@gmod/cram 1.6.3 → 1.7.0

package/dist/indexedCramFile.js

@@ -8,40 +8,13 @@ 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 errors_1 = require("./errors");
-var cramFile_1 = __importDefault(require("./cramFile"));
-var IndexedCramFile = /** @class */ (function () {
+const errors_1 = require("./errors");
+const cramFile_1 = __importDefault(require("./cramFile"));
+class IndexedCramFile {
     /**
      *
      * @param {object} args
@@ -52,7 +25,7 @@ var IndexedCramFile = /** @class */ (function () {
      * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
      * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
      */
-    function IndexedCramFile(args) {
+    constructor(args) {
         // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
         if (args.cram) {
             this.cram = args.cram;
@@ -83,141 +56,128 @@ var IndexedCramFile = /** @class */ (function () {
      * @param {number} end end of the range of interest. 1-based closed coordinates.
      * @returns {Promise[Array[CramRecord]]}
      */
-    IndexedCramFile.prototype.getRecordsForRange = function (seq, start, end, opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var seqId, slices, totalSize, filter, sliceResults, ret, readNames, readIds_1, i, name_1, id, unmatedPairs_1, matePromises, i, name_2, mateSlices, mateBlocks, mateChunks, i, mateRecordPromises_1, mateFeatPromises_1, mateTotalSize, newMateFeats, newMates;
-            var _a;
-            var _this = this;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        opts.viewAsPairs = opts.viewAsPairs || false;
-                        opts.pairAcrossChr = opts.pairAcrossChr || false;
-                        opts.maxInsertSize = opts.maxInsertSize || 200000;
-                        if (typeof seq === 'string') {
-                            // TODO: support string reference sequence names somehow
-                            throw new errors_1.CramUnimplementedError('string sequence names not yet supported');
-                        }
-                        seqId = seq;
-                        return [4 /*yield*/, this.index.getEntriesForRange(seqId, start, end)];
-                    case 1:
-                        slices = _b.sent();
-                        totalSize = slices.map(function (s) { return s.sliceBytes; }).reduce(function (a, b) { return a + b; }, 0);
-                        if (totalSize > this.fetchSizeLimit) {
-                            throw new errors_1.CramSizeLimitError("data size of ".concat(totalSize.toLocaleString(), " bytes exceeded fetch size limit of ").concat(this.fetchSizeLimit.toLocaleString(), " bytes"));
-                        }
-                        filter = function (feature) {
-                            return feature.sequenceId === seq &&
-                                feature.alignmentStart <= end &&
-                                feature.alignmentStart + feature.lengthOnRef - 1 >= start;
-                        };
-                        return [4 /*yield*/, Promise.all(slices.map(function (slice) { return _this.getRecordsInSlice(slice, filter); }))];
-                    case 2:
-                        sliceResults = _b.sent();
-                        ret = (_a = Array.prototype).concat.apply(_a, sliceResults);
-                        if (!opts.viewAsPairs) return [3 /*break*/, 5];
-                        readNames = {};
-                        readIds_1 = {};
-                        for (i = 0; i < ret.length; i += 1) {
-                            name_1 = ret[i].readName;
-                            id = ret[i].uniqueId;
-                            if (!readNames[name_1]) {
-                                readNames[name_1] = 0;
-                            }
-                            readNames[name_1] += 1;
-                            readIds_1[id] = 1;
-                        }
-                        unmatedPairs_1 = {};
-                        Object.entries(readNames).forEach(function (_a) {
-                            var k = _a[0], v = _a[1];
-                            if (v === 1) {
-                                unmatedPairs_1[k] = true;
-                            }
-                        });
-                        matePromises = [];
-                        for (i = 0; i < ret.length; i += 1) {
-                            name_2 = ret[i].readName;
-                            if (unmatedPairs_1[name_2] &&
-                                ret[i].mate &&
-                                (ret[i].mate.sequenceId === seqId || opts.pairAcrossChr) &&
-                                Math.abs(ret[i].alignmentStart - ret[i].mate.alignmentStart) <
-                                    opts.maxInsertSize) {
-                                mateSlices = this.index.getEntriesForRange(ret[i].mate.sequenceId, ret[i].mate.alignmentStart, ret[i].mate.alignmentStart + 1);
-                                matePromises.push(mateSlices);
