@gmod/cram 1.5.9 → 1.6.2

package/esm/indexedCramFile.d.ts

@@ -0,0 +1,39 @@
+export default class IndexedCramFile {
+    /**
+     *
+     * @param {object} args
+     * @param {CramFile} args.cram
+     * @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
+     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
+     * @param {number} [args.fetchSizeLimit] optional maximum number of bytes to fetch in a single getRecordsForRange call.  Default 3 MiB.
+     * @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.
+     */
+    constructor(args: {
+        cram: CramFile;
+    });
+    cram: CramFile;
+    index: any;
+    fetchSizeLimit: any;
+    /**
+     *
+     * @param {number} seq numeric ID of the reference sequence
+     * @param {number} start start of the range of interest. 1-based closed coordinates.
+     * @param {number} end end of the range of interest. 1-based closed coordinates.
+     * @returns {Promise[Array[CramRecord]]}
+     */
+    getRecordsForRange(seq: number, start: number, end: number, opts?: {}): Promise<any>[any[][CramRecord]];
+    getRecordsInSlice({ containerStart, sliceStart, sliceBytes }: {
+        containerStart: any;
+        sliceStart: any;
+        sliceBytes: any;
+    }, filterFunction: any): Promise<any>;
+    /**
+     *
+     * @param {number} seqId
+     * @returns {Promise} true if the CRAM file contains data for the given
+     * reference sequence numerical ID
+     */
+    hasDataForReferenceSequence(seqId: number): Promise<any>;
+}
+import CramFile from "./cramFile";

package/esm/indexedCramFile.js

@@ -0,0 +1,155 @@
+import { CramUnimplementedError, CramSizeLimitError } from './errors';
+import CramFile from './cramFile';
+export default class IndexedCramFile {
+    /**
+     *
+     * @param {object} args
+     * @param {CramFile} args.cram
+     * @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
+     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
+     * @param {number} [args.fetchSizeLimit] optional maximum number of bytes to fetch in a single getRecordsForRange call.  Default 3 MiB.
+     * @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.
+     */
+    constructor(args) {
+        // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
+        if (args.cram) {
+            this.cram = args.cram;
+        }
+        else {
+            this.cram = new CramFile({
+                url: args.cramUrl,
+                path: args.cramPath,
+                filehandle: args.cramFilehandle,
+                seqFetch: args.seqFetch,
+                checkSequenceMD5: args.checkSequenceMD5,
+                cacheSize: args.cacheSize,
+            });
+        }
+        if (!(this.cram instanceof CramFile)) {
+            throw new Error('invalid arguments: no cramfile');
+        }
+        this.index = args.index;
+        if (!this.index.getEntriesForRange) {
+            throw new Error('invalid arguments: not an index');
+        }
+        this.fetchSizeLimit = args.fetchSizeLimit || 3000000;
+    }
+    /**
+     *
+     * @param {number} seq numeric ID of the reference sequence
+     * @param {number} start start of the range of interest. 1-based closed coordinates.
+     * @param {number} end end of the range of interest. 1-based closed coordinates.
+     * @returns {Promise[Array[CramRecord]]}
+     */
+    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 CramUnimplementedError('string sequence names not yet supported');
+        }
+        const seqId = seq;
+        const slices = await 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 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.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 (let i = 0; i < ret.length; i += 1) {
+                const name = ret[i].readName;
+                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 name = ret[i].readName;
+                if (unmatedPairs[name] &&
+                    ret[i].mate &&
+                    (ret[i].mate.sequenceId === seqId || opts.pairAcrossChr) &&
+                    Math.abs(ret[i].alignmentStart - ret[i].mate.alignmentStart) <
+                        opts.maxInsertSize) {
+                    const mateSlices = this.index.getEntriesForRange(ret[i].mate.sequenceId, ret[i].mate.alignmentStart, ret[i].mate.alignmentStart + 1);
+                    matePromises.push(mateSlices);
+                }
+            }
+            const mateBlocks = await 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 (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);
+        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
+     */
+    hasDataForReferenceSequence(seqId) {
+        return this.index.hasDataForReferenceSequence(seqId);
+    }
+}
+//# sourceMappingURL=indexedCramFile.js.map

package/esm/indexedCramFile.js.map

@@ -0,0 +1 @@
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package/esm/io/bufferCache.d.ts

