npm - @gmod/cram - Versions diffs - 2.0.3 → 3.0.0 - Mend

@gmod/cram 2.0.3 → 3.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (118) hide show

package/CHANGELOG.md +10 -0
package/README.md +0 -4
package/dist/craiIndex.js +1 -1
package/dist/craiIndex.js.map +1 -1
package/dist/cram-bundle.js +1 -1
package/dist/cram-bundle.js.LICENSE.txt +0 -2
package/dist/cramFile/codecs/byteArrayLength.js +1 -1
package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
package/dist/cramFile/codecs/byteArrayStop.d.ts +0 -1
package/dist/cramFile/codecs/external.js +1 -1
package/dist/cramFile/codecs/external.js.map +1 -1
package/dist/cramFile/codecs/getBits.d.ts +0 -1
package/dist/cramFile/codecs/getBits.js +2 -2
package/dist/cramFile/codecs/getBits.js.map +1 -1
package/dist/cramFile/codecs/huffman.js +2 -1
package/dist/cramFile/codecs/huffman.js.map +1 -1
package/dist/cramFile/codecs/index.js +1 -2
package/dist/cramFile/codecs/index.js.map +1 -1
package/dist/cramFile/container/compressionScheme.d.ts +0 -3
package/dist/cramFile/container/compressionScheme.js +0 -4
package/dist/cramFile/container/compressionScheme.js.map +1 -1
package/dist/cramFile/container/index.d.ts +57 -5
package/dist/cramFile/container/index.js +15 -9
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/file.d.ts +24 -61
package/dist/cramFile/file.js +23 -28
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.d.ts +1 -1
package/dist/cramFile/sectionParsers.d.ts +195 -49
package/dist/cramFile/sectionParsers.js +622 -304
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +1 -1
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.d.ts +23 -1
package/dist/cramFile/slice/index.js +9 -6
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.d.ts +6 -6
package/dist/cramFile/util.js +93 -12
package/dist/cramFile/util.js.map +1 -1
package/dist/indexedCramFile.d.ts +0 -3
package/dist/indexedCramFile.js +4 -16
package/dist/indexedCramFile.js.map +1 -1
package/dist/io/index.d.ts +1 -3
package/dist/io/index.js +3 -16
package/dist/io/index.js.map +1 -1
package/dist/rans/d04.js +1 -1
package/dist/rans/d04.js.map +1 -1
package/dist/rans/d14.js +1 -1
package/dist/rans/d14.js.map +1 -1
package/dist/rans/frequencies.js +2 -3
package/dist/rans/frequencies.js.map +1 -1
package/dist/rans/index.js +1 -1
package/dist/rans/index.js.map +1 -1
package/dist/sam.js +1 -2
package/dist/sam.js.map +1 -1
package/dist/typescript.d.ts +0 -1
package/dist/typescript.js +0 -8
package/dist/typescript.js.map +1 -1
package/dist/unzip-pako.d.ts +0 -1
package/dist/unzip-pako.js +1 -2
package/dist/unzip-pako.js.map +1 -1
package/dist/unzip.d.ts +0 -1
package/esm/craiIndex.js +1 -1
package/esm/craiIndex.js.map +1 -1
package/esm/cramFile/codecs/byteArrayLength.js +1 -1
package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
package/esm/cramFile/codecs/byteArrayStop.d.ts +0 -1
package/esm/cramFile/codecs/external.js +1 -1
package/esm/cramFile/codecs/external.js.map +1 -1
package/esm/cramFile/codecs/getBits.d.ts +0 -1
package/esm/cramFile/codecs/huffman.js +2 -1
package/esm/cramFile/codecs/huffman.js.map +1 -1
package/esm/cramFile/container/compressionScheme.d.ts +0 -3
package/esm/cramFile/container/compressionScheme.js +0 -4
package/esm/cramFile/container/compressionScheme.js.map +1 -1
package/esm/cramFile/container/index.d.ts +57 -5
package/esm/cramFile/container/index.js +15 -9
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/file.d.ts +24 -61
package/esm/cramFile/file.js +22 -25
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/record.d.ts +1 -1
package/esm/cramFile/sectionParsers.d.ts +195 -49
package/esm/cramFile/sectionParsers.js +620 -303
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/index.d.ts +23 -1
package/esm/cramFile/slice/index.js +10 -7
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.d.ts +6 -6
package/esm/cramFile/util.js +87 -6
package/esm/cramFile/util.js.map +1 -1
package/esm/indexedCramFile.d.ts +0 -3
package/esm/indexedCramFile.js +3 -15
package/esm/indexedCramFile.js.map +1 -1
package/esm/io/index.d.ts +1 -3
package/esm/io/index.js +2 -11
package/esm/io/index.js.map +1 -1
package/esm/typescript.d.ts +0 -1
package/esm/typescript.js +1 -6
package/esm/typescript.js.map +1 -1
package/esm/unzip-pako.d.ts +0 -1
package/esm/unzip.d.ts +0 -1
package/package.json +9 -15
package/src/craiIndex.ts +1 -1
package/src/cramFile/codecs/byteArrayLength.ts +1 -2
package/src/cramFile/codecs/external.ts +1 -1
package/src/cramFile/codecs/huffman.ts +2 -1
package/src/cramFile/container/compressionScheme.ts +1 -8
package/src/cramFile/container/index.ts +21 -10
package/src/cramFile/file.ts +28 -43
package/src/cramFile/record.ts +1 -1
package/src/cramFile/sectionParsers.ts +668 -390
package/src/cramFile/slice/index.ts +11 -5
package/src/cramFile/util.ts +90 -91
package/src/indexedCramFile.ts +3 -25
package/src/io/index.ts +2 -12
package/src/typescript.ts +0 -7
package/src/typings/binary-parser.d.ts +0 -44

