@gmod/cram 3.0.6 → 4.0.0

package/dist/indexedCramFile.js

@@ -1,19 +1,10 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        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 errors_1 = require("./errors");
 const cramFile_1 = __importDefault(require("./cramFile"));
+const errors_1 = require("./errors");
 class IndexedCramFile {
     /**
      *
@@ -25,17 +16,17 @@ class IndexedCramFile {
      * 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.
      */
     constructor(args) {
-        var _a;
         // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
         this.cram =
-            (_a = args.cram) !== null && _a !== void 0 ? _a : new cramFile_1.default({
-                url: args.cramUrl,
-                path: args.cramPath,
-                filehandle: args.cramFilehandle,
-                seqFetch: args.seqFetch,
-                checkSequenceMD5: args.checkSequenceMD5,
-                cacheSize: args.cacheSize,
-            });
+            args.cram ??
+                new cramFile_1.default({
+                    url: args.cramUrl,
+                    path: args.cramPath,
+                    filehandle: args.cramFilehandle,
+                    seqFetch: args.seqFetch,
+                    checkSequenceMD5: args.checkSequenceMD5,
+                    cacheSize: args.cacheSize,
+                });
         if (!(this.cram instanceof cramFile_1.default)) {
             throw new Error('invalid arguments: no cramfile');
         }
@@ -48,101 +39,99 @@ class IndexedCramFile {
      * @param {number} end end of the range of interest. 1-based closed coordinates.
      * @returns {Promise[Array[CramRecord]]}
      */
-    getRecordsForRange(seq_1, start_1, end_1) {
-        return __awaiter(this, arguments, void 0, function* (seq, start, end, opts = {}) {
-            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);
-            // 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 (const read of ret) {
-                    const name = read.readName;
-                    if (name === undefined) {
-                        throw new Error('readName undefined');
-                    }
-                    const id = read.uniqueId;
-                    if (!readNames[name]) {
-                        readNames[name] = 0;
-                    }
-                    readNames[name] += 1;
-                    readIds[id] = 1;
+    async getRecordsForRange(seq, start, end, opts = {}) {
+        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 = await this.index.getEntriesForRange(seqId, start, end);
+        // 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 = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, filter)));
+        let ret = Array.prototype.concat(...sliceResults);
+        if (opts.viewAsPairs) {
+            const readNames = {};
+            const readIds = {};
+            for (const read of ret) {
+                const name = read.readName;
+                if (name === undefined) {
+                    throw new Error('readName undefined');
                 }
-                const unmatedPairs = {};
-                Object.entries(readNames).forEach(([k, v]) => {
-                    if (v === 1) {
-                        unmatedPairs[k] = true;
-                    }
-                });
-                const matePromises = [];
-                for (const cramRecord of ret) {
-                    const name = cramRecord.readName;
-                    if (name === undefined) {
-                        throw new Error('readName undefined');
-                    }
-                    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 id = read.uniqueId;
+                if (!readNames[name]) {
+                    readNames[name] = 0;
                 }
-                const mateBlocks = yield Promise.all(matePromises);
-                let mateChunks = [];
-                for (const block of mateBlocks) {
-                    mateChunks.push(...block);
+                readNames[name] += 1;
+                readIds[id] = 1;
+            }
+            const unmatedPairs = {};
+            Object.entries(readNames).forEach(([k, v]) => {
+                if (v === 1) {
+                    unmatedPairs[k] = true;
                 }
-                // 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 = [];
-                for (const c of mateChunks) {
-                    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 (const feature of feats) {
-                            if (feature.readName === undefined) {
-                                throw new Error('readName undefined');
-                            }
-                            if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
-                                mateRecs.push(feature);
-                            }
-                        }
-                        return mateRecs;
-                    });
-                    mateFeatPromises.push(featPromise);
+            });
+            const matePromises = [];
+            for (const cramRecord of ret) {
+                const name = cramRecord.readName;
+                if (name === undefined) {
+                    throw new Error('readName undefined');
                 }
-                const newMateFeats = yield Promise.all(mateFeatPromises);
-                if (newMateFeats.length) {
-                    const newMates = newMateFeats.reduce((result, current) => result.concat(current));
-                    ret = ret.concat(newMates);
+                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);
                 }
             }
-            return ret;
-        });
+            const mateBlocks = await Promise.all(matePromises);
+            let mateChunks = [];
+            for (const block of mateBlocks) {
+                mateChunks.push(...block);
+            }
+            // 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 = [];
+            for (const c of mateChunks) {
+                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 (const feature of feats) {
+                        if (feature.readName === undefined) {
+                            throw new Error('readName undefined');
+                        }
+                        if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
+                            mateRecs.push(feature);
+                        }
+                    }
+                    return mateRecs;
+                });
+                mateFeatPromises.push(featPromise);
+            }
+            const newMateFeats = await Promise.all(mateFeatPromises);
+            if (newMateFeats.length) {
+                const newMates = newMateFeats.reduce((result, current) => result.concat(current));
+                ret = ret.concat(newMates);
+            }
+        }
+        return ret;
     }
     getRecordsInSlice({ containerStart, sliceStart, sliceBytes, }, filterFunction) {
         const container = this.cram.getContainerAtPosition(containerStart);