@@ -0,0 +1,12 @@
+export default class BufferCache {
+    constructor({ fetch, size, chunkSize }: {
+        fetch: any;
+        size?: number | undefined;
+        chunkSize?: number | undefined;
+    });
+    fetch: any;
+    chunkSize: number;
+    lruCache: any;
+    get(outputBuffer: any, offset: any, length: any, position: any): Promise<void>;
+    _getChunk(chunkNumber: any): any;
+}

package/esm/io/bufferCache.js

@@ -0,0 +1,54 @@
+import LRU from 'quick-lru';
+export default class BufferCache {
+    constructor({ fetch, size = 10000000, chunkSize = 32768 }) {
+        if (!fetch) {
+            throw new Error('fetch function required');
+        }
+        this.fetch = fetch;
+        this.chunkSize = chunkSize;
+        this.lruCache = new LRU({ maxSize: Math.floor(size / chunkSize) });
+    }
+    async get(outputBuffer, offset, length, position) {
+        if (outputBuffer.length < offset + length) {
+            throw new Error('output buffer not big enough for request');
+        }
+        // calculate the list of chunks involved in this fetch
+        const firstChunk = Math.floor(position / this.chunkSize);
+        const lastChunk = Math.floor((position + length) / this.chunkSize);
+        // fetch them all as necessary
+        const fetches = new Array(lastChunk - firstChunk + 1);
+        for (let chunk = firstChunk; chunk <= lastChunk; chunk += 1) {
+            fetches[chunk - firstChunk] = this._getChunk(chunk).then(data => ({
+                data,
+                chunkNumber: chunk,
+            }));
+        }
+        // stitch together the response buffer using them
+        const chunks = await Promise.all(fetches);
+        const chunksOffset = position - chunks[0].chunkNumber * this.chunkSize;
+        chunks.forEach(({ data, chunkNumber }) => {
+            const chunkPositionStart = chunkNumber * this.chunkSize;
+            let copyStart = 0;
+            let copyEnd = this.chunkSize;
+            let copyOffset = offset + (chunkNumber - firstChunk) * this.chunkSize - chunksOffset;
+            if (chunkNumber === firstChunk) {
+                copyOffset = offset;
+                copyStart = chunksOffset;
+            }
+            if (chunkNumber === lastChunk) {
+                copyEnd = position + length - chunkPositionStart;
+            }
+            data.copy(outputBuffer, copyOffset, copyStart, copyEnd);
+        });
+    }
+    _getChunk(chunkNumber) {
+        const cachedPromise = this.lruCache.get(chunkNumber);
+        if (cachedPromise) {
+            return cachedPromise;
+        }
+        const freshPromise = this.fetch(chunkNumber * this.chunkSize, this.chunkSize);
+        this.lruCache.set(chunkNumber, freshPromise);
+        return freshPromise;
+    }
+}
+//# sourceMappingURL=bufferCache.js.map

