@gmod/cram 3.0.3 → 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 @@
-{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,4FAAiE;AACjE,0DAAgC;AAChC,mCAA+B;AAC/B,6BAA2B;AAC3B,qCAA6C;AAI7C,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAYnC,SAAS,gBAAgB,CAAC,KAAkB,EAAE,MAAgB;IAC5D,MAAM,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,cAAc,EAAE,UAAU,EAAE,UAAU,CAAC,GAAG,MAAM,CAAA;IAE3E,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;QAClB,KAAK,CAAC,KAAK,CAAC,GAAG,EAAE,CAAA;IACnB,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC;QAChB,KAAK;QACL,IAAI;QACJ,cAAc;QACd,UAAU;QACV,UAAU;KACX,CAAC,CAAA;AACJ,CAAC;AAED,MAAqB,SAAS;IAY5B;;;;;;OAMG;IACH,YAAY,IAAoB;QAC9B,IAAI,CAAC,UAAU,GAAG,IAAA,SAAI,EAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QAC5D,IAAI,CAAC,WAAW,GAAG,IAAI,iCAAqB,CAAuB;YACjE,KAAK,EAAE,IAAI,mBAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;YACnC,IAAI,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,EAAE;SAC5C,CAAC,CAAA;IACJ,CAAC;IAED,UAAU;QACR,MAAM,KAAK,GAAgB,EAAE,CAAA;QAC7B,OAAO,IAAI,CAAC,UAAU;aACnB,QAAQ,EAAE;aACV,IAAI,CAAC,IAAI,CAAC,EAAE;YACX,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;gBACtC,OAAO,IAAA,aAAK,EAAC,IAAI,CAAC,CAAA;YACpB,CAAC;YACD,OAAO,IAAI,CAAA;QACb,CAAC,CAAC;aACD,IAAI,CAAC,kBAAkB,CAAC,EAAE;YACzB,IACE,kBAAkB,CAAC,MAAM,GAAG,CAAC;gBAC7B,kBAAkB,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAChD,CAAC;gBACD,MAAM,IAAI,2BAAkB,CAC1B,+IAA+I,CAChJ,CAAA;YACH,CAAC;YACD,mDAAmD;YACnD,uDAAuD;YACvD,uEAAuE;YACvE,gDAAgD;YAChD,IAAI,aAAa,GAAa,EAAE,CAAA;YAChC,IAAI,aAAa,GAAG,EAAE,CAAA;YACtB,KAAK,MAAM,QAAQ,IAAI,kBAAkB,EAAE,CAAC;gBAC1C,IACE,CAAC,QAAQ,IAAI,EAAE,IAAI,QAAQ,IAAI,EAAE,CAAC,CAAC,SAAS;oBAC5C,CAAC,CAAC,aAAa,IAAI,QAAQ,KAAK,EAAE,CAAC,CAAC,eAAe,EACnD,CAAC;oBACD,aAAa,IAAI,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAA;gBAChD,CAAC;qBAAM,IAAI,QAAQ,KAAK,CAAC,CAAC,QAAQ,EAAE,CAAC;oBACnC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;oBACtD,aAAa,GAAG,EAAE,CAAA;gBACpB,CAAC;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC;oBACpC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;oBACtD,aAAa,GAAG,EAAE,CAAA;oBAClB,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;oBACtC,aAAa,GAAG,EAAE,CAAA;gBACpB,CAAC;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,IAAI,QAAQ,KAAK,EAAE,CAAC,WAAW,EAAE,CAAC;oBACnE,oDAAoD;oBACpD,oCAAoC;oBACpC,MAAM,IAAI,2BAAkB,CAAC,0BAA0B,CAAC,CAAA;gBAC1D,CAAC;YACH,CAAC;YAED,8DAA8D;YAC9D,IAAI,aAAa,EAAE,CAAC;gBAClB,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;YACxD,CAAC;YACD,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC/B,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;YACxC,CAAC;YAED,6BAA6B;YAC7B,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,EAAE;gBAC7C,KAAK,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,CACrB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,CAC/C,CAAA;YACH,CAAC,CAAC,CAAA;YACF,OAAO,KAAK,CAAA;QACd,CAAC,CAAC,CAAA;IACN,CAAC;IAED,QAAQ,CAAC,OAAiC,EAAE;QAC1C,OAAO,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACzD,CAAC;IAED;;;;OAIG;IACG,2BAA2B,CAAC,KAAa;;YAC7C,OAAO,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;QACzC,CAAC;KAAA;IAED;;;;;;;;;;OAUG;IACG,kBAAkB,CACtB,KAAa,EACb,UAAkB,EAClB,QAAgB;;YAEhB,MAAM,UAAU,GAAG,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;YACjD,IAAI,CAAC,UAAU,EAAE,CAAC;gBAChB,OAAO,EAAE,CAAA;YACX,CAAC;YAED,MAAM,OAAO,GAAG,CAAC,KAAY,EAAE,EAAE;gBAC/B,MAAM,UAAU,GAAG,KAAK,CAAC,KAAK,CAAA;gBAC9B,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,IAAI,CAAA;gBACzC,IAAI,UAAU,GAAG,QAAQ,EAAE,CAAC;oBAC1B,OAAO,CAAC,CAAC,CAAA;gBACX,CAAC,CAAC,0BAA0B;gBAC5B,IAAI,QAAQ,IAAI,UAAU,EAAE,CAAC;oBAC3B,OAAO,CAAC,CAAA;gBACV,CAAC,CAAC,wBAAwB;gBAC1B,OAAO,CAAC,CAAA,CAAC,uBAAuB;YAClC,CAAC,CAAA;YACD,MAAM,IAAI,GAAG,EAAa,CAAA;YAC1B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;gBAC/B,IAAI,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;oBACzB,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBAClB,CAAC;YACH,CAAC;YACD,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;CACF;AAhJD,4BAgJC"}