package/dist/indexedCramFile.js.map

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package/dist/io/index.d.ts

@@ -1,4 +1,4 @@
-import { Filehandle } from '../cramFile/filehandle';
-declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: Filehandle): Filehandle;
+import type { GenericFilehandle } from 'generic-filehandle2';
+declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: GenericFilehandle): GenericFilehandle;
 export { open };
 export { LocalFile, RemoteFile } from 'generic-filehandle';

package/dist/io/index.js

@@ -2,20 +2,20 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.RemoteFile = exports.LocalFile = void 0;
 exports.open = open;
-const generic_filehandle_1 = require("generic-filehandle");
+const generic_filehandle2_1 = require("generic-filehandle2");
 function open(maybeUrl, maybePath, maybeFilehandle) {
     if (maybeFilehandle) {
         return maybeFilehandle;
     }
     if (maybeUrl) {
-        return new generic_filehandle_1.RemoteFile(maybeUrl);
+        return new generic_filehandle2_1.RemoteFile(maybeUrl);
     }
     if (maybePath) {
-        return new generic_filehandle_1.LocalFile(maybePath);
+        return new generic_filehandle2_1.LocalFile(maybePath);
     }
     throw new Error('no url, path, or filehandle provided, cannot open');
 }
-var generic_filehandle_2 = require("generic-filehandle");
-Object.defineProperty(exports, "LocalFile", { enumerable: true, get: function () { return generic_filehandle_2.LocalFile; } });
-Object.defineProperty(exports, "RemoteFile", { enumerable: true, get: function () { return generic_filehandle_2.RemoteFile; } });
+var 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; } });
 //# sourceMappingURL=index.js.map

package/dist/io/index.js.map

@@ -1 +1 @@
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package/dist/rans/constants.d.ts

@@ -1,4 +1,4 @@
 declare const TF_SHIFT = 12;
 declare const TOTFREQ: number;
 declare const RANS_BYTE_L: number;
-export { TF_SHIFT, TOTFREQ, RANS_BYTE_L };
+export { RANS_BYTE_L, TF_SHIFT, TOTFREQ };

package/dist/rans/constants.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.RANS_BYTE_L = exports.TOTFREQ = exports.TF_SHIFT = void 0;
+exports.TOTFREQ = exports.TF_SHIFT = exports.RANS_BYTE_L = void 0;
 const TF_SHIFT = 12;
 exports.TF_SHIFT = TF_SHIFT;
 const TOTFREQ = 1 << TF_SHIFT;

package/dist/rans/constants.js.map

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package/dist/rans/d04.js.map

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package/dist/rans/decoding.js.map

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package/dist/rans/frequencies.js.map

