@gmod/cram 3.0.4 → 3.0.5

package/dist/craiIndex.d.ts

@@ -6,9 +6,9 @@ export interface Slice {
     sliceStart: number;
     sliceBytes: number;
 }
-type ParsedIndex = Record<string, Slice[]>;
+type ParsedIndex = Record<string, Slice[] | undefined>;
 export default class CraiIndex {
-    private _parseCache;
+    private parseIndexP?;
     private filehandle;
     /**
      *
@@ -19,9 +19,7 @@ export default class CraiIndex {
      */
     constructor(args: CramFileSource);
     parseIndex(): Promise<ParsedIndex>;
-    getIndex(opts?: {
-        signal?: AbortSignal;
-    }): Promise<ParsedIndex>;
+    getIndex(): Promise<ParsedIndex>;
     /**
      * @param {number} seqId
      * @returns {Promise} true if the index contains entries for

package/dist/craiIndex.js

@@ -8,29 +8,31 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
-const quick_lru_1 = __importDefault(require("quick-lru"));
 const unzip_1 = require("./unzip");
 const io_1 = require("./io");
 const errors_1 = require("./errors");
 const BAI_MAGIC = 21578050; // BAI\1
 function addRecordToIndex(index, record) {
     const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record;
-    if (!index[seqId]) {
-        index[seqId] = [];
+    const s = seqId;
+    if (!index[s]) {
+        index[s] = [];
     }
-    index[seqId].push({
-        start,
-        span,
-        containerStart,
-        sliceStart,
-        sliceBytes,
+    index[s].push({
+        start: start,
+        span: span,
+        containerStart: containerStart,
+        sliceStart: sliceStart,
+        sliceBytes: sliceBytes,
     });
 }
+function maybeUnzip(data) {
+    if (data[0] === 31 && data[1] === 139) {
+        return (0, unzip_1.unzip)(data);
+    }
+    return data;
+}
 class CraiIndex {
     /**
      *
@@ -41,22 +43,11 @@ class CraiIndex {
      */
     constructor(args) {
         this.filehandle = (0, io_1.open)(args.url, args.path, args.filehandle);
-        this._parseCache = new abortable_promise_cache_1.default({
-            cache: new quick_lru_1.default({ maxSize: 1 }),
-            fill: (_data, _signal) => this.parseIndex(),
-        });
     }
     parseIndex() {
-        const index = {};
-        return this.filehandle
-            .readFile()
-            .then(data => {
-            if (data[0] === 31 && data[1] === 139) {
-                return (0, unzip_1.unzip)(data);
-            }
-            return data;
-        })
-            .then(uncompressedBuffer => {
+        return __awaiter(this, void 0, void 0, function* () {
+            const index = {};
+            const uncompressedBuffer = maybeUnzip(yield this.filehandle.readFile());
             if (uncompressedBuffer.length > 4 &&
                 uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC) {
                 throw new errors_1.CramMalformedError('invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support');
@@ -97,13 +88,20 @@ class CraiIndex {
             }
             // sort each of them by start
             Object.entries(index).forEach(([seqId, ent]) => {
-                index[seqId] = ent.sort((a, b) => a.start - b.start || a.span - b.span);
+                const e2 = ent;
+                index[seqId] = e2.sort((a, b) => a.start - b.start || a.span - b.span);
             });
             return index;
         });
     }
-    getIndex(opts = {}) {
-        return this._parseCache.get('index', null, opts.signal);
+    getIndex() {
+        if (!this.parseIndexP) {
+            this.parseIndexP = this.parseIndex().catch((e) => {
+                this.parseIndexP = undefined;
+                throw e;
+            });
+        }
+        return this.parseIndexP;
     }
     /**
      * @param {number} seqId

package/dist/craiIndex.js.map

@@ -1 +1 @@
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