+    getRecordsForRange(seq, start, end, opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            opts.viewAsPairs = opts.viewAsPairs || false;
+            opts.pairAcrossChr = opts.pairAcrossChr || false;
+            opts.maxInsertSize = opts.maxInsertSize || 200000;
+            if (typeof seq === 'string') {
+                // TODO: support string reference sequence names somehow
+                throw new errors_1.CramUnimplementedError('string sequence names not yet supported');
+            }
+            const seqId = seq;
+            const slices = yield this.index.getEntriesForRange(seqId, start, end);
+            const totalSize = slices.map(s => s.sliceBytes).reduce((a, b) => a + b, 0);
+            if (totalSize > this.fetchSizeLimit) {
+                throw new errors_1.CramSizeLimitError(`data size of ${totalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
+            }
+            // TODO: do we need to merge or de-duplicate the blocks?
+            // fetch all the slices and parse the feature data
+            const filter = (feature) => feature.sequenceId === seq &&
+                feature.alignmentStart <= end &&
+                feature.lengthOnRef !== undefined &&
+                feature.alignmentStart + feature.lengthOnRef - 1 >= start;
+            const sliceResults = yield Promise.all(slices.map(slice => this.getRecordsInSlice(slice, filter)));
+            let ret = Array.prototype.concat(...sliceResults);
+            if (opts.viewAsPairs) {
+                const readNames = {};
+                const readIds = {};
+                for (let i = 0; i < ret.length; i += 1) {
+                    const name = ret[i].readName;
+                    if (name === undefined) {
+                        throw new Error();
+                    }
+                    const id = ret[i].uniqueId;
+                    if (!readNames[name]) {
+                        readNames[name] = 0;
+                    }
+                    readNames[name] += 1;
+                    readIds[id] = 1;
+                }
+                const unmatedPairs = {};
+                Object.entries(readNames).forEach(([k, v]) => {
+                    if (v === 1) {
+                        unmatedPairs[k] = true;
+                    }
+                });
+                const matePromises = [];
+                for (let i = 0; i < ret.length; i += 1) {
+                    const cramRecord = ret[i];
+                    const name = cramRecord.readName;
+                    if (name === undefined) {
+                        throw new Error();
+                    }
+                    if (unmatedPairs[name] &&
+                        cramRecord.mate &&
+                        (cramRecord.mate.sequenceId === seqId || opts.pairAcrossChr) &&
+                        Math.abs(cramRecord.alignmentStart - cramRecord.mate.alignmentStart) <
+                            opts.maxInsertSize) {
+                        const mateSlices = this.index.getEntriesForRange(cramRecord.mate.sequenceId, cramRecord.mate.alignmentStart, cramRecord.mate.alignmentStart + 1);
+                        matePromises.push(mateSlices);
+                    }
+                }
+                const mateBlocks = yield Promise.all(matePromises);
+                let mateChunks = [];
+                for (let i = 0; i < mateBlocks.length; i += 1) {
+                    mateChunks.push(...mateBlocks[i]);
+                }
+                // filter out duplicates
+                mateChunks = mateChunks
+                    .sort((a, b) => a.toString().localeCompare(b.toString()))
+                    .filter((item, pos, ary) => !pos || item.toString() !== ary[pos - 1].toString());
+                const mateRecordPromises = [];
+                const mateFeatPromises = [];
+                const mateTotalSize = mateChunks
+                    .map(s => s.sliceBytes)
+                    .reduce((a, b) => a + b, 0);
+                if (mateTotalSize > this.fetchSizeLimit) {
+                    throw new Error(`mate data size of ${mateTotalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
+                }
+                mateChunks.forEach(c => {
+                    let recordPromise = this.cram.featureCache.get(c.toString());
+                    if (!recordPromise) {
+                        recordPromise = this.getRecordsInSlice(c, () => true);
+                        this.cram.featureCache.set(c.toString(), recordPromise);
+                    }
+                    mateRecordPromises.push(recordPromise);
+                    const featPromise = recordPromise.then(feats => {
+                        const mateRecs = [];
+                        for (let i = 0; i < feats.length; i += 1) {
+                            const feature = feats[i];
+                            if (feature.readName === undefined) {
+                                throw new Error();
