@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/dist/CramAdapter/CramAdapter.js

@@ -17,7 +17,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         // maps a seqId to original refname, passed specially to render args, to a seqid
         this.seqIdToOriginalRefName = [];
     }
-    async configure() {
+    async configurePre() {
         const cramLocation = this.getConf('cramLocation');
         const craiLocation = this.getConf('craiLocation');
         if (!cramLocation) {
@@ -26,38 +26,43 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         if (!craiLocation) {
             throw new Error('missing craiLocation argument');
         }
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const pm = this.pluginManager;
         const cram = new cram_1.IndexedCramFile({
-            cramFilehandle: (0, io_1.openLocation)(cramLocation, this.pluginManager),
-            index: new cram_1.CraiIndex({
-                filehandle: (0, io_1.openLocation)(craiLocation, this.pluginManager),
-            }),
-            seqFetch: this.seqFetch.bind(this),
+            cramFilehandle: (0, io_1.openLocation)(cramLocation, pm),
+            index: new cram_1.CraiIndex({ filehandle: (0, io_1.openLocation)(craiLocation, pm) }),
+            seqFetch: (...args) => this.seqFetch(...args),
             checkSequenceMD5: false,
             fetchSizeLimit: 200000000, // just make this a large size to avoid hitting it
         });
-        // instantiate the sequence adapter
-        const sequenceAdapterType = this.getConf(['sequenceAdapter', 'type']);
         if (!this.getSubAdapter) {
             throw new Error('Error getting subadapter');
         }
         const seqConf = this.getConf('sequenceAdapter');
-        const { dataAdapter: sequenceAdapter } = await this.getSubAdapter(seqConf);
-        if (!(sequenceAdapter instanceof BaseAdapter_1.BaseFeatureDataAdapter)) {
-            throw new Error(`CRAM feature adapters cannot use sequence adapters of type '${sequenceAdapterType}'`);
+        const subadapter = await this.getSubAdapter(seqConf);
+        return {
+            cram,
+            sequenceAdapter: subadapter.dataAdapter,
+        };
+    }
+    async configure() {
+        if (!this.configureP) {
+            this.configureP = this.configurePre().catch(e => {
+                this.configureP = undefined;
+                throw e;
+            });
         }
-        return { cram, sequenceAdapter };
+        return this.configureP;
     }
     async getHeader(opts) {
         const { cram } = await this.configure();
-        return cram.cram.getHeaderText(opts);
+        return cram.cram.getHeaderText();
     }
     async seqFetch(seqId, start, end) {
         start -= 1; // convert from 1-based closed to interbase
         const { sequenceAdapter } = await this.configure();
         const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
         if (!refName) {
-            return undefined;
+            throw new Error('unknown');
         }
         const seqChunks = await sequenceAdapter
             .getFeatures({
@@ -87,10 +92,10 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async setupPre(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const configured = await this.configure();
+        const conf = await this.configure();
         statusCallback('Downloading index');
-        const { cram } = configured;
-        const samHeader = await cram.cram.getSamHeader(opts === null || opts === void 0 ? void 0 : opts.signal);
+        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 = [];
@@ -113,7 +118,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const data = { idToName, nameToId, readGroups };
         statusCallback('');
         this.samHeader = data;
-        return { samHeader: data, ...configured };
+        return { samHeader: data, ...conf };
     }
     async setup(opts) {
         if (!this.setupP) {
@@ -145,13 +150,8 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     // use info from the SAM header if possible, but fall back to using
     // the ref seq order from when the browser's refseqs were loaded
     refIdToName(refId) {
-        if (this.samHeader.idToName) {
-            return this.samHeader.idToName[refId];
-        }
-        if (this.seqIdToRefName) {
-            return this.seqIdToRefName[refId];
-        }
-        return undefined;
+        var _a, _b;
+        return ((_a = this.samHeader.idToName) === null || _a === void 0 ? void 0 : _a[refId]) || ((_b = this.seqIdToRefName) === null || _b === void 0 ? void 0 : _b[refId]);
     }
     refIdToOriginalName(refId) {
         return this.seqIdToOriginalRefName[refId];
@@ -160,44 +160,37 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const { signal, filterBy, statusCallback = () => { } } = opts || {};
         const { refName, start, end, originalRefName } = region;
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { cram, sequenceAdapter } = await this.setup(opts);
-            statusCallback('Downloading alignments');
-            if (!this.seqIdToRefName) {
-                this.seqIdToRefName = await sequenceAdapter.getRefNames(opts);
-            }
+            const { cram } = await this.setup(opts);
             const refId = this.refNameToId(refName);
-            if (refId !== undefined) {
-                if (originalRefName) {
-                    this.seqIdToOriginalRefName[refId] = originalRefName;
-                }
-                const records = await cram.getRecordsForRange(refId, start, end, opts);
-                (0, util_1.checkAbortSignal)(signal);
-                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
-                // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                let filtered = records.filter((record) => {
-                    const flags = record.flags;
-                    return (flags & flagInclude) === flagInclude && !(flags & flagExclude);
-                });
-                if (tagFilter) {
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                    filtered = filtered.filter((record) => {
-                        const val = record[tagFilter.tag];
-                        return val === '*' ? val !== undefined : val === tagFilter.value;
-                    });
-                }
-                if (readName) {
-                    filtered = filtered.filter(
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                    (record) => record.readName === readName);
-                }
-                // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                filtered.forEach((record) => {
-                    observer.next(this.cramRecordToFeature(record));
+            if (refId === undefined) {
+                console.warn('Unknown refName', refName);
+                observer.complete();
+                return;
+            }
+            if (originalRefName) {
+                this.seqIdToOriginalRefName[refId] = originalRefName;
+            }
+            statusCallback('Downloading alignments');
+            const records = await 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-ignore
+                    const val = record[tagFilter.tag];
+                    return val === '*' ? val !== undefined : val === tagFilter.value;
                 });
             }
-            else {
-                console.warn('Unknown refName', refName);
+            if (readName) {
+                filtered = filtered.filter(record => record.readName === readName);
             }
+            filtered.forEach(record => {
+                observer.next(this.cramRecordToFeature(record));
+            });
             statusCallback('');
             observer.complete();
         }, signal);
@@ -225,7 +218,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const blockResults = await Promise.all(regions.map(region => {
             const { refName, start, end } = region;
             const chrId = this.refNameToId(refName);
-            return cram.index.getEntriesForRange(chrId, start, end);
+            return chrId !== undefined
+                ? cram.index.getEntriesForRange(chrId, start, end)
+                : [{ sliceBytes: 0 }];
         }));
         return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0);
     }

