@gmod/cram 1.6.3 → 1.7.0

package/CHANGELOG.md

@@ -1,3 +1,12 @@
+# v1.7.0
+
+- Typescript entire codebase, big thanks to @0xorial for taking on this effort!
+- Update to use webpack 5 for UMD build
+
+# v1.6.4
+
+- Fix off by one in returning features from getRecordsFromRange
+
 # v1.6.3
 
 - Optimize CRAM parsing slightly (15% improvement on many short reads). This removes support for big endian machines

package/dist/craiIndex.d.ts

@@ -1,4 +1,15 @@
+import { CramFileSource } from './cramFile/file';
+export declare type Slice = {
+    start: number;
+    span: number;
+    containerStart: number;
+    sliceStart: number;
+    sliceBytes: number;
+};
+declare type ParsedIndex = Record<string, Slice[]>;
 export default class CraiIndex {
+    private _parseCache;
+    private filehandle;
     /**
      *
      * @param {object} args
@@ -6,21 +17,17 @@ export default class CraiIndex {
      * @param {string} [args.url]
      * @param {FileHandle} [args.filehandle]
      */
-    constructor(args: {
-        path?: string | undefined;
-        url?: string | undefined;
-        filehandle?: any;
-    });
-    _parseCache: AbortablePromiseCache<any, any>;
-    readFile: any;
-    parseIndex(): any;
-    getIndex(opts?: {}): Promise<any>;
+    constructor(args: CramFileSource);
+    parseIndex(): Promise<ParsedIndex>;
+    getIndex(opts?: {
+        signal?: AbortSignal;
+    }): Promise<ParsedIndex>;
     /**
      * @param {number} seqId
      * @returns {Promise} true if the index contains entries for
      * the given reference sequence ID, false otherwise
      */
-    hasDataForReferenceSequence(seqId: number): Promise<any>;
+    hasDataForReferenceSequence(seqId: number): Promise<boolean>;
     /**
      * fetch index entries for the given range
      *
@@ -32,6 +39,6 @@ export default class CraiIndex {
      * an array of objects of the form
      * `{start, span, containerStart, sliceStart, sliceBytes }`
      */
-    getEntriesForRange(seqId: number, queryStart: number, queryEnd: number): Promise<any>;
+    getEntriesForRange(seqId: number, queryStart: number, queryEnd: number): Promise<Slice[]>;
 }
-import AbortablePromiseCache from "abortable-promise-cache";
+export {};