package/esm/io/bufferCache.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"bufferCache.js","sourceRoot":"","sources":["../../src/io/bufferCache.js"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,WAAW,CAAA;AAE3B,MAAM,CAAC,OAAO,OAAO,WAAW;IAC9B,YAAY,EAAE,KAAK,EAAE,IAAI,GAAG,QAAQ,EAAE,SAAS,GAAG,KAAK,EAAE;QACvD,IAAI,CAAC,KAAK,EAAE;YACV,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;SAC3C;QACD,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;QAClB,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;QAC1B,IAAI,CAAC,QAAQ,GAAG,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,GAAG,SAAS,CAAC,EAAE,CAAC,CAAA;IACpE,CAAC;IAED,KAAK,CAAC,GAAG,CAAC,YAAY,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ;QAC9C,IAAI,YAAY,CAAC,MAAM,GAAG,MAAM,GAAG,MAAM,EAAE;YACzC,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAA;SAC5D;QAED,sDAAsD;QACtD,MAAM,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,CAAA;QACxD,MAAM,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,QAAQ,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,SAAS,CAAC,CAAA;QAElE,8BAA8B;QAC9B,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,SAAS,GAAG,UAAU,GAAG,CAAC,CAAC,CAAA;QACrD,KAAK,IAAI,KAAK,GAAG,UAAU,EAAE,KAAK,IAAI,SAAS,EAAE,KAAK,IAAI,CAAC,EAAE;YAC3D,OAAO,CAAC,KAAK,GAAG,UAAU,CAAC,GAAG,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBAChE,IAAI;gBACJ,WAAW,EAAE,KAAK;aACnB,CAAC,CAAC,CAAA;SACJ;QAED,iDAAiD;QACjD,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QACzC,MAAM,YAAY,GAAG,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,SAAS,CAAA;QACtE,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,EAAE,EAAE;YACvC,MAAM,kBAAkB,GAAG,WAAW,GAAG,IAAI,CAAC,SAAS,CAAA;YACvD,IAAI,SAAS,GAAG,CAAC,CAAA;YACjB,IAAI,OAAO,GAAG,IAAI,CAAC,SAAS,CAAA;YAC5B,IAAI,UAAU,GACZ,MAAM,GAAG,CAAC,WAAW,GAAG,UAAU,CAAC,GAAG,IAAI,CAAC,SAAS,GAAG,YAAY,CAAA;YAErE,IAAI,WAAW,KAAK,UAAU,EAAE;gBAC9B,UAAU,GAAG,MAAM,CAAA;gBACnB,SAAS,GAAG,YAAY,CAAA;aACzB;YACD,IAAI,WAAW,KAAK,SAAS,EAAE;gBAC7B,OAAO,GAAG,QAAQ,GAAG,MAAM,GAAG,kBAAkB,CAAA;aACjD;YAED,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,UAAU,EAAE,SAAS,EAAE,OAAO,CAAC,CAAA;QACzD,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,SAAS,CAAC,WAAW;QACnB,MAAM,aAAa,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;QACpD,IAAI,aAAa,EAAE;YACjB,OAAO,aAAa,CAAA;SACrB;QAED,MAAM,YAAY,GAAG,IAAI,CAAC,KAAK,CAC7B,WAAW,GAAG,IAAI,CAAC,SAAS,EAC5B,IAAI,CAAC,SAAS,CACf,CAAA;QACD,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;QAC5C,OAAO,YAAY,CAAA;IACrB,CAAC;CACF"}

package/esm/io/index.d.ts

@@ -0,0 +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 };

package/esm/io/index.js

@@ -0,0 +1,24 @@
+import url from 'url';
+import RemoteFile from './remoteFile';
+import LocalFile from './localFile';
+function fromUrl(source) {
+    const { protocol, pathname } = url.parse(source);
+    if (protocol === 'file:') {
+        return new LocalFile(unescape(pathname));
+    }
+    return new RemoteFile(source);
+}
+function open(maybeUrl, maybePath, maybeFilehandle) {
+    if (maybeFilehandle) {
+        return maybeFilehandle;
+    }
+    if (maybeUrl) {
+        return fromUrl(maybeUrl);
+    }
+    if (maybePath) {
+        return new LocalFile(maybePath);
+    }
+    throw new Error('no url, path, or filehandle provided, cannot open');
+}
+export { LocalFile, RemoteFile, fromUrl, open };
+//# sourceMappingURL=index.js.map

package/esm/io/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.js"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,KAAK,CAAA;AACrB,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,SAAS,OAAO,CAAC,MAAM;IACrB,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAChD,IAAI,QAAQ,KAAK,OAAO,EAAE;QACxB,OAAO,IAAI,SAAS,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,CAAA;KACzC;IACD,OAAO,IAAI,UAAU,CAAC,MAAM,CAAC,CAAA;AAC/B,CAAC;AAED,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,SAAS,CAAC,SAAS,CAAC,CAAA;KAChC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAED,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,OAAO,EAAE,IAAI,EAAE,CAAA"}

package/esm/io/localFile.d.ts

@@ -0,0 +1,10 @@
+export default class LocalFile {
+    constructor(source: any);
+    position: number;
+    filename: any;
+    fd: any;
+    read(buffer: any, offset: number | undefined, length: any, position: any): Promise<any>;
+    readFile(): Promise<any>;
+    stat(): Promise<any>;
+    _stat: any;
+}