                             }
-                        }
-                        return [4 /*yield*/, Promise.all(matePromises)];
-                    case 3:
-                        mateBlocks = _b.sent();
-                        mateChunks = [];
-                        for (i = 0; i < mateBlocks.length; i += 1) {
-                            mateChunks.push.apply(mateChunks, mateBlocks[i]);
-                        }
-                        // filter out duplicates
-                        mateChunks = mateChunks
-                            .sort(function (a, b) { return a.toString().localeCompare(b.toString()); })
-                            .filter(function (item, pos, ary) {
-                            return !pos || item.toString() !== ary[pos - 1].toString();
-                        });
-                        mateRecordPromises_1 = [];
-                        mateFeatPromises_1 = [];
-                        mateTotalSize = mateChunks
-                            .map(function (s) { return s.sliceBytes; })
-                            .reduce(function (a, b) { return a + b; }, 0);
-                        if (mateTotalSize > this.fetchSizeLimit) {
-                            throw new Error("mate data size of ".concat(mateTotalSize.toLocaleString(), " bytes exceeded fetch size limit of ").concat(this.fetchSizeLimit.toLocaleString(), " bytes"));
-                        }
-                        mateChunks.forEach(function (c) {
-                            var recordPromise = _this.cram.featureCache.get(c.toString());
-                            if (!recordPromise) {
-                                recordPromise = _this.getRecordsInSlice(c, function () { return true; });
-                                _this.cram.featureCache.set(c.toString(), recordPromise);
+                            if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
+                                mateRecs.push(feature);
                             }
-                            mateRecordPromises_1.push(recordPromise);
-                            var featPromise = recordPromise.then(function (feats) {
-                                var mateRecs = [];
-                                for (var i = 0; i < feats.length; i += 1) {
-                                    var feature = feats[i];
-                                    if (unmatedPairs_1[feature.readName] && !readIds_1[feature.uniqueId]) {
-                                        mateRecs.push(feature);
-                                    }
-                                }
-                                return mateRecs;
-                            });
-                            mateFeatPromises_1.push(featPromise);
-                        });
-                        return [4 /*yield*/, Promise.all(mateFeatPromises_1)];
-                    case 4:
-                        newMateFeats = _b.sent();
-                        if (newMateFeats.length) {
-                            newMates = newMateFeats.reduce(function (result, current) {
-                                return result.concat(current);
-                            });
-                            ret = ret.concat(newMates);
                         }
-                        _b.label = 5;
-                    case 5: return [2 /*return*/, ret];
+                        return mateRecs;
+                    });
+                    mateFeatPromises.push(featPromise);
+                });
+                const newMateFeats = yield Promise.all(mateFeatPromises);
+                if (newMateFeats.length) {
+                    const newMates = newMateFeats.reduce((result, current) => result.concat(current));
+                    ret = ret.concat(newMates);
                 }
-            });
+            }
+            return ret;
         });
-    };
-    IndexedCramFile.prototype.getRecordsInSlice = function (_a, filterFunction) {
-        var containerStart = _a.containerStart, sliceStart = _a.sliceStart, sliceBytes = _a.sliceBytes;
-        var container = this.cram.getContainerAtPosition(containerStart);
-        var slice = container.getSlice(sliceStart, sliceBytes);
+    }
+    getRecordsInSlice({ containerStart, sliceStart, sliceBytes, }, filterFunction) {
+        const container = this.cram.getContainerAtPosition(containerStart);
+        const slice = container.getSlice(sliceStart, sliceBytes);
         return slice.getRecords(filterFunction);
-    };
+    }
     /**
      *
      * @param {number} seqId
      * @returns {Promise} true if the CRAM file contains data for the given
      * reference sequence numerical ID
      */
-    IndexedCramFile.prototype.hasDataForReferenceSequence = function (seqId) {
+    hasDataForReferenceSequence(seqId) {
         return this.index.hasDataForReferenceSequence(seqId);
-    };
-    return IndexedCramFile;
-}());
+    }
+}
 exports.default = IndexedCramFile;
 //# sourceMappingURL=indexedCramFile.js.map