package/dist/cramFile/sectionParsers.js.map CHANGED Viewed

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package/dist/cramFile/slice/decodeRecord.js CHANGED Viewed

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = decodeRecord;
 const long_1 = __importDefault(require("long"));
 const errors_1 = require("../../errors");
 const record_1 = require("../record");
@@ -337,5 +338,4 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         tags,
     };
 }
-exports.default = decodeRecord;
 //# sourceMappingURL=decodeRecord.js.map

package/dist/cramFile/slice/decodeRecord.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/cramFile/slice/index.d.ts CHANGED Viewed

@@ -10,7 +10,29 @@ export default class CramSlice {
     containerPosition: number;
     private file;
     constructor(container: CramContainer, containerPosition: number, _unused: number);
-    getHeader(): Promise<SliceHeader>;
+    getHeader(): Promise<{
+        parsedContent: {
+            recordCounter: number;
+            md5: [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number] | undefined;
+            contentIds: number[];
+            numContentIds: number;
+            numBlocks: number;
+            numRecords: number;
+        } & {
+            _endPosition: number;
+            _size: number;
+        };
+        compressionMethod: import("../sectionParsers").CompressionMethod;
+        contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
+        contentId: number;
+        compressedSize: number;
+        uncompressedSize: number;
+        _endPosition: number;
+        contentPosition: number;
+        _size: number;
+        content: Buffer;
+        crc32?: number;
+    }>;
     getBlocks(): Promise<CramFileBlock[]>;
     getCoreDataBlock(): Promise<CramFileBlock>;
     _getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;

package/dist/cramFile/slice/index.js CHANGED Viewed

@@ -147,8 +147,12 @@ class CramSlice {
     getHeader() {
         return __awaiter(this, void 0, void 0, function* () {
             // fetch and parse the slice header
-            const sectionParsers = yield this.file.getSectionParsers();
+            const { majorVersion } = yield this.file.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const containerHeader = yield this.container.getHeader();
+            if (!containerHeader) {
+                throw new Error('no container header detected');
+            }
             const header = yield this.file.readBlock(containerHeader._endPosition + this.containerPosition);
             if (header === undefined) {
                 throw new Error('block header undefined');
@@ -173,7 +177,7 @@ class CramSlice {
             // read all the blocks into memory and store them
             let blockPosition = header._endPosition;
             const blocks = new Array(header.parsedContent.numBlocks);
-            for (let i = 0; i < blocks.length; i += 1) {
+            for (let i = 0; i < blocks.length; i++) {
                 const block = yield this.file.readBlock(blockPosition);
                 if (block === undefined) {
                     throw new Error('block undefined');
@@ -266,6 +270,7 @@ class CramSlice {
     }
     _fetchRecords() {
         return __awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             const { majorVersion } = yield this.file.getDefinition();
             const compressionScheme = yield this.container.getCompressionScheme();
             if (compressionScheme === undefined) {
@@ -281,14 +286,12 @@ class CramSlice {
                 this.file.options.checkSequenceMD5 &&
                 (0, sectionParsers_1.isMappedSliceHeader)(sliceHeader.parsedContent) &&
                 sliceHeader.parsedContent.refSeqId >= 0 &&
-                sliceHeader.parsedContent.md5.join('') !== '0000000000000000') {
+                ((_a = sliceHeader.parsedContent.md5) === null || _a === void 0 ? void 0 : _a.join('')) !== '0000000000000000') {
                 const refRegion = yield this.getReferenceRegion();
                 if (refRegion) {
                     const { seq, start, end } = refRegion;
                     const seqMd5 = (0, util_1.sequenceMD5)(seq);
-                    const storedMd5 = sliceHeader.parsedContent.md5
-                        .map(byte => (byte < 16 ? '0' : '') + byte.toString(16))
-                        .join('');
+                    const storedMd5 = (_b = sliceHeader.parsedContent.md5) === null || _b === void 0 ? void 0 : _b.map(byte => (byte < 16 ? '0' : '') + byte.toString(16)).join('');
                     if (seqMd5 !== storedMd5) {
                         throw new errors_1.CramMalformedError(`MD5 checksum reference mismatch for ref ${sliceHeader.parsedContent.refSeqId} pos ${start}..${end}. recorded MD5: ${storedMd5}, calculated MD5: ${