package/dist/CramAdapter/CramAdapter.js.map

@@ -1 +1 @@
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+{"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,wFAA+D;AAe/D,MAAqB,WAAY,SAAQ,oCAAsB;IAA/D;;QACE,cAAS,GAAW,EAAE,CAAA;QAgBtB,gFAAgF;QACxE,2BAAsB,GAAa,EAAE,CAAA;IAuQ/C,CAAC;IArQQ,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,eAAe;aACpC,WAAW,CAAC;YACX,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC;aACD,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC;aACf,SAAS,EAAE,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,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;QAC/C,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,CAA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package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,40 +1,32 @@
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import { CramRecord } from '@gmod/cram';
 import CramAdapter from './CramAdapter';
-export interface Mismatch {
-    qual?: number;
-    start: number;
-    length: number;
-    type: string;
-    base: string;
-    altbase?: string;
-    seq?: string;
-    cliplen?: number;
-}
+import { Mismatch } from './util';
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;
-    constructor(record: any, _store: CramAdapter);
-    _get_name(): any;
+    constructor(record: CramRecord, _store: CramAdapter);
+    _get_name(): string | undefined;
     _get_start(): number;
     _get_end(): number;
-    _get_cram_read_features(): any;
+    _get_cram_read_features(): import("@gmod/cram/dist/cramFile/record").ReadFeature[] | undefined;
     _get_type(): string;
-    _get_score(): any;
-    _get_flags(): any;
+    _get_score(): number | undefined;
+    _get_flags(): number;
     _get_strand(): 1 | -1;
-    _read_group_id(): number | undefined;
-    _get_qual(): any;
-    qualRaw(): any;
+    _read_group_id(): string | undefined;
+    _get_qual(): string;
+    qualRaw(): number[] | null | undefined;
     _get_seq_id(): string | undefined;
     _get_refName(): string | undefined;
     _get_is_paired(): boolean;
-    _get_pair_orientation(): any;
-    _get_template_length(): any;
+    _get_pair_orientation(): string | null | undefined;
+    _get_template_length(): number | undefined;
     _get_next_seq_id(): string | undefined;
-    _get_next_pos(): any;
+    _get_next_pos(): number | undefined;
     _get_next_segment_position(): string | undefined;
-    _get_tags(): any;
-    _get_seq(): any;
+    _get_tags(): Record<string, string>;
+    _get_seq(): string | null | undefined;
     _get_CIGAR(): string;
     tags(): string[];
     id(): string;