package/dist/craiIndex.js

@@ -8,77 +8,33 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
 };
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
-var quick_lru_1 = __importDefault(require("quick-lru"));
-var unzip_1 = require("./unzip");
-var io_1 = require("./io");
-var errors_1 = require("./errors");
-var BAI_MAGIC = 21578050; // BAI\1
-var Slice = /** @class */ (function () {
-    function Slice(args) {
-        Object.assign(this, args);
-    }
-    Slice.prototype.toString = function () {
-        return "".concat(this.start, ":").concat(this.span, ":").concat(this.containerStart, ":").concat(this.sliceStart, ":").concat(this.sliceBytes);
-    };
-    return Slice;
-}());
+const abortable_promise_cache_1 = __importDefault(require("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) {
-    if (record.some(function (el) { return el === undefined; })) {
+    if (record.some(el => el === undefined)) {
         throw new errors_1.CramMalformedError('invalid .crai index file');
     }
-    var seqId = record[0], start = record[1], span = record[2], containerStart = record[3], sliceStart = record[4], sliceBytes = record[5];
+    const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record;
     if (!index[seqId]) {
         index[seqId] = [];
     }
-    index[seqId].push(new Slice({
-        start: start,
-        span: span,
-        containerStart: containerStart,
-        sliceStart: sliceStart,
-        sliceBytes: sliceBytes,
-    }));
+    index[seqId].push({
+        start,
+        span,
+        containerStart,
+        sliceStart,
+        sliceBytes,
+    });
 }
-var CraiIndex = /** @class */ (function () {
-    // A CRAM index (.crai) is a gzipped tab delimited file containing the following columns:
-    // 1. Sequence id
-    // 2. Alignment start
-    // 3. Alignment span
-    // 4. Container start byte position in the file
-    // 5. Slice start byte position in the container data (‘blocks’)
-    // 6. Slice size in bytes
-    // Each line represents a slice in the CRAM file. Please note that all slices must be listed in index file.
+class CraiIndex {
     /**
      *
      * @param {object} args
@@ -86,25 +42,24 @@ var CraiIndex = /** @class */ (function () {
      * @param {string} [args.url]
      * @param {FileHandle} [args.filehandle]
      */
-    function CraiIndex(args) {
-        var _this = this;
-        var filehandle = (0, io_1.open)(args.url, args.path, args.filehandle);
+    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: function (data, signal) { return _this.parseIndex({ signal: signal }); },
+            fill: (data, signal) => this.parseIndex(),
         });
-        this.readFile = filehandle.readFile.bind(filehandle);
     }
-    CraiIndex.prototype.parseIndex = function () {
-        var index = {};
-        return this.readFile()
-            .then(function (data) {
+    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(function (uncompressedBuffer) {
+            .then(uncompressedBuffer => {
             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');
@@ -113,10 +68,10 @@ var CraiIndex = /** @class */ (function () {
             // supposed to be only digits and whitespace characters
             // this is written in a deliberately low-level fashion for performance,
             // because some .crai files can be pretty large.
-            var currentRecord = [];
-            var currentString = '';
-            for (var i = 0; i < uncompressedBuffer.length; i += 1) {
-                var charCode = uncompressedBuffer[i];
+            let currentRecord = [];
+            let currentString = '';
+            for (let i = 0; i < uncompressedBuffer.length; i += 1) {
+                const charCode = uncompressedBuffer[i];
                 if ((charCode >= 48 && charCode <= 57) /* 0-9 */ ||
                     (!currentString && charCode === 45) /* leading - */) {
                     currentString += String.fromCharCode(charCode);
@@ -145,32 +100,25 @@ var CraiIndex = /** @class */ (function () {
                 addRecordToIndex(index, currentRecord);
             }
             // sort each of them by start
-            Object.entries(index).forEach(function (_a) {
-                var seqId = _a[0], ent = _a[1];
-                index[seqId] = ent.sort(function (a, b) { return a.start - b.start || a.span - b.span; });
+            Object.entries(index).forEach(([seqId, ent]) => {
+                index[seqId] = ent.sort((a, b) => a.start - b.start || a.span - b.span);
             });
             return index;
         });
-    };
-    CraiIndex.prototype.getIndex = function (opts) {
-        if (opts === void 0) { opts = {}; }
+    }
+    getIndex(opts = {}) {
         return this._parseCache.get('index', null, opts.signal);
-    };
+    }
     /**
      * @param {number} seqId
      * @returns {Promise} true if the index contains entries for
      * the given reference sequence ID, false otherwise
      */
-    CraiIndex.prototype.hasDataForReferenceSequence = function (seqId) {
-        return __awaiter(this, void 0, void 0, function () {
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.getIndex()];
-                    case 1: return [2 /*return*/, !!(_a.sent())[seqId]];
-                }
-            });
+    hasDataForReferenceSequence(seqId) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return !!(yield this.getIndex())[seqId];
         });
-    };
+    }
     /**
      * fetch index entries for the given range
      *
@@ -182,40 +130,32 @@ var CraiIndex = /** @class */ (function () {
      * an array of objects of the form
      * `{start, span, containerStart, sliceStart, sliceBytes }`
      */
-    CraiIndex.prototype.getEntriesForRange = function (seqId, queryStart, queryEnd) {
-        return __awaiter(this, void 0, void 0, function () {
-            var seqEntries, compare, bins, i;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.getIndex()];
-                    case 1:
-                        seqEntries = (_a.sent())[seqId];
-                        if (!seqEntries) {
-                            return [2 /*return*/, []];
-                        }
-                        compare = function (entry) {
-                            var entryStart = entry.start;
-                            var entryEnd = entry.start + entry.span;
-                            if (entryStart >= queryEnd) {
-                                return -1;
-                            } // entry is ahead of query
-                            if (entryEnd <= queryStart) {
-                                return 1;
-                            } // entry is behind query
-                            return 0; // entry overlaps query
-                        };
-                        bins = [];
-                        for (i = 0; i < seqEntries.length; i += 1) {
-                            if (compare(seqEntries[i]) === 0) {
-                                bins.push(seqEntries[i]);
-                            }
-                        }
-                        return [2 /*return*/, bins];
+    getEntriesForRange(seqId, queryStart, queryEnd) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const seqEntries = (yield this.getIndex())[seqId];
+            if (!seqEntries) {
+                return [];
+            }
+            const compare = (entry) => {
+                const entryStart = entry.start;
+                const entryEnd = entry.start + entry.span;
+                if (entryStart > queryEnd) {
+                    return -1;
+                } // entry is ahead of query
+                if (entryEnd <= queryStart) {
+                    return 1;
+                } // entry is behind query
+                return 0; // entry overlaps query
+            };
+            const bins = [];
+            for (let i = 0; i < seqEntries.length; i += 1) {
+                if (compare(seqEntries[i]) === 0) {
+                    bins.push(seqEntries[i]);
                 }
-            });
+            }
+            return bins;
         });
-    };
-    return CraiIndex;
-}());
+    }
+}
 exports.default = CraiIndex;
 //# sourceMappingURL=craiIndex.js.map

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