBAC5B,IAAI,GAAuB,CAAA;oBAC3B,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;wBACrB,GAAG,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvB,eAAe,IAAI,OAAO,EAC1B,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,EACnB,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAClB,CAAA;qBACF;oBAED,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAA;oBAC1B,IAAI,CAAC,KAAK,GAAG,WAAW,CAAC,KAAK,WAAW,IAAI,CAAC,CAAC,KAAK,GAAG,WAAW,CAAC,EAAE;wBACnE,SAAQ;qBACT;oBAED,IAAI,SAAS,EAAE;wBACb,MAAM,CAAC,GAAG,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAA;wBACnC,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,KAAK,SAAS,CAAC,KAAK,CAAC,EAAE;4BAC/D,SAAQ;yBACT;qBACF;oBAED,IAAI,QAAQ,IAAI,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,QAAQ,EAAE;wBAC/C,SAAQ;qBACT;oBAED,QAAQ,CAAC,IAAI,CAAC,IAAI,gCAAsB,CAAC,MAAM,EAAE,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;iBAC7D;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;YACrB,CAAC,CAAC,CAAA;QACJ,CAAC,EAAE,MAAM,CAAC,CAAA;IACZ,CAAC;IAED,KAAK,CAAC,iCAAiC,CACrC,OAAiB,EACjB,IAAkB;QAElB,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,uDAAuD;QACvD,IAAI,GAAG,CAAC,KAAK,EAAE;YACb,MAAM,KAAK,GAAG,MAAM,IAAA,sBAAe,EAAC,OAAO,EAAE,GAAG,CAAC,CAAA;YACjD,MAAM,cAAc,GAAG,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAA;YACrD,OAAO,EAAE,KAAK,EAAE,cAAc,EAAE,CAAA;SACjC;aAAM;YACL,OAAO,KAAK,CAAC,iCAAiC,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;SAC9D;IACH,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;IAExC,2DAA2D;IAC3D,WAAW,CAAC,KAAa;;QACvB,OAAO,MAAA,IAAI,CAAC,SAAS,0CAAE,QAAQ,CAAC,KAAK,CAAC,CAAA;IACxC,CAAC;CACF;AAtOD,6BAsOC"}

package/dist/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;

package/dist/BamAdapter/configSchema.d.ts

@@ -1,2 +1,51 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    bamLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot index.indexType
+         */
+        indexType: {
+            model: import("mobx-state-tree").ISimpleType<string>;
+            type: string;
+            defaultValue: string;
+        };
+        /**
+         * #slot index.location
+         */
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     */
+    fetchSizeLimit: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+        type: string;
+        description: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/CramAdapter/CramAdapter.d.ts

@@ -45,7 +45,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
     cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
+    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<{
         bytes: number;
         fetchSizeLimit: any;
     }>;

package/dist/CramAdapter/CramAdapter.js

@@ -92,33 +92,33 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async setupPre(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const conf = await this.configure();
-        statusCallback('Downloading index');
-        const { cram } = conf;
-        const samHeader = await cram.cram.getSamHeader();
-        // use the @SQ lines in the header to figure out the
-        // mapping between ref ID numbers and names
-        const idToName = [];
-        const nameToId = {};
-        samHeader
-            .filter(l => l.tag === 'SQ')
-            .forEach((sqLine, refId) => {
-            sqLine.data.forEach(item => {
-                if (item.tag === 'SN') {
-                    // this is the ref name
-                    const refName = item.value;
-                    nameToId[refName] = refId;
-                    idToName[refId] = refName;
-                }
+        return (0, util_1.updateStatus)('Downloading index', statusCallback, async () => {
+            const conf = await this.configure();
+            const { cram } = conf;
+            const samHeader = await cram.cram.getSamHeader();
+            // use the @SQ lines in the header to figure out the
+            // mapping between ref ID numbers and names