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+{"version":3,"file":"frequencies.js","sourceRoot":"","sources":["../../src/rans/frequencies.ts"],"names":[],"mappings":";;;;;AAWA,kCA0CC;AAED,kCAiEC;AAxHD,cAAc;AACd,sCAA8C;AAC9C,2CAAqC;AACrC,0DAAiC;AAEjC,SAAS,MAAM,CAAC,MAAM;IACpB,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,MAAM,IAAI,2BAAkB,CAAC,kBAAkB,CAAC,CAAA;IAClD,CAAC;AACH,CAAC;AAED,SAAgB,WAAW;AACzB,gBAAgB,CAAC,EAAE;AACnB,yBAAyB,CAAC,OAAO;AACjC,8BAA8B,CAAC,IAAI;IAEnC,2CAA2C;IAC3C,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;IACvB,GAAG,CAAC;QACF,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;YAC1B,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,EAAE,EAAE,CAAA;QACnC,CAAC;QACD,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;QACjC,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,CAAC;YAC3B,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAA;YACvB,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAC,CAAA;QACtE,CAAC;QACD,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnB,kBAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAE9D,gCAAgC;QAChC,IAAI,CAAC,OAAO,CAAC,CAAC,EAAE,CAAC;YACf,OAAO,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,mBAAO,CAAC,CAAA;QAChC,CAAC;QACD,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEzC,CAAC,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEpB,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE,CAAC;YAChE,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;YACnB,GAAG,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;QACvB,CAAC;aAAM,IAAI,GAAG,KAAK,CAAC,EAAE,CAAC;YACrB,GAAG,IAAI,CAAC,CAAA;YACR,CAAC,IAAI,CAAC,CAAA;QACR,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;QACrB,CAAC;IACH,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAC;IAEjB,MAAM,CAAC,CAAC,GAAG,mBAAO,CAAC,CAAA;AACrB,CAAC;AAED,SAAgB,WAAW;AACzB,gBAAgB,CAAC,EAAE;AACnB,4BAA4B,CAAC,CAAC;AAC9B,gCAAgC,CAAC,IAAI;IAErC,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,IAAI,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;IACvB,GAAG,CAAC;QACF,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;QACvB,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;YACjB,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,UAAU,EAAE,CAAA;QAClC,CAAC;QACD,GAAG,CAAC;YACF,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;gBACvB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,EAAE,EAAE,CAAA;YAChC,CAAC;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YAC9B,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,CAAC;gBACxB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAA;gBACpB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;YAChE,CAAC;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAEhB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;gBACvB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,mBAAO,CAAA;YACxB,CAAC;YAED,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;gBACvB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,aAAa,EAAE,CAAA;YAC3C,CAAC;YAED,kBAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAE3D,gCAAgC;YAChC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;gBACnB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,mBAAO,CAAC,CAAA;YAC7B,CAAC;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAEnC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACjB,MAAM,CAAC,CAAC,IAAI,mBAAO,CAAC,CAAA;YAEpB,IAAI,IAAI,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE,CAAC;gBACjE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;gBACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACxB,CAAC;iBAAM,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;gBACtB,IAAI,IAAI,CAAC,CAAA;gBACT,CAAC,IAAI,CAAC,CAAA;YACR,CAAC;iBAAM,CAAC;gBACN,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACrB,CAAC;QACH,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAC;QAEjB,IAAI,IAAI,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE,CAAC;YACjE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;QACxB,CAAC;aAAM,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;YACtB,IAAI,IAAI,CAAC,CAAA;YACT,CAAC,IAAI,CAAC,CAAA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package/dist/rans/index.js

@@ -5,12 +5,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = uncompress;
 // @ts-nocheck
-const buffer_1 = require("buffer");
 const errors_1 = require("../errors");
-const decoding_1 = __importDefault(require("./decoding"));
-const frequencies_1 = require("./frequencies");
 const d04_1 = __importDefault(require("./d04"));
 const d14_1 = __importDefault(require("./d14"));
+const decoding_1 = __importDefault(require("./decoding"));
+const frequencies_1 = require("./frequencies");
 // const /* int */ ORDER_BYTE_LENGTH = 1
 // const /* int */ COMPRESSED_BYTE_LENGTH = 4
 const /* int */ RAW_BYTE_LENGTH = 4;
@@ -130,6 +129,7 @@ function uncompressOrder1Way4(
 class ByteBuffer {
     constructor(nodeBuffer, initialInputPosition = 0) {
         this._buffer = nodeBuffer;
+        this._dataView = new DataView(nodeBuffer.buffer);
         this._position = initialInputPosition;
         this.length = nodeBuffer.length;
     }
@@ -161,7 +161,7 @@ class ByteBuffer {
         return pos;
     }
     getInt() {
-        const i = this._buffer.readInt32LE(this._position);
+        const i = this._dataView.getInt32(this._position, true);
         this._position += 4;
         return i;
     }
@@ -186,7 +186,7 @@ function uncompress(inputBuffer, outputBuffer, initialInputPosition = 0) {
         throw new errors_1.CramMalformedError('Incorrect input length.');
     }
     const /* int */ outputSize = input.getInt();
-    const output = new ByteBuffer(outputBuffer || buffer_1.Buffer.allocUnsafe(outputSize));
+    const output = new ByteBuffer(outputBuffer || new Uint8Array(outputSize));
     // TODO output.limit(outputSize)
     if (output.length < outputSize) {
         throw new errors_1.CramMalformedError(`Output buffer too small to fit ${outputSize} bytes.`);