package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -1,9 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+const util_1 = require("./util");
 class CramSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     constructor(record, _store) {
         this.record = record;
         this._store = _store;
@@ -15,7 +15,8 @@ class CramSlightlyLazyFeature {
         return this.record.alignmentStart - 1;
     }
     _get_end() {
-        return this.record.alignmentStart + this.record.lengthOnRef - 1;
+        var _a;
+        return this.record.alignmentStart + ((_a = this.record.lengthOnRef) !== null && _a !== void 0 ? _a : 1) - 1;
     }
     _get_cram_read_features() {
         return this.record.readFeatures;
@@ -81,115 +82,10 @@ class CramSlightlyLazyFeature {
     }
     // generate a CIGAR, based on code from jkbonfield
     _get_CIGAR() {
-        let seq = '';
-        let cigar = '';
-        let op = 'M';
-        let oplen = 0;
-        // not sure I should access these, but...
-        const ref = this.record._refRegion.seq;
-        const refStart = this.record._refRegion.start;
-        let last_pos = this.record.alignmentStart;
-        let sublen = 0;
-        if (typeof this.record.readFeatures !== 'undefined') {
-            // @ts-ignore
-            for (let i = 0; i < this.record.readFeatures.length; i++) {
-                const { code, refPos, sub, data } = this.record.readFeatures[i];
-                sublen = refPos - last_pos;
-                seq += ref.substring(last_pos - refStart, refPos - refStart);
-                last_pos = refPos;
-                if (oplen && op !== 'M') {
-                    cigar += oplen + op;
-                    oplen = 0;
-                }
-                if (sublen) {
-                    op = 'M';
-                    oplen += sublen;
-                }
-                if (code === 'b') {
-                    // An array of bases stored verbatim
-                    const ret = data.split(',');
-                    const added = String.fromCharCode(...ret);
-                    seq += added;
-                    last_pos += added.length;
-                    oplen += added.length;
-                }
-                else if (code === 'B') {
-                    // Single base (+ qual score)
-                    seq += sub;
-                    last_pos++;
-                    oplen++;
-                }
-                else if (code === 'X') {
-                    // Substitution
-                    seq += sub;
-                    last_pos++;
-                    oplen++;
-                }
-                else if (code === 'D' || code === 'N') {
-                    // Deletion or Ref Skip
-                    last_pos += data;
-                    if (oplen) {
-                        cigar += oplen + op;
-                    }
-                    cigar += data + code;
-                    oplen = 0;
-                }
-                else if (code === 'I' || code === 'S') {
-                    // Insertion or soft-clip
-                    seq += data;
-                    if (oplen) {
-                        cigar += oplen + op;
-                    }
-                    cigar += data.length + code;
-                    oplen = 0;
-                }
-                else if (code === 'i') {
-                    // Single base insertion
-                    seq += data;
-                    if (oplen) {
-                        cigar += oplen + op;
-                    }
-                    cigar += `${1}I`;
-                    oplen = 0;
-                }
-                else if (code === 'P') {
-                    // Padding
-                    if (oplen) {
-                        cigar += oplen + op;
-                    }
-                    cigar += `${data}P`;
-                }
-                else if (code === 'H') {
-                    // Hard clip
-                    if (oplen) {
-                        cigar += oplen + op;
-                    }
-                    cigar += `${data}H`;
-                    oplen = 0;
-                } // else q or Q
-            }
-        }
-        else {
-            sublen = this.record.readLength - seq.length;
-        }
-        if (seq.length !== this.record.readLength) {
-            sublen = this.record.readLength - seq.length;
-            seq += ref.substring(last_pos - refStart, last_pos - refStart + sublen);
-            if (oplen && op !== 'M') {
-                cigar += oplen + op;
-                oplen = 0;
-            }
-            op = 'M';
-            oplen += sublen;
-        }
-        if (oplen) {
-            cigar += oplen + op;
-        }