+            const idToName = [];
+            const nameToId = {};
+            samHeader
+                .filter(l => l.tag === 'SQ')
+                .forEach((sqLine, refId) => {
+                sqLine.data.forEach(item => {
+                    if (item.tag === 'SN') {
+                        // this is the ref name
+                        const refName = item.value;
+                        nameToId[refName] = refId;
+                        idToName[refId] = refName;
+                    }
+                });
             });
+            const readGroups = samHeader
+                .filter(l => l.tag === 'RG')
+                .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
+            const data = { idToName, nameToId, readGroups };
+            this.samHeader = data;
+            return { samHeader: data, ...conf };
         });
-        const readGroups = samHeader
-            .filter(l => l.tag === 'RG')
-            .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
-        const data = { idToName, nameToId, readGroups };
-        statusCallback('');
-        this.samHeader = data;
-        return { samHeader: data, ...conf };
     }
     async setup(opts) {
         if (!this.setupP) {
@@ -170,29 +170,31 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             if (originalRefName) {
                 this.seqIdToOriginalRefName[refId] = originalRefName;
             }
-            statusCallback('Downloading alignments');
-            const records = await cram.getRecordsForRange(refId, start, end);
+            const records = await (0, util_1.updateStatus)('Downloading alignments', statusCallback, () => cram.getRecordsForRange(refId, start, end));
             (0, util_1.checkAbortSignal)(signal);
-            const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
-            let filtered = records.filter(record => {
-                const flags = record.flags;
-                return (flags & flagInclude) === flagInclude && !(flags & flagExclude);
-            });
-            if (tagFilter) {
-                filtered = filtered.filter(record => {
-                    // @ts-expect-error
-                    const val = record[tagFilter.tag];
-                    return val === '*' ? val !== undefined : val === tagFilter.value;
-                });
-            }
-            if (readName) {
-                filtered = filtered.filter(record => record.readName === readName);
-            }
-            filtered.forEach(record => {
-                observer.next(this.cramRecordToFeature(record));
+            await (0, util_1.updateStatus)('Processing alignments', statusCallback, () => {
+                var _a;
+                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
+                for (const record of records) {
+                    const flags = record.flags;
+                    if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
+                        continue;
+                    }
+                    if (tagFilter) {
+                        const v = tagFilter.tag === 'RG'
+                            ? (_a = this.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
+                            : record.tags[tagFilter.tag];
+                        if (!(v === '*' ? v !== undefined : `${v}` === tagFilter.value)) {
+                            continue;
+                        }
+                    }
+                    if (readName && record.readName !== readName) {
+                        continue;
+                    }
+                    observer.next(this.cramRecordToFeature(record));
+                }
+                observer.complete();
             });
-            statusCallback('');
-            observer.complete();
         }, signal);
     }
     freeResources( /* { region } */) { }