package/dist/rans/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.ts"],"names":[],"mappings":";;;;;AA6MA,6BA2CC;AAxPD,cAAc;AACd,sCAA8C;AAC9C,gDAAuB;AACvB,gDAAuB;AACvB,0DAAiC;AACjC,+CAAwD;AAExD,wCAAwC;AACxC,6CAA6C;AAC7C,MAAM,SAAS,CAAC,eAAe,GAAG,CAAC,CAAA;AACnC,uCAAuC;AACvC,iEAAiE;AAEjE,eAAe;AACf,iBAAiB;AAEjB,oDAAoD;AACpD,gBAAgB;AAChB,4CAA4C;AAC5C,6DAA6D;AAC7D,0EAA0E;AAC1E,YAAY;AACZ,QAAQ;AACR,IAAI;AAEJ,gGAAgG;AAChG,kCAAkC;AAClC,+BAA+B;AAE/B,iCAAiC;AACjC,iDAAiD;AAEjD,uBAAuB;AACvB,qBAAqB;AACrB,qDAAqD;AACrD,oBAAoB;AACpB,qDAAqD;AAErD,mBAAmB;AACnB,0EAA0E;AAC1E,QAAQ;AACR,IAAI;AAEJ,oEAAoE;AACpE,+EAA+E;AAC/E,yFAAyF;AACzF,2BAA2B;AAC3B,sDAAsD;AACtD,gDAAgD;AAChD,mEAAmE;AACnE,8CAA8C;AAC9C,sBAAsB;AACtB,IAAI;AAEJ,+DAA+D;AAC/D,qEAAqE;AACrE,mDAAmD;AACnD,oDAAoD;AACpD,2DAA2D;AAC3D,wCAAwC;AAExC,gEAAgE;AAChE,gEAAgE;AAEhE,6CAA6C;AAC7C,oFAAoF;AAEpF,sBAAsB;AACtB,2EAA2E;AAE3E,mEAAmE;AACnE,oCAAoC;AACpC,sBAAsB;AACtB,IAAI;AAEJ,+DAA+D;AAC/D,qEAAqE;AACrE,mDAAmD;AACnD,oDAAoD;AACpD,2DAA2D;AAC3D,wCAAwC;AAExC,kEAAkE;AAClE,kEAAkE;AAElE,6CAA6C;AAC7C,oFAAoF;AAEpF,sBAAsB;AACtB,2EAA2E;AAE3E,mEAAmE;AACnE,oCAAoC;AACpC,sBAAsB;AACtB,IAAI;AAEJ,kFAAkF;AAClF,8IAA8I;AAC9I,6DAA6D;AAC7D,sCAAsC;AACtC,oCAAoC;AACpC,8CAA8C;AAC9C,gEAAgE;AAChE,+DAA+D;AAC/D,sCAAsC;AACtC,kFAAkF;AAClF,8CAA8C;AAC9C,wBAAwB;AACxB,IAAI;AAEJ,SAAiC,oBAAoB;AACnD,uBAAuB,CAAC,KAAK;AAC7B,uBAAuB,CAAC,GAAG;IAE3B,wCAAwC;IACxC,MAAM,CAAC,GAAG,IAAI,kBAAQ,CAAC,UAAU,EAAE,CAAA;IACnC,MAAM,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACxC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,cAAc,EAAE,CAAA;IACzC,CAAC;IAED,IAAA,yBAAW,EAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,IAAA,aAAG,EAAC,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,CAAC,CAAA;IAExB,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,SAAiC,oBAAoB;AACnD,sBAAsB,CAAC,KAAK;AAC5B,sBAAsB,CAAC,MAAM;IAE7B,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACrC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,UAAU,EAAE,CAAA;IAClC,CAAC;IACD,MAAM,iCAAiC,CAAC,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IAC7D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACxC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC3C,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,cAAc,EAAE,CAAA;QAC5C,CAAC;IACH,CAAC;IACD,IAAA,yBAAW,EAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,IAAA,aAAG,EAAC,KAAK,EAAE,MAAM,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,OAAO,MAAM,CAAA;AACf,CAAC;AAED,mEAAmE;AACnE,MAAM,UAAU;IACd,YAAY,UAAU,EAAE,oBAAoB,GAAG,CAAC;QAC9C,IAAI,CAAC,OAAO,GAAG,UAAU,CAAA;QACzB,IAAI,CAAC,SAAS,GAAG,IAAI,QAAQ,CAAC,UAAU,CAAC,MAAM,CAAC,CAAA;QAChD,IAAI,CAAC,SAAS,GAAG,oBAAoB,CAAA;QACrC,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,GAAG;QACD,MAAM,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QACtC,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,CAAC,CAAA;IACV,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,GAAG,EAAE,CAAA;IACnB,CAAC;IAED,SAAS,CAAC,QAAQ;QAChB,OAAO,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;IAC/B,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,GAAG,CAAC,GAAG;QACL,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,GAAG,CAAA;QAClC,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,KAAK,CAAC,QAAQ,EAAE,GAAG;QACjB,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,GAAG,GAAG,CAAA;QAC5B,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,WAAW,CAAC,GAAG;QACb,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACpB,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,MAAM;QACJ,MAAM,CAAC,GAAG,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,CAAA;QACvD,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,CAAC,CAAA;IACV,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,SAAS,CAAA;IAC7C,CAAC;CACF;AAED,uEAAuE;AACvE,SAAwB,UAAU,CAChC,WAAW,EACX,YAAY,EACZ,oBAAoB,GAAG,CAAC;IAExB,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC7B,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACpB,OAAO,YAAY,CAAA;IACrB,CAAC;IAED,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,WAAW,EAAE,oBAAoB,CAAC,CAAA;IAC/D,wCAAwC;IAExC,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,EAAE,CAAA;IACzB,IAAI,KAAK,KAAK,CAAC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;QAC/B,MAAM,IAAI,2BAAkB,CAAC,sBAAsB,KAAK,EAAE,CAAC,CAAA;IAC7D,CAAC;IAED,MAAM,SAAS,CAAC,SAAS,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1C,IAAI,SAAS,KAAK,KAAK,CAAC,SAAS,EAAE,GAAG,eAAe,EAAE,CAAC;QACtD,MAAM,IAAI,2BAAkB,CAAC,yBAAyB,CAAC,CAAA;IACzD,CAAC;IAED,MAAM,SAAS,CAAC,UAAU,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC3C,MAAM,MAAM,GAAG,IAAI,UAAU,CAAC,YAAY,IAAI,IAAI,UAAU,CAAC,UAAU,CAAC,CAAC,CAAA;IACzE,gCAAgC;IAEhC,IAAI,MAAM,CAAC,MAAM,GAAG,UAAU,EAAE,CAAC;QAC/B,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,UAAU,SAAS,CACtD,CAAA;IACH,CAAC;IAED,QAAQ,KAAK,EAAE,CAAC;QACd,KAAK,CAAC;YACJ,OAAO,oBAAoB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAE5C,KAAK,CAAC;YACJ,OAAO,oBAAoB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAE5C;YACE,MAAM,IAAI,2BAAkB,CAAC,uBAAuB,KAAK,EAAE,CAAC,CAAA;IAChE,CAAC;AACH,CAAC"}