-        return cigar;
+        return (0, util_1.readFeaturesToCIGAR)(this.record.readFeatures, this.record.alignmentStart, this.record.readLength, this.record._refRegion);
     }
     tags() {
-        const properties = Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype);
-        return properties
+        return Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype)
             .filter(prop => prop.startsWith('_get_') &&
             prop !== '_get_mismatches' &&
             prop !== '_get_cram_read_features')
@@ -231,121 +127,18 @@ class CramSlightlyLazyFeature {
         return 0;
     }
     toJSON() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        const tags = {};
-        this.tags().forEach((t) => {
-            const val = this.get(t);
-            if (val !== undefined) {
-                tags[t] = val;
-            }
-        });
         return {
-            ...tags,
-            name: this.get('name'),
-            type: this.get('type'),
+            ...Object.fromEntries(this.tags()
+                .map(t => [t, this.get(t)])
+                .filter(elt => elt[1] !== undefined)),
             uniqueId: this.id(),
         };
     }
     _get_mismatches() {
-        const readFeatures = this.get('cram_read_features');
+        const readFeatures = this.record.readFeatures;
         const qual = this.qualRaw();
-        if (!readFeatures) {
-            return [];
-        }
         const start = this.get('start');
-        const mismatches = new Array(readFeatures.length);
-        let j = 0;
-        for (let i = 0; i < readFeatures.length; i++) {
-            const f = readFeatures[i];
-            const { code, pos, data, sub, ref } = f;
-            const refPos = f.refPos - 1 - start;
-            if (code === 'X') {
-                // substitution
-                mismatches[j++] = {
-                    start: refPos,
-                    length: 1,
-                    base: sub,
-                    qual: qual === null || qual === void 0 ? void 0 : qual[pos],
-                    altbase: ref,
-                    type: 'mismatch',
-                };
-            }
-            else if (code === 'I') {
-                // insertion
-                mismatches[j++] = {
-                    start: refPos,
-                    type: 'insertion',
-                    base: `${data.length}`,
-                    length: 0,
-                };
-            }
-            else if (code === 'N') {
-                // reference skip
-                mismatches[j++] = {
-                    type: 'skip',
-                    length: data,
-                    start: refPos,
-                    base: 'N',
-                };
-            }
-            else if (code === 'S') {
-                // soft clip
-                const len = data.length;
-                mismatches[j++] = {
-                    start: refPos,
-                    type: 'softclip',
-                    base: `S${len}`,
-                    cliplen: len,
-                    length: 1,
-                };
-            }
-            else if (code === 'P') {
-                // padding
-            }
-            else if (code === 'H') {
-                // hard clip
-                const len = data;
-                mismatches[j++] = {
-                    start: refPos,
-                    type: 'hardclip',
-                    base: `H${len}`,
-                    cliplen: len,
-                    length: 1,
-                };
-            }
-            else if (code === 'D') {
-                // deletion
-                mismatches[j++] = {
-                    type: 'deletion',
-                    length: data,
-                    start: refPos,
-                    base: '*',
-                };
-            }
-            else if (code === 'b') {
-                // stretch of bases
-            }
-            else if (code === 'q') {
-                // stretch of qual scores
-            }
-            else if (code === 'B') {
-                // a pair of [base, qual]
-            }
-            else if (code === 'i') {
-                // single-base insertion
-                // insertion
-                mismatches[j++] = {
-                    start: refPos,
-                    type: 'insertion',
-                    base: data,
-                    length: 1,
-                };
-            }
-            else if (code === 'Q') {
-                // single quality value
-            }
-        }
-        return mismatches.slice(0, j);
+        return (0, util_1.readFeaturesToMismatches)(readFeatures, start, qual);
     }
 }
 exports.default = CramSlightlyLazyFeature;