+{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"names":[],"mappings":";;;;;;;;;;;AAAA,mCAA+B;AAC/B,6BAA2B;AAC3B,qCAA6C;AAI7C,MAAM,SAAS,GAAG,QAAU,CAAA,CAAC,QAAQ;AAYrC,SAAS,gBAAgB,CAAC,KAAkB,EAAE,MAAgB;IAC5D,MAAM,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,cAAc,EAAE,UAAU,EAAE,UAAU,CAAC,GAAG,MAAM,CAAA;IAE3E,MAAM,CAAC,GAAG,KAAM,CAAA;IAChB,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;QACd,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;IACf,CAAC;IAED,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QACZ,KAAK,EAAE,KAAM;QACb,IAAI,EAAE,IAAK;QACX,cAAc,EAAE,cAAe;QAC/B,UAAU,EAAE,UAAW;QACvB,UAAU,EAAE,UAAW;KACxB,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,UAAU,CAAC,IAAY;IAC9B,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;QACtC,OAAO,IAAA,aAAK,EAAC,IAAI,CAAC,CAAA;IACpB,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAqB,SAAS;IAe5B;;;;;;OAMG;IACH,YAAY,IAAoB;QAC9B,IAAI,CAAC,UAAU,GAAG,IAAA,SAAI,EAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;IAC9D,CAAC;IAEK,UAAU;;YACd,MAAM,KAAK,GAAgB,EAAE,CAAA;YAC7B,MAAM,kBAAkB,GAAG,UAAU,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC,CAAA;YACvE,IACE,kBAAkB,CAAC,MAAM,GAAG,CAAC;gBAC7B,kBAAkB,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAChD,CAAC;gBACD,MAAM,IAAI,2BAAkB,CAC1B,+IAA+I,CAChJ,CAAA;YACH,CAAC;YACD,mDAAmD;YACnD,uDAAuD;YACvD,uEAAuE;YACvE,gDAAgD;YAChD,IAAI,aAAa,GAAa,EAAE,CAAA;YAChC,IAAI,aAAa,GAAG,EAAE,CAAA;YACtB,KAAK,MAAM,QAAQ,IAAI,kBAAkB,EAAE,CAAC;gBAC1C,IACE,CAAC,QAAQ,IAAI,EAAE,IAAI,QAAQ,IAAI,EAAE,CAAC,CAAC,SAAS;oBAC5C,CAAC,CAAC,aAAa,IAAI,QAAQ,KAAK,EAAE,CAAC,CAAC,eAAe,EACnD,CAAC;oBACD,aAAa,IAAI,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAA;gBAChD,CAAC;qBAAM,IAAI,QAAQ,KAAK,CAAC,CAAC,QAAQ,EAAE,CAAC;oBACnC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;oBACtD,aAAa,GAAG,EAAE,CAAA;gBACpB,CAAC;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC;oBACpC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;oBACtD,aAAa,GAAG,EAAE,CAAA;oBAClB,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;oBACtC,aAAa,GAAG,EAAE,CAAA;gBACpB,CAAC;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,IAAI,QAAQ,KAAK,EAAE,CAAC,WAAW,EAAE,CAAC;oBACnE,oDAAoD;oBACpD,oCAAoC;oBACpC,MAAM,IAAI,2BAAkB,CAAC,0BAA0B,CAAC,CAAA;gBAC1D,CAAC;YACH,CAAC;YAED,8DAA8D;YAC9D,IAAI,aAAa,EAAE,CAAC;gBAClB,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;YACxD,CAAC;YACD,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC/B,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;YACxC,CAAC;YAED,6BAA6B;YAC7B,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,EAAE;gBAC7C,MAAM,EAAE,GAAG,GAAI,CAAA;gBACf,KAAK,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;YACxE,CAAC,CAAC,CAAA;YACF,OAAO,KAAK,CAAA;QACd,CAAC;KAAA;IAED,QAAQ;QACN,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC;YACtB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACxD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAED;;;;OAIG;IACG,2BAA2B,CAAC,KAAa;;YAC7C,OAAO,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;QACzC,CAAC;KAAA;IAED;;;;;;;;;;OAUG;IACG,kBAAkB,CACtB,KAAa,EACb,UAAkB,EAClB,QAAgB;;YAEhB,MAAM,UAAU,GAAG,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;YACjD,IAAI,CAAC,UAAU,EAAE,CAAC;gBAChB,OAAO,EAAE,CAAA;YACX,CAAC;YAED,MAAM,OAAO,GAAG,CAAC,KAAY,EAAE,EAAE;gBAC/B,MAAM,UAAU,GAAG,KAAK,CAAC,KAAK,CAAA;gBAC9B,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,IAAI,CAAA;gBACzC,IAAI,UAAU,GAAG,QAAQ,EAAE,CAAC;oBAC1B,OAAO,CAAC,CAAC,CAAA;gBACX,CAAC,CAAC,0BAA0B;gBAC5B,IAAI,QAAQ,IAAI,UAAU,EAAE,CAAC;oBAC3B,OAAO,CAAC,CAAA;gBACV,CAAC,CAAC,wBAAwB;gBAC1B,OAAO,CAAC,CAAA,CAAC,uBAAuB;YAClC,CAAC,CAAA;YACD,MAAM,IAAI,GAAG,EAAa,CAAA;YAC1B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;gBAC/B,IAAI,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;oBACzB,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBAClB,CAAC;YACH,CAAC;YACD,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;CACF;AA3ID,4BA2IC"}