package/dist/unzip.d.ts

@@ -1 +1 @@
-export { gunzipSync as unzip } from 'zlib';
+export declare function unzip(input: Uint8Array): Uint8Array<ArrayBufferLike>;

package/dist/unzip.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.unzip = void 0;
-var zlib_1 = require("zlib");
-Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.gunzipSync; } });
+exports.unzip = unzip;
+const pako_1 = require("pako");
+function unzip(input) {
+    return (0, pako_1.inflate)(input);
+}
 //# sourceMappingURL=unzip.js.map

package/dist/unzip.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,6BAA0C;AAAjC,6FAAA,UAAU,OAAS"}
+{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;AAEA,sBAEC;AAJD,+BAA8B;AAE9B,SAAgB,KAAK,CAAC,KAAiB;IACrC,OAAO,IAAA,cAAO,EAAC,KAAK,CAAC,CAAA;AACvB,CAAC"}

package/esm/craiIndex.js

@@ -1,7 +1,7 @@
-import { unzip } from './unzip';
-import { open } from './io';
 import { CramMalformedError } from './errors';
-const BAI_MAGIC = 21578050; // BAI\1
+import { open } from './io';
+import { unzip } from './unzip';
+const BAI_MAGIC = 21_578_050; // BAI\1
 function addRecordToIndex(index, record) {
     const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record;
     const s = seqId;
@@ -17,10 +17,7 @@ function addRecordToIndex(index, record) {
     });
 }
 function maybeUnzip(data) {
-    if (data[0] === 31 && data[1] === 139) {
-        return unzip(data);
-    }
-    return data;
+    return data[0] === 31 && data[1] === 139 ? unzip(data) : data;
 }
 export default class CraiIndex {
     /**
@@ -36,14 +33,15 @@ export default class CraiIndex {
     async parseIndex() {
         const index = {};
         const uncompressedBuffer = maybeUnzip(await this.filehandle.readFile());
+        const dataView = new DataView(uncompressedBuffer.buffer);
         if (uncompressedBuffer.length > 4 &&
-            uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC) {
+            dataView.getUint32(0, true) === BAI_MAGIC) {
             throw new 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');
         }
-        // interpret the text as regular ascii, since it is
-        // 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.
+        // interpret the text as regular ascii, since it is 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.
         let currentRecord = [];
         let currentString = '';
         for (const charCode of uncompressedBuffer) {

package/esm/craiIndex.js.map

@@ -1 +1 @@
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package/esm/cramFile/codecs/_base.d.ts

@@ -1,5 +1,5 @@
-import CramSlice from '../slice';
 import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 import { DataType } from './dataSeriesTypes';
 export interface DataTypeMapping {
     byte: number;

package/esm/cramFile/codecs/beta.d.ts

@@ -1,7 +1,7 @@
 import CramCodec, { Cursors } from './_base';
-import CramSlice from '../slice';
-import { CramFileBlock } from '../file';
 import { BetaEncoding } from '../encoding';
+import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 export default class BetaCodec extends CramCodec<'int', BetaEncoding['parameters']> {
     constructor(parameters: BetaEncoding['parameters'], dataType: 'int');
     decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;

package/esm/cramFile/codecs/beta.js

@@ -1,6 +1,6 @@
-import { CramUnimplementedError } from '../../errors';
 import CramCodec from './_base';
 import { getBits } from './getBits';
+import { CramUnimplementedError } from '../../errors';
 export default class BetaCodec extends CramCodec {
     constructor(parameters, dataType) {
         super(parameters, dataType);

package/esm/cramFile/codecs/beta.js.map

@@ -1 +1 @@
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+{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAKrD,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,SAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,6CAA6C,CAC9D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,QAAQ,GAAG,OAAO,CACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;QACD,OAAO,QAAQ,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IAC1C,CAAC;CACF"}

package/esm/cramFile/codecs/byteArrayLength.d.ts

@@ -1,13 +1,13 @@
 import CramCodec, { Cursors } from './_base';
 import { ByteArrayLengthEncoding, CramEncoding } from '../encoding';
-import CramSlice from '../slice';
 import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 import { DataType } from './dataSeriesTypes';
 type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
 export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayLengthEncoding['parameters']> {
     private instantiateCodec;
     constructor(parameters: ByteArrayLengthEncoding['parameters'], dataType: 'byteArray', instantiateCodec: CramCodecFactory);
-    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array;
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array<ArrayBuffer>;
     _getLengthCodec(): CramCodec<"int", unknown>;
     _getDataCodec(): CramCodec<"byte", unknown>;
 }