package/dist/indexedCramFile.js.map

@@ -1 +1 @@
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package/dist/io/index.d.ts

@@ -1,5 +1,5 @@
-import LocalFile from "./localFile";
-import RemoteFile from "./remoteFile";
-export function fromUrl(source: any): RemoteFile | LocalFile;
-export function open(maybeUrl: any, maybePath: any, maybeFilehandle: any): any;
-export { LocalFile, RemoteFile };
+import { Filehandle } from '../cramFile/filehandle';
+import { LocalFile, RemoteFile } from 'generic-filehandle';
+declare function fromUrl(source: string): LocalFile | RemoteFile;
+declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: Filehandle): Filehandle;
+export { LocalFile, RemoteFile, fromUrl, open };

package/dist/io/index.js

@@ -4,17 +4,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.open = exports.fromUrl = exports.RemoteFile = exports.LocalFile = void 0;
-var url_1 = __importDefault(require("url"));
-var remoteFile_1 = __importDefault(require("./remoteFile"));
-exports.RemoteFile = remoteFile_1.default;
-var localFile_1 = __importDefault(require("./localFile"));
-exports.LocalFile = localFile_1.default;
+const url_1 = __importDefault(require("url"));
+const typescript_1 = require("../typescript");
+const generic_filehandle_1 = require("generic-filehandle");
+Object.defineProperty(exports, "LocalFile", { enumerable: true, get: function () { return generic_filehandle_1.LocalFile; } });
+Object.defineProperty(exports, "RemoteFile", { enumerable: true, get: function () { return generic_filehandle_1.RemoteFile; } });
 function fromUrl(source) {
-    var _a = url_1.default.parse(source), protocol = _a.protocol, pathname = _a.pathname;
+    const { protocol, pathname } = url_1.default.parse(source);
     if (protocol === 'file:') {
-        return new localFile_1.default(unescape(pathname));
+        return new generic_filehandle_1.LocalFile(unescape((0, typescript_1.ensureNotNullish)(pathname)));
     }
-    return new remoteFile_1.default(source);
+    return new generic_filehandle_1.RemoteFile(source);
 }
 exports.fromUrl = fromUrl;
 function open(maybeUrl, maybePath, maybeFilehandle) {
@@ -25,7 +25,7 @@ function open(maybeUrl, maybePath, maybeFilehandle) {
         return fromUrl(maybeUrl);
     }
     if (maybePath) {
-        return new localFile_1.default(maybePath);
+        return new generic_filehandle_1.LocalFile(maybePath);
     }
     throw new Error('no url, path, or filehandle provided, cannot open');
 }