package/esm/io/localFile.js

@@ -0,0 +1,31 @@
+import { promisify } from 'es6-promisify';
+import fs from 'fs';
+const fsOpen = fs && promisify(fs.open);
+const fsRead = fs && promisify(fs.read);
+const fsFStat = fs && promisify(fs.fstat);
+const fsReadFile = fs && promisify(fs.readFile);
+export default class LocalFile {
+    constructor(source) {
+        this.position = 0;
+        this.filename = source;
+        this.fd = fsOpen(this.filename, 'r');
+    }
+    async read(buffer, offset = 0, length, position) {
+        let readPosition = position;
+        if (readPosition === null) {
+            readPosition = this.position;
+            this.position += length;
+        }
+        return fsRead(await this.fd, buffer, offset, length, position);
+    }
+    async readFile() {
+        return fsReadFile(await this.fd);
+    }
+    async stat() {
+        if (!this._stat) {
+            this._stat = await fsFStat(await this.fd);
+        }
+        return this._stat;
+    }
+}
+//# sourceMappingURL=localFile.js.map

package/esm/io/localFile.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"localFile.js","sourceRoot":"","sources":["../../src/io/localFile.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACzC,OAAO,EAAE,MAAM,IAAI,CAAA;AAEnB,MAAM,MAAM,GAAG,EAAE,IAAI,SAAS,CAAC,EAAE,CAAC,IAAI,CAAC,CAAA;AACvC,MAAM,MAAM,GAAG,EAAE,IAAI,SAAS,CAAC,EAAE,CAAC,IAAI,CAAC,CAAA;AACvC,MAAM,OAAO,GAAG,EAAE,IAAI,SAAS,CAAC,EAAE,CAAC,KAAK,CAAC,CAAA;AACzC,MAAM,UAAU,GAAG,EAAE,IAAI,SAAS,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAA;AAE/C,MAAM,CAAC,OAAO,OAAO,SAAS;IAC5B,YAAY,MAAM;QAChB,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;QACjB,IAAI,CAAC,QAAQ,GAAG,MAAM,CAAA;QACtB,IAAI,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;IACtC,CAAC;IAED,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,GAAG,CAAC,EAAE,MAAM,EAAE,QAAQ;QAC7C,IAAI,YAAY,GAAG,QAAQ,CAAA;QAC3B,IAAI,YAAY,KAAK,IAAI,EAAE;YACzB,YAAY,GAAG,IAAI,CAAC,QAAQ,CAAA;YAC5B,IAAI,CAAC,QAAQ,IAAI,MAAM,CAAA;SACxB;QACD,OAAO,MAAM,CAAC,MAAM,IAAI,CAAC,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;IAChE,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,OAAO,UAAU,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAA;IAClC,CAAC;IAED,KAAK,CAAC,IAAI;QACR,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE;YACf,IAAI,CAAC,KAAK,GAAG,MAAM,OAAO,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAA;SAC1C;QACD,OAAO,IAAI,CAAC,KAAK,CAAA;IACnB,CAAC;CACF"}

package/esm/io/remoteFile.d.ts

@@ -0,0 +1,16 @@
+export default class RemoteFile {
+    constructor(source: any);
+    position: number;
+    url: any;
+    cache: BufferCache;
+    _fetch(position: any, length: any): Promise<Buffer>;
+    _stat: {
+        size: number;
+    } | undefined;
+    read(buffer: any, offset?: number, length?: number, position?: number): Promise<void>;
+    readFile(): Promise<Buffer>;
+    stat(): Promise<{
+        size: number;
+    }>;
+}
+import BufferCache from "./bufferCache";