@@ -200,7 +202,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return new CramSlightlyLazyFeature_1.default(record, this);
     }
     // we return the configured fetchSizeLimit, and the bytes for the region
-    async estimateRegionsStats(regions, opts) {
+    async getMultiRegionFeatureDensityStats(regions, opts) {
         const bytes = await this.bytesForRegions(regions, opts);
         const fetchSizeLimit = this.getConf('fetchSizeLimit');
         return {

package/dist/CramAdapter/CramAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"CramAdapter.js","sourceRoot":"","sources":["../../src/CramAdapter/CramAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qCAAmE;AACnE,yEAIgD;AAChD,6CAAsE;AACtE,8CAAoD;AACpD,kDAA0D;AAC1D,8CAAwC;AACxC,+BAAqC;AACrC,wFAA+D;AAe/D,MAAqB,WAAY,SAAQ,oCAAsB;IAA/D;;QACE,cAAS,GAAW,EAAE,CAAA;QAgBtB,gFAAgF;QACxE,2BAAsB,GAAa,EAAE,CAAA;IAwQ/C,CAAC;IAtQQ,KAAK,CAAC,YAAY;QACvB,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,MAAM,IAAI,GAAG,IAAI,sBAAe,CAAC;YAC/B,cAAc,EAAE,IAAA,iBAAY,EAAC,YAAY,EAAE,EAAE,CAAC;YAC9C,KAAK,EAAE,IAAI,gBAAS,CAAC,EAAE,UAAU,EAAE,IAAA,iBAAY,EAAC,YAAY,EAAE,EAAE,CAAC,EAAE,CAAC;YACpE,QAAQ,EAAE,CAAC,GAAG,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,IAAI,CAAC;YAC7C,gBAAgB,EAAE,KAAK;YACvB,cAAc,EAAE,SAAW,EAAE,kDAAkD;SAChF,CAAC,CAAA;QAEF,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QAC/C,MAAM,UAAU,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QAEpD,OAAO;YACL,IAAI;YACJ,eAAe,EAAE,UAAU,CAAC,WAAkC;SAC/D,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACvC,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;IAClC,CAAC;IAEO,KAAK,CAAC,QAAQ,CACpB,KAAa,EACb,KAAa,EACb,GAAW;QAEX,KAAK,IAAI,CAAC,CAAA,CAAC,2CAA2C;QAEtD,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,MAAM,OAAO,GAAG,IAAI,CAAC,mBAAmB,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QAC1E,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;SAC3B;QAED,MAAM,SAAS,GAAG,MAAM,IAAA,qBAAc,EACpC,eAAe;aACZ,WAAW,CAAC;YACX,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC;aACD,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACnB,CAAA;QAED,MAAM,QAAQ,GAAG,SAAS;aACvB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;aAC/C,GAAG,CAAC,KAAK,CAAC,EAAE;YACX,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;YACjD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;YACjE,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;YACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;YAC1D,OAAO,QAAQ,CAAC,KAAK,CAAC,SAAS,EAAE,SAAS,GAAG,UAAU,CAAC,CAAA;QAC1D,CAAC,CAAC;aACD,IAAI,CAAC,EAAE,CAAC,CAAA;QAEX,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;YACnC,MAAM,IAAI,KAAK,CACb,mCAAmC,OAAO,IAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,IAAI,GAAG,CAAC,cAAc,EAAE,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;SACF;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACnC,cAAc,CAAC,mBAAmB,CAAC,CAAA;QACnC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;QACrB,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,CAAA;QAEhD,oDAAoD;QACpD,2CAA2C;QAC3C,MAAM,QAAQ,GAAa,EAAE,CAAA;QAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,SAAS;aACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;aAC3B,OAAO,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;YACzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;gBACzB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oBACrB,uBAAuB;oBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;oBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;oBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;iBAC1B;YACH,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;QAEJ,MAAM,UAAU,GAAG,SAAS;aACzB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;aAC3B,GAAG,CAAC,MAAM,CAAC,EAAE,WAAC,OAAA,MAAA,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,KAAK,IAAI,CAAC,0CAAE,KAAK,CAAA,EAAA,CAAC,CAAA;QAEpE,MAAM,IAAI,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAA;QAC/C,cAAc,CAAC