package/dist/io/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.js"],"names":[],"mappings":";;;;;;AAAA,4CAAqB;AACrB,4DAAqC;AAwBjB,qBAxBb,oBAAU,CAwBa;AAvB9B,0DAAmC;AAuB1B,oBAvBF,mBAAS,CAuBE;AArBlB,SAAS,OAAO,CAAC,MAAM;IACf,IAAA,KAAyB,aAAG,CAAC,KAAK,CAAC,MAAM,CAAC,EAAxC,QAAQ,cAAA,EAAE,QAAQ,cAAsB,CAAA;IAChD,IAAI,QAAQ,KAAK,OAAO,EAAE;QACxB,OAAO,IAAI,mBAAS,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,CAAA;KACzC;IACD,OAAO,IAAI,oBAAU,CAAC,MAAM,CAAC,CAAA;AAC/B,CAAC;AAe+B,0BAAO;AAbvC,SAAS,IAAI,CAAC,QAAQ,EAAE,SAAS,EAAE,eAAe;IAChD,IAAI,eAAe,EAAE;QACnB,OAAO,eAAe,CAAA;KACvB;IACD,IAAI,QAAQ,EAAE;QACZ,OAAO,OAAO,CAAC,QAAQ,CAAC,CAAA;KACzB;IACD,IAAI,SAAS,EAAE;QACb,OAAO,IAAI,mBAAS,CAAC,SAAS,CAAC,CAAA;KAChC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAEwC,oBAAI"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":";;;;;;AAAA,8CAAqB;AACrB,8CAAgD;AAEhD,2DAA0D;AA2BjD,0FA3BA,8BAAS,OA2BA;AAAE,2FA3BA,+BAAU,OA2BA;AAzB9B,SAAS,OAAO,CAAC,MAAc;IAC7B,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,aAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAChD,IAAI,QAAQ,KAAK,OAAO,EAAE;QACxB,OAAO,IAAI,8BAAS,CAAC,QAAQ,CAAC,IAAA,6BAAgB,EAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;KAC3D;IACD,OAAO,IAAI,+BAAU,CAAC,MAAM,CAAC,CAAA;AAC/B,CAAC;AAmB+B,0BAAO;AAjBvC,SAAS,IAAI,CACX,QAAiB,EACjB,SAAkB,EAClB,eAA4B;IAE5B,IAAI,eAAe,EAAE;QACnB,OAAO,eAAe,CAAA;KACvB;IACD,IAAI,QAAQ,EAAE;QACZ,OAAO,OAAO,CAAC,QAAQ,CAAC,CAAA;KACzB;IACD,IAAI,SAAS,EAAE;QACb,OAAO,IAAI,8BAAS,CAAC,SAAS,CAAC,CAAA;KAChC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAEwC,oBAAI"}

package/dist/rans/constants.js

@@ -1,10 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.RANS_BYTE_L = exports.TOTFREQ = exports.TF_SHIFT = void 0;
-var TF_SHIFT = 12;
+const TF_SHIFT = 12;
 exports.TF_SHIFT = TF_SHIFT;
-var TOTFREQ = 1 << TF_SHIFT;
+const TOTFREQ = 1 << TF_SHIFT;
 exports.TOTFREQ = TOTFREQ;
-var RANS_BYTE_L = 1 << 23;
+const RANS_BYTE_L = 1 << 23;
 exports.RANS_BYTE_L = RANS_BYTE_L;
 //# sourceMappingURL=constants.js.map

package/dist/rans/constants.js.map

@@ -1 +1 @@
-{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/rans/constants.js"],"names":[],"mappings":";;;AAAA,IAAM,QAAQ,GAAG,EAAE,CAAA;AAIV,4BAAQ;AAHjB,IAAM,OAAO,GAAG,CAAC,IAAI,QAAQ,CAAA;AAGV,0BAAO;AAF1B,IAAM,WAAW,GAAG,CAAC,IAAI,EAAE,CAAA;AAEC,kCAAW"}
+{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/rans/constants.js"],"names":[],"mappings":";;;AAAA,MAAM,QAAQ,GAAG,EAAE,CAAA;AAIV,4BAAQ;AAHjB,MAAM,OAAO,GAAG,CAAC,IAAI,QAAQ,CAAA;AAGV,0BAAO;AAF1B,MAAM,WAAW,GAAG,CAAC,IAAI,EAAE,CAAA;AAEC,kCAAW"}