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+{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":";;AAOA,iCAAgF;AAEhF,MAAqB,uBAAuB;IAC1C,wEAAwE;IACxE,iFAAiF;IACjF,YAAoB,MAAkB,EAAU,MAAmB;QAA/C,WAAM,GAAN,MAAM,CAAY;QAAU,WAAM,GAAN,MAAM,CAAa;IAAG,CAAC;IAEvE,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,QAAQ;;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,WAAW,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,CAAC;IAED,uBAAuB;QACrB,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IACjC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,CAAA;IACnC,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,cAAc;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAA;QAC3C,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACrD,CAAC;IAED,SAAS;QACP,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACpD,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,aAAa,CAAA;IAClC,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACxD,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,WAAW,EAAE,CAAA;IAC3B,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAA;IAC3B,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,oBAAoB;QAClB,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,IAAI,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IAC/D,CAAC;IAED,gBAAgB;QACd,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,CAAA;IACvE,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,IACrD,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cACnB,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,SAAS;QACP,MAAM,EAAE,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAA;QAC5B,4DAA4D;QAC5D,OAAO,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;IAClD,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,kDAAkD;IAClD,UAAU;QACR,OAAO,IAAA,0BAAmB,EACxB,IAAI,CAAC,MAAM,CAAC,YAAY,EACxB,IAAI,CAAC,MAAM,CAAC,cAAc,EAC1B,IAAI,CAAC,MAAM,CAAC,UAAU,EACtB,IAAI,CAAC,MAAM,CAAC,UAAU,CACvB,CAAA;IACH,CAAC;IAED,IAAI;QACF,OAAO,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC,SAAS,CAAC;aACjE,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;YACxB,IAAI,KAAK,iBAAiB;YAC1B,IAAI,KAAK,yBAAyB,CACrC;aACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;IACpD,CAAC;IAED,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,GAAG,KAAU,CAAC;IAEd,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,YAAY;QACV,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;QACzC,IAAI,UAAU,CAAC,MAAM,EAAE;YACrB,MAAM,MAAM,GACV,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;gBACvB,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;gBACnC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YAChC,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,EAAE;gBAC9C,OAAO,OAAO,CAAA;aACf;SACF;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,EAAE,CAAA;QAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAC/B,OAAO,IAAA,+BAAwB,EAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF;AApLD,0CAoLC"}

package/dist/CramAdapter/CramTestAdapters.d.ts

@@ -7,7 +7,7 @@ export declare function parseSmallFasta(text: string): {
     description: string;
     sequence: string;
 }[];
-declare type FileHandle = GenericFilehandle;
+type FileHandle = GenericFilehandle;
 export declare class FetchableSmallFasta {
     data: Promise<ReturnType<typeof parseSmallFasta>>;
     constructor(filehandle: FileHandle);

package/dist/CramAdapter/CramTestAdapters.js

@@ -36,7 +36,7 @@ class FetchableSmallFasta {
         if (!entry) {
             throw new Error(`no sequence with id ${id} exists`);
         }
-        return entry.sequence.substr(start - 1, length);
+        return entry.sequence.slice(start, start + length);
     }
     async getSequenceList() {
         const data = await this.data;

package/dist/CramAdapter/CramTestAdapters.js.map

@@ -1 +1 @@
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package/dist/CramAdapter/configSchema.d.ts

@@ -1,3 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;