,EAAE,CAAC,CAAA;QAClB,IAAI,CAAC,SAAS,GAAG,IAAI,CAAA;QACrB,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,GAAG,IAAI,EAAE,CAAA;IACrC,CAAC;IAEO,KAAK,CAAC,KAAK,CAAC,IAAkB;QACpC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,SAAS,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC5C,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,OAAO,SAAS,CAAC,QAAQ,CAAA;IAC3B,CAAC;IAED,mEAAmE;IACnE,gEAAgE;IAChE,WAAW,CAAC,OAAe;QACzB,IAAI,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE;YAC3B,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAA;SACxC;QACD,IAAI,IAAI,CAAC,cAAc,EAAE;YACvB,OAAO,IAAI,CAAC,cAAc,CAAC,OAAO,CAAC,OAAO,CAAC,CAAA;SAC5C;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,mEAAmE;IACnE,gEAAgE;IAChE,WAAW,CAAC,KAAa;;QACvB,OAAO,CAAA,MAAA,IAAI,CAAC,SAAS,CAAC,QAAQ,0CAAG,KAAK,CAAC,MAAI,MAAA,IAAI,CAAC,cAAc,0CAAG,KAAK,CAAC,CAAA,CAAA;IACzE,CAAC;IAED,mBAAmB,CAAC,KAAa;QAC/B,OAAO,IAAI,CAAC,sBAAsB,CAAC,KAAK,CAAC,CAAA;IAC3C,CAAC;IAED,WAAW,CACT,MAA6C,EAC7C,IAEC;QAED,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAClE,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,eAAe,EAAE,GAAG,MAAM,CAAA;QAEvD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAEvC,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YACvC,IAAI,KAAK,KAAK,SAAS,EAAE;gBACvB,OAAO,CAAC,IAAI,CAAC,iBAAiB,EAAE,OAAO,CAAC,CAAA;gBACxC,QAAQ,CAAC,QAAQ,EAAE,CAAA;gBACnB,OAAM;aACP;YAED,IAAI,eAAe,EAAE;gBACnB,IAAI,CAAC,sBAAsB,CAAC,KAAK,CAAC,GAAG,eAAe,CAAA;aACrD;YACD,cAAc,CAAC,wBAAwB,CAAC,CAAA;YACxC,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;YAChE,IAAA,uBAAgB,EAAC,MAAM,CAAC,CAAA;YACxB,MAAM,EACJ,WAAW,GAAG,CAAC,EACf,WAAW,GAAG,CAAC,EACf,SAAS,EACT,QAAQ,GACT,GAAG,QAAQ,IAAI,EAAE,CAAA;YAElB,IAAI,QAAQ,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE;gBACrC,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAA;gBAC1B,OAAO,CAAC,KAAK,GAAG,WAAW,CAAC,KAAK,WAAW,IAAI,CAAC,CAAC,KAAK,GAAG,WAAW,CAAC,CAAA;YACxE,CAAC,CAAC,CAAA;YAEF,IAAI,SAAS,EAAE;gBACb,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE;oBAClC,mBAAmB;oBACnB,MAAM,GAAG,GAAG,MAAM,CAAC,SAAS,CAAC,GAAG,CAAC,CAAA;oBACjC,OAAO,GAAG,KAAK,GAAG,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,CAAC,KAAK,CAAA;gBAClE,CAAC,CAAC,CAAA;aACH;YAED,IAAI,QAAQ,EAAE;gBACZ,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,KAAK,QAAQ,CAAC,CAAA;aACnE;YAED,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;gBACxB,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,mBAAmB,CAAC,MAAM,CAAC,CAAC,CAAA;YACjD,CAAC,CAAC,CAAA;YACF,cAAc,CAAC,EAAE,CAAC,CAAA;YAClB,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,MAAM,CAAC,CAAA;IACZ,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;IAExC,mBAAmB,CAAC,MAAkB;QACpC,OAAO,IAAI,iCAAuB,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAClD,CAAC;IAED,wEAAwE;IACxE,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QACvD,MAAM,cAAc,GAAG,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAA;QACrD,OAAO;YACL,KAAK;YACL,cAAc;SACf,CAAA;IACH,CAAC;IAED;;;;OAIG;IACK,KAAK,CAAC,eAAe,CAAC,OAAiB,EAAE,KAAmB;QAClE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACvC,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;YACnB,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;YACtC,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YACvC,OAAO,KAAK,KAAK,SAAS;gBACxB,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC;gBAClD,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,CAAC,EAAE,CAAC,CAAA;QACzB,CAAC,CAAC,CACH,CAAA;QAED,OAAO,YAAY,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;IAClE,CAAC;CACF;AA1RD,8BA0RC"}