package/esm/io/remoteFile.js

@@ -0,0 +1,64 @@
+import fetch from 'cross-fetch';
+import BufferCache from './bufferCache';
+export default class RemoteFile {
+    constructor(source) {
+        this.position = 0;
+        this.url = source;
+        this.cache = new BufferCache({
+            fetch: (start, length) => this._fetch(start, length),
+        });
+    }
+    async _fetch(position, length) {
+        const headers = {};
+        if (length < Infinity) {
+            headers.range = `bytes=${position}-${position + length}`;
+        }
+        else if (length === Infinity && position !== 0) {
+            headers.range = `bytes=${position}-`;
+        }
+        const response = await fetch(this.url, {
+            method: 'GET',
+            headers,
+            redirect: 'follow',
+            mode: 'cors',
+        });
+        if ((response.status === 200 && position === 0) ||
+            response.status === 206) {
+            const nodeBuffer = Buffer.from(await response.arrayBuffer());
+            // try to parse out the size of the remote file
+            const sizeMatch = /\/(\d+)$/.exec(response.headers.get('content-range'));
+            if (sizeMatch[1]) {
+                this._stat = { size: parseInt(sizeMatch[1], 10) };
+            }
+            return nodeBuffer;
+        }
+        throw new Error(`HTTP ${response.status} fetching ${this.url}`);
+    }
+    read(buffer, offset = 0, length = Infinity, position = 0) {
+        let readPosition = position;
+        if (readPosition === null) {
+            readPosition = this.position;
+            this.position += length;
+        }
+        return this.cache.get(buffer, offset, length, position);
+    }
+    async readFile() {
+        const response = await fetch(this.url, {
+            method: 'GET',
+            redirect: 'follow',
+            mode: 'cors',
+        });
+        return Buffer.from(await response.arrayBuffer());
+    }
+    async stat() {
+        if (!this._stat) {
+            const buf = Buffer.allocUnsafe(10);
+            await this.read(buf, 0, 10, 0);
+            if (!this._stat) {
+                throw new Error(`unable to determine size of file at ${this.url}`);
+            }
+        }
+        return this._stat;
+    }
+}
+//# sourceMappingURL=remoteFile.js.map

package/esm/io/remoteFile.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"remoteFile.js","sourceRoot":"","sources":["../../src/io/remoteFile.js"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,aAAa,CAAA;AAC/B,OAAO,WAAW,MAAM,eAAe,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,UAAU;IAC7B,YAAY,MAAM;QAChB,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;QACjB,IAAI,CAAC,GAAG,GAAG,MAAM,CAAA;QACjB,IAAI,CAAC,KAAK,GAAG,IAAI,WAAW,CAAC;YAC3B,KAAK,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC;SACrD,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,QAAQ,EAAE,MAAM;QAC3B,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,IAAI,MAAM,GAAG,QAAQ,EAAE;YACrB,OAAO,CAAC,KAAK,GAAG,SAAS,QAAQ,IAAI,QAAQ,GAAG,MAAM,EAAE,CAAA;SACzD;aAAM,IAAI,MAAM,KAAK,QAAQ,IAAI,QAAQ,KAAK,CAAC,EAAE;YAChD,OAAO,CAAC,KAAK,GAAG,SAAS,QAAQ,GAAG,CAAA;SACrC;QACD,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,IAAI,CAAC,GAAG,EAAE;YACrC,MAAM,EAAE,KAAK;YACb,OAAO;YACP,QAAQ,EAAE,QAAQ;YAClB,IAAI,EAAE,MAAM;SACb,CAAC,CAAA;QACF,IACE,CAAC,QAAQ,CAAC,MAAM,KAAK,GAAG,IAAI,QAAQ,KAAK,CAAC,CAAC;YAC3C,QAAQ,CAAC,MAAM,KAAK,GAAG,EACvB;YACA,MAAM,UAAU,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,QAAQ,CAAC,WAAW,EAAE,CAAC,CAAA;YAE5D,+CAA+C;YAC/C,MAAM,SAAS,GAAG,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC,CAAA;YACxE,IAAI,SAAS,CAAC,CAAC,CAAC,EAAE;gBAChB,IAAI,CAAC,KAAK,GAAG,EAAE,IAAI,EAAE,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,EAAE,CAAA;aAClD;YAED,OAAO,UAAU,CAAA;SAClB;QACD,MAAM,IAAI,KAAK,CAAC,QAAQ,QAAQ,CAAC,MAAM,aAAa,IAAI,CAAC,GAAG,EAAE,CAAC,CAAA;IACjE,CAAC;IAED,IAAI,CAAC,MAAM,EAAE,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,QAAQ,EAAE,QAAQ,GAAG,CAAC;QACtD,IAAI,YAAY,GAAG,QAAQ,CAAA;QAC3B,IAAI,YAAY,KAAK,IAAI,EAAE;YACzB,YAAY,GAAG,IAAI,CAAC,QAAQ,CAAA;YAC5B,IAAI,CAAC,QAAQ,IAAI,MAAM,CAAA;SACxB;QACD,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;IACzD,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,IAAI,CAAC,GAAG,EAAE;YACrC,MAAM,EAAE,KAAK;YACb,QAAQ,EAAE,QAAQ;YAClB,IAAI,EAAE,MAAM;SACb,CAAC,CAAA;QACF,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,QAAQ,CAAC,WAAW,EAAE,CAAC,CAAA;IAClD,CAAC;IAED,KAAK,CAAC,IAAI;QACR,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE;YACf,MAAM,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YAClC,MAAM,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;YAC9B,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE;gBACf,MAAM,IAAI,KAAK,CAAC,uCAAuC,IAAI,CAAC,GAAG,EAAE,CAAC,CAAA;aACnE;SACF;QACD,OAAO,IAAI,CAAC,KAAK,CAAA;IACnB,CAAC;CACF"}