package/dist/rans/d04.js

@@ -3,25 +3,25 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var errors_1 = require("../errors");
-var constants_1 = require("./constants");
-var decoding_1 = __importDefault(require("./decoding"));
+const errors_1 = require("../errors");
+const constants_1 = require("./constants");
+const decoding_1 = __importDefault(require("./decoding"));
 function uncompress(
 /* ByteBuffer */ input, 
 /* Decoding.AriDecoder */ D, 
 /* Decoding.Symbol[] */ syms, 
 /* ByteBuffer */ out) {
-    var rans0 = input.getInt();
-    var rans1 = input.getInt();
-    var rans2 = input.getInt();
-    var rans3 = input.getInt();
-    var /* int */ outputSize = out.remaining();
-    var /* int */ outputEnd = outputSize & ~3;
-    for (var i = 0; i < outputEnd; i += 4) {
-        var /* byte */ c0 = D.R[decoding_1.default.get(rans0, constants_1.TF_SHIFT)];
-        var /* byte */ c1 = D.R[decoding_1.default.get(rans1, constants_1.TF_SHIFT)];
-        var /* byte */ c2 = D.R[decoding_1.default.get(rans2, constants_1.TF_SHIFT)];
-        var /* byte */ c3 = D.R[decoding_1.default.get(rans3, constants_1.TF_SHIFT)];
+    let rans0 = input.getInt();
+    let rans1 = input.getInt();
+    let rans2 = input.getInt();
+    let rans3 = input.getInt();
+    const /* int */ outputSize = out.remaining();
+    const /* int */ outputEnd = outputSize & ~3;
+    for (let i = 0; i < outputEnd; i += 4) {
+        const /* byte */ c0 = D.R[decoding_1.default.get(rans0, constants_1.TF_SHIFT)];
+        const /* byte */ c1 = D.R[decoding_1.default.get(rans1, constants_1.TF_SHIFT)];
+        const /* byte */ c2 = D.R[decoding_1.default.get(rans2, constants_1.TF_SHIFT)];
+        const /* byte */ c3 = D.R[decoding_1.default.get(rans3, constants_1.TF_SHIFT)];
         out.putAt(i, c0);
         out.putAt(i + 1, c1);
         out.putAt(i + 2, c2);
@@ -36,7 +36,7 @@ function uncompress(
         rans3 = decoding_1.default.renormalize(rans3, input);
     }
     out.setPosition(outputEnd);
-    var /* byte */ c;
+    let /* byte */ c;
     switch (outputSize & 3) {
         case 0:
             break;

package/dist/rans/d04.js.map

@@ -1 +1 @@
-{"version":3,"file":"d04.js","sourceRoot":"","sources":["../../src/rans/d04.js"],"names":[],"mappings":";;;;;AAAA,oCAA8C;AAE9C,yCAAsC;AACtC,wDAAiC;AAEjC,SAAwB,UAAU;AAChC,gBAAgB,CAAC,KAAK;AACtB,yBAAyB,CAAC,CAAC;AAC3B,uBAAuB,CAAC,IAAI;AAC5B,gBAAgB,CAAC,GAAG;IAEpB,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAE1B,IAAM,SAAS,CAAC,UAAU,GAAG,GAAG,CAAC,SAAS,EAAE,CAAA;IAC5C,IAAM,SAAS,CAAC,SAAS,GAAG,UAAU,GAAG,CAAC,CAAC,CAAA;IAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;QACrC,IAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QACxD,IAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QACxD,IAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QACxD,IAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QAExD,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;QAChB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QAEpB,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QAEpE,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;KAC3C;IAED,GAAG,CAAC,WAAW,CAAC,SAAS,CAAC,CAAA;IAC1B,IAAI,UAAU,CAAC,CAAC,CAAA;IAChB,QAAQ,UAAU,GAAG,CAAC,EAAE;QACtB,KAAK,CAAC;YACJ,MAAK;QACP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP;YACE,MAAM,IAAI,2BAAkB,CAC1B,sDAAsD,CACvD,CAAA;KACJ;IAED,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;AACpB,CAAC;AA7ED,6BA6EC"}
+{"version":3,"file":"d04.js","sourceRoot":"","sources":["../../src/rans/d04.js"],"names":[],"mappings":";;;;;AAAA,sCAA8C;AAE9C,2CAAsC;AACtC,0DAAiC;AAEjC,SAAwB,UAAU;AAChC,gBAAgB,CAAC,KAAK;AACtB,yBAAyB,CAAC,CAAC;AAC3B,uBAAuB,CAAC,IAAI;AAC5B,gBAAgB,CAAC,GAAG;IAEpB,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAE1B,MAAM,SAAS,CAAC,UAAU,GAAG,GAAG,CAAC,SAAS,EAAE,CAAA;IAC5C,MAAM,SAAS,CAAC,SAAS,GAAG,UAAU,GAAG,CAAC,CAAC,CAAA;IAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;QACrC,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QACxD,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QACxD,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QACxD,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QAExD,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;QAChB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QAEpB,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QAEpE,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;KAC3C;IAED,GAAG,CAAC,WAAW,CAAC,SAAS,CAAC,CAAA;IAC1B,IAAI,UAAU,CAAC,CAAC,CAAA;IAChB,QAAQ,UAAU,GAAG,CAAC,EAAE;QACtB,KAAK,CAAC;YACJ,MAAK;QACP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;YACtC,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,oBAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP;YACE,MAAM,IAAI,2BAAkB,CAC1B,sDAAsD,CACvD,CAAA;KACJ;IAED,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;AACpB,CAAC;AA7ED,6BA6EC"}