+{"version":3,"file":"CramAdapter.js","sourceRoot":"","sources":["../../src/CramAdapter/CramAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qCAAmE;AACnE,yEAIgD;AAChD,6CAK2B;AAC3B,8CAAoD;AACpD,kDAA0D;AAC1D,8CAAwC;AACxC,+BAAqC;AACrC,wFAA+D;AAe/D,MAAqB,WAAY,SAAQ,oCAAsB;IAA/D;;QACE,cAAS,GAAW,EAAE,CAAA;QAgBtB,gFAAgF;QACxE,2BAAsB,GAAa,EAAE,CAAA;IAiR/C,CAAC;IA/QQ,KAAK,CAAC,YAAY;QACvB,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,MAAM,IAAI,GAAG,IAAI,sBAAe,CAAC;YAC/B,cAAc,EAAE,IAAA,iBAAY,EAAC,YAAY,EAAE,EAAE,CAAC;YAC9C,KAAK,EAAE,IAAI,gBAAS,CAAC,EAAE,UAAU,EAAE,IAAA,iBAAY,EAAC,YAAY,EAAE,EAAE,CAAC,EAAE,CAAC;YACpE,QAAQ,EAAE,CAAC,GAAG,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,IAAI,CAAC;YAC7C,gBAAgB,EAAE,KAAK;YACvB,cAAc,EAAE,SAAW,EAAE,kDAAkD;SAChF,CAAC,CAAA;QAEF,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QAC/C,MAAM,UAAU,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QAEpD,OAAO;YACL,IAAI;YACJ,eAAe,EAAE,UAAU,CAAC,WAAkC;SAC/D,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACvC,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;IAClC,CAAC;IAEO,KAAK,CAAC,QAAQ,CACpB,KAAa,EACb,KAAa,EACb,GAAW;QAEX,KAAK,IAAI,CAAC,CAAA,CAAC,2CAA2C;QAEtD,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,MAAM,OAAO,GAAG,IAAI,CAAC,mBAAmB,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QAC1E,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;SAC3B;QAED,MAAM,SAAS,GAAG,MAAM,IAAA,qBAAc,EACpC,eAAe;aACZ,WAAW,CAAC;YACX,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC;aACD,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACnB,CAAA;QAED,MAAM,QAAQ,GAAG,SAAS;aACvB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;aAC/C,GAAG,CAAC,KAAK,CAAC,EAAE;YACX,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;YACjD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;YACjE,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;YACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;YAC1D,OAAO,QAAQ,CAAC,KAAK,CAAC,SAAS,EAAE,SAAS,GAAG,UAAU,CAAC,CAAA;QAC1D,CAAC,CAAC;aACD,IAAI,CAAC,EAAE,CAAC,CAAA;QAEX,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;YACnC,MAAM,IAAI,KAAK,CACb,mCAAmC,OAAO,IAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,IAAI,GAAG,CAAC,cAAc,EAAE,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;SACF;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,IAAA,mBAAY,EAAC,mBAAmB,EAAE,cAAc,EAAE,KAAK,IAAI,EAAE;YAClE,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YACnC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;YACrB,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,CAAA;YAEhD,oDAAoD;YACpD,2CAA2C;YAC3C,MAAM,QAAQ,GAAa,EAAE,CAAA;YAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;YAC3C,SAAS;iBACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;iBAC3B,OAAO,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;gBACzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACzB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;wBACrB,uBAAuB;wBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;wBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;wBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;qBAC1B;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YAEJ,MAAM,UAAU,GAAG,SAAS;iBACzB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;iBAC3B,GAAG,CAAC,MAAM,CAAC,EAAE,WAAC,OAAA,MAAA,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,KAAK,IAAI,CAAC,0CAAE,KAAK,CAAA,EAAA,CAAC,CAAA;YAEpE,MAAM,IAAI,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAA;YAC/C,IAAI,CAAC,SAAS,GAAG,IAAI,CAAA;YACrB,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,GAAG,IAAI,EAAE,CAAA;QACrC,CAAC,CAAC,CAAA;IACJ,CAAC;IAEO,KAAK,CAAC,KAAK,CAAC,IAAkB;QACpC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,SAAS,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC5C,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,OAAO,SAAS,CAAC,QAAQ,CAAA;IAC3B,CAAC;IAED,mEAAmE;IACnE,gEAAgE;IAChE,WAAW,CAAC,OAAe;QACzB,IAAI,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE;YAC3B,OAAO,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAA;SACxC;QACD,IAAI,IAAI,CAAC,cAAc,EAAE;YACvB,OAAO,IAAI,CAAC,cAAc,CAAC,OAAO,CAAC,OAAO,CAAC,CAAA;SAC5C;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,mEAAmE;IACnE,gEAAgE;IAChE,WAAW,CAAC,KAAa;;QACvB,OAAO,CAAA,MAAA,IAAI,CAAC,SAAS,CAAC,QAAQ,0CAAG,KAAK,CAAC,MAAI,MAAA,IAAI,CAAC,cAAc,0CAAG,KAAK,CAAC,CAAA,CAAA;IACzE,CAAC;IAED,mBAAmB,CAAC,KAAa;QAC/B,OAAO,IAAI,CAAC,sBAAsB,CAAC,KAAK,CAAC,CAAA;IAC3C,CAAC;IAED,WAAW,CACT,MAA6C,EAC7C,IAEC;QAED,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAClE,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,eAAe,EAAE,GAAG,MAAM,CAAA;QAEvD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAEvC,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YACvC,IAAI,KAAK,KAAK,SAAS,EAAE;gBACvB,OAAO,CAAC,IAAI,CAAC,iBAAiB,EAAE,OAAO,CAAC,CAAA;gBACxC,QAAQ,CAAC,QAAQ,EAAE,CAAA;gBACnB,OAAM;aACP;YAED,IAAI,eAAe,EAAE;gBACnB,IAAI,CAAC,sBAAsB,CAAC,KAAK,CAAC,GAAG,eAAe,CAAA;aACrD;YACD,MAAM,OAAO,GAAG,MAAM,IAAA,mBAAY,EAChC,wBAAwB,EACxB,cAAc,EACd,GAAG,EAAE,CAAC,IAAI,CAAC,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CACjD,CAAA;YACD,IAAA,uBAAgB,EAAC,MAAM,CAAC,CAAA;YACxB,MAAM,IAAA,mBAAY,EAAC,uBAAuB,EAAE,cAAc,EAAE,GAAG,EAAE;;gBAC/D,MAAM,EACJ,WAAW,GAAG,CAAC,EACf,WAAW,GAAG,CAAC,EACf,SAAS,EACT,QAAQ,GACT,GAAG,QAAQ,IAAI,EAAE,CAAA;gBAElB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;oBAC5B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAA;oBAC1B,IAAI,CAAC,KAAK,GAAG,WAAW,CAAC,KAAK,WAAW,IAAI,CAAC,CAAC,KAAK,GAAG,WAAW,CAAC,EAAE;wBACnE,SAAQ;qBACT;oBAED,IAAI,SAAS,EAAE;wBACb,MAAM,CAAC,GACL,SAAS,CAAC,GAAG,KAAK,IAAI;4BACpB,CAAC,CAAC,MAAA,IAAI,CAAC,SAAS,CAAC,UAAU,0CAAG,MAAM,CAAC,WAAW,CAAC;4BACjD,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,CAAA;wBAChC,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,KAAK,SAAS,CAAC,KAAK,CAAC,EAAE;4BAC/D,SAAQ;yBACT;qBACF;oBAED,IAAI,QAAQ,IAAI,MAAM,CAAC,QAAQ,KAAK,QAAQ,EAAE;wBAC5C,SAAQ;qBACT;oBACD,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,mBAAmB,CAAC,MAAM,CAAC,CAAC,CAAA;iBAChD;gBAED,QAAQ,CAAC,QAAQ,EAAE,CAAA;YACrB,CAAC,CAAC,CAAA;QACJ,CAAC,EAAE,MAAM,CAAC,CAAA;IACZ,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;IAExC,mBAAmB,CAAC,MAAkB;QACpC,OAAO,IAAI,iCAAuB,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAClD,CAAC;IAED,wEAAwE;IACxE,KAAK,CAAC,iCAAiC,CACrC,OAAiB,EACjB,IAAkB;QAElB,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QACvD,MAAM,cAAc,GAAG,IAAI,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAA;QACrD,OAAO;YACL,KAAK;YACL,cAAc;SACf,CAAA;IACH,CAAC;IAED;;;;OAIG;IACK,KAAK,CAAC,eAAe,CAAC,OAAiB,EAAE,KAAmB;QAClE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACvC,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;YACnB,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;YACtC,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YACvC,OAAO,KAAK,KAAK,SAAS;gBACxB,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC;gBAClD,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,CAAC,EAAE,CAAC,CAAA;QACzB,CAAC,CAAC,CACH,CAAA;QAED,OAAO,YAAY,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;IAClE,CAAC;CACF;AAnSD,8BAmSC"}

package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -34,8 +34,8 @@ class CramSlightlyLazyFeature {
         return this.record.isReverseComplemented() ? -1 : 1;
     }
     _read_group_id() {
-        const rg = this._store.samHeader.readGroups;
-        return rg ? rg[this.record.readGroupId] : undefined;
+        var _a;
+        return (_a = this._store.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[this.record.readGroupId];
     }
     _get_qual() {
         return (this.record.qualityScores || []).join(' ');
@@ -114,9 +114,7 @@ class CramSlightlyLazyFeature {
     _get_clipPos() {
         const mismatches = this.get('mismatches');
         if (mismatches.length) {
-            const record = this.get('strand') === -1
-                ? mismatches[mismatches.length - 1]
-                : mismatches[0];
+            const record = this.get('strand') === -1 ? mismatches.at(-1) : mismatches[0];
             const { type, cliplen } = record;
             if (type === 'softclip' || type === 'hardclip') {
                 return cliplen;