package/esm/rans/constants.d.ts

@@ -0,0 +1,3 @@
+export const TF_SHIFT: 12;
+export const TOTFREQ: number;
+export const RANS_BYTE_L: number;

package/esm/rans/constants.js

@@ -0,0 +1,5 @@
+const TF_SHIFT = 12;
+const TOTFREQ = 1 << TF_SHIFT;
+const RANS_BYTE_L = 1 << 23;
+export { TF_SHIFT, TOTFREQ, RANS_BYTE_L };
+//# sourceMappingURL=constants.js.map

package/esm/rans/constants.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/rans/constants.js"],"names":[],"mappings":"AAAA,MAAM,QAAQ,GAAG,EAAE,CAAA;AACnB,MAAM,OAAO,GAAG,CAAC,IAAI,QAAQ,CAAA;AAC7B,MAAM,WAAW,GAAG,CAAC,IAAI,EAAE,CAAA;AAE3B,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,CAAA"}

package/esm/rans/d04.d.ts

@@ -0,0 +1 @@
+export default function uncompress(input: any, D: any, syms: any, out: any): void;

package/esm/rans/d04.js

@@ -0,0 +1,67 @@
+import { CramMalformedError } from '../errors';
+import { TF_SHIFT } from './constants';
+import Decoding from './decoding';
+export default function uncompress(
+/* ByteBuffer */ input, 
+/* Decoding.AriDecoder */ D, 
+/* Decoding.Symbol[] */ syms, 
+/* ByteBuffer */ out) {
+    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.get(rans0, TF_SHIFT)];
+        const /* byte */ c1 = D.R[Decoding.get(rans1, TF_SHIFT)];
+        const /* byte */ c2 = D.R[Decoding.get(rans2, TF_SHIFT)];
+        const /* byte */ c3 = D.R[Decoding.get(rans3, TF_SHIFT)];
+        out.putAt(i, c0);
+        out.putAt(i + 1, c1);
+        out.putAt(i + 2, c2);
+        out.putAt(i + 3, c3);
+        rans0 = Decoding.advanceSymbolStep(rans0, syms[0xff & c0], TF_SHIFT);
+        rans1 = Decoding.advanceSymbolStep(rans1, syms[0xff & c1], TF_SHIFT);
+        rans2 = Decoding.advanceSymbolStep(rans2, syms[0xff & c2], TF_SHIFT);
+        rans3 = Decoding.advanceSymbolStep(rans3, syms[0xff & c3], TF_SHIFT);
+        rans0 = Decoding.renormalize(rans0, input);
+        rans1 = Decoding.renormalize(rans1, input);
+        rans2 = Decoding.renormalize(rans2, input);
+        rans3 = Decoding.renormalize(rans3, input);
+    }
+    out.setPosition(outputEnd);
+    let /* byte */ c;
+    switch (outputSize & 3) {
+        case 0:
+            break;
+        case 1:
+            c = D.R[Decoding.get(rans0, TF_SHIFT)];
+            Decoding.advanceSymbol(rans0, input, syms[0xff & c], TF_SHIFT);
+            out.put(c);
+            break;
+        case 2:
+            c = D.R[Decoding.get(rans0, TF_SHIFT)];
+            Decoding.advanceSymbol(rans0, input, syms[0xff & c], TF_SHIFT);
+            out.put(c);
+            c = D.R[Decoding.get(rans1, TF_SHIFT)];
+            Decoding.advanceSymbol(rans1, input, syms[0xff & c], TF_SHIFT);
+            out.put(c);
+            break;
+        case 3:
+            c = D.R[Decoding.get(rans0, TF_SHIFT)];
+            Decoding.advanceSymbol(rans0, input, syms[0xff & c], TF_SHIFT);
+            out.put(c);
+            c = D.R[Decoding.get(rans1, TF_SHIFT)];
+            Decoding.advanceSymbol(rans1, input, syms[0xff & c], TF_SHIFT);
+            out.put(c);
+            c = D.R[Decoding.get(rans2, TF_SHIFT)];
+            Decoding.advanceSymbol(rans2, input, syms[0xff & c], TF_SHIFT);
+            out.put(c);
+            break;
+        default:
+            throw new CramMalformedError('invalid output size encountered during rANS decoding');
+    }
+    out.setPosition(0);
+}
+//# sourceMappingURL=d04.js.map

package/esm/rans/d04.js.map

@@ -0,0 +1 @@
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package/esm/rans/d14.d.ts

@@ -0,0 +1 @@
+export default function uncompress(input: any, output: any, D: any, syms: any): void;

package/esm/rans/d14.js

@@ -0,0 +1,52 @@
+import { TF_SHIFT } from './constants';
+import Decoding from './decoding';
+export default function uncompress(
+/* ByteBuffer */ input, 
+/* ByteBuffer */ output, 
+/* Decoding.AriDecoder[] */ D, 
+/* Decoding.Symbol[][] */ syms) {
+    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) {
+        const /* int */ c0 = 0xff & D[l0].R[Decoding.get(rans0, TF_SHIFT)];
+        const /* int */ c1 = 0xff & D[l1].R[Decoding.get(rans1, TF_SHIFT)];
+        const /* int */ c2 = 0xff & D[l2].R[Decoding.get(rans2, TF_SHIFT)];
+        const /* int */ c7 = 0xff & D[l7].R[Decoding.get(rans7, TF_SHIFT)];
+        output.putAt(i0, c0);
+        output.putAt(i1, c1);
+        output.putAt(i2, c2);
+        output.putAt(i7, c7);
+        rans0 = Decoding.advanceSymbolStep(rans0, syms[l0][c0], TF_SHIFT);
+        rans1 = Decoding.advanceSymbolStep(rans1, syms[l1][c1], TF_SHIFT);
+        rans2 = Decoding.advanceSymbolStep(rans2, syms[l2][c2], TF_SHIFT);
+        rans7 = Decoding.advanceSymbolStep(rans7, syms[l7][c7], TF_SHIFT);
+        rans0 = Decoding.renormalize(rans0, input);
+        rans1 = Decoding.renormalize(rans1, input);
+        rans2 = Decoding.renormalize(rans2, input);
+        rans7 = Decoding.renormalize(rans7, input);
+        l0 = c0;
+        l1 = c1;
+        l2 = c2;
+        l7 = c7;
+    }
+    // Remainder
+    for (; i7 < outputSize; i7 += 1) {
+        const /* int */ c7 = 0xff & D[l7].R[Decoding.get(rans7, TF_SHIFT)];
+        output.putAt(i7, c7);
+        rans7 = Decoding.advanceSymbol(rans7, input, syms[l7][c7], TF_SHIFT);
+        l7 = c7;
+    }
+}
+//# sourceMappingURL=d14.js.map

package/esm/rans/d14.js.map

@@ -0,0 +1 @@
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package/esm/rans/decoding.d.ts

@@ -0,0 +1,30 @@
+export default Decode;
+declare namespace Decode {
+    export { FC };
+    export { AriDecoder };
+    export { Symbol };
+    export { symbolInit };
+    export { advanceStep };
+    export { advanceSymbolStep };
+    export { get };
+    export { advanceSymbol };
+    export { renormalize };
+}
+declare class FC {
+    F: any;
+    C: any;
+}
+declare class AriDecoder {
+    fc: any[];
+    R: any;
+}
+declare class Symbol {
+    start: any;
+    freq: any;
+}
+declare function symbolInit(sym: any, start: any, freq: any): void;
+declare function advanceStep(r: any, start: any, freq: any, scaleBits: any): number;
+declare function advanceSymbolStep(r: any, sym: any, scaleBits: any): number;
+declare function get(r: any, scaleBits: any): number;
+declare function advanceSymbol(r: any, pptr: any, sym: any, scaleBits: any): any;
+declare function renormalize(r: any, pptr: any): any;