package/dist/rans/d14.js

@@ -3,32 +3,32 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var constants_1 = require("./constants");
-var decoding_1 = __importDefault(require("./decoding"));
+const constants_1 = require("./constants");
+const decoding_1 = __importDefault(require("./decoding"));
 function uncompress(
 /* ByteBuffer */ input, 
 /* ByteBuffer */ output, 
 /* Decoding.AriDecoder[] */ D, 
 /* Decoding.Symbol[][] */ syms) {
-    var /* int */ outputSize = output.remaining();
-    var rans0 = input.getInt();
-    var rans1 = input.getInt();
-    var rans2 = input.getInt();
-    var rans7 = input.getInt();
-    var /* int */ isz4 = outputSize >> 2;
-    var /* int */ i0 = 0;
-    var /* int */ i1 = isz4;
-    var /* int */ i2 = 2 * isz4;
-    var /* int */ i7 = 3 * isz4;
-    var /* int */ l0 = 0;
-    var /* int */ l1 = 0;
-    var /* int */ l2 = 0;
-    var /* int */ l7 = 0;
+    const /* int */ outputSize = output.remaining();
+    let rans0 = input.getInt();
+    let rans1 = input.getInt();
+    let rans2 = input.getInt();
+    let rans7 = input.getInt();
+    const /* int */ isz4 = outputSize >> 2;
+    let /* int */ i0 = 0;
+    let /* int */ i1 = isz4;
+    let /* int */ i2 = 2 * isz4;
+    let /* int */ i7 = 3 * isz4;
+    let /* int */ l0 = 0;
+    let /* int */ l1 = 0;
+    let /* int */ l2 = 0;
+    let /* int */ l7 = 0;
     for (; i0 < isz4; i0 += 1, i1 += 1, i2 += 1, i7 += 1) {
-        var /* int */ c0 = 0xff & D[l0].R[decoding_1.default.get(rans0, constants_1.TF_SHIFT)];
-        var /* int */ c1 = 0xff & D[l1].R[decoding_1.default.get(rans1, constants_1.TF_SHIFT)];
-        var /* int */ c2 = 0xff & D[l2].R[decoding_1.default.get(rans2, constants_1.TF_SHIFT)];
-        var /* int */ c7 = 0xff & D[l7].R[decoding_1.default.get(rans7, constants_1.TF_SHIFT)];
+        const /* int */ c0 = 0xff & D[l0].R[decoding_1.default.get(rans0, constants_1.TF_SHIFT)];
+        const /* int */ c1 = 0xff & D[l1].R[decoding_1.default.get(rans1, constants_1.TF_SHIFT)];
+        const /* int */ c2 = 0xff & D[l2].R[decoding_1.default.get(rans2, constants_1.TF_SHIFT)];
+        const /* int */ c7 = 0xff & D[l7].R[decoding_1.default.get(rans7, constants_1.TF_SHIFT)];
         output.putAt(i0, c0);
         output.putAt(i1, c1);
         output.putAt(i2, c2);
@@ -48,7 +48,7 @@ function uncompress(
     }
     // Remainder
     for (; i7 < outputSize; i7 += 1) {
-        var /* int */ c7 = 0xff & D[l7].R[decoding_1.default.get(rans7, constants_1.TF_SHIFT)];
+        const /* int */ c7 = 0xff & D[l7].R[decoding_1.default.get(rans7, constants_1.TF_SHIFT)];
         output.putAt(i7, c7);
         rans7 = decoding_1.default.advanceSymbol(rans7, input, syms[l7][c7], constants_1.TF_SHIFT);
         l7 = c7;

package/dist/rans/d14.js.map

@@ -1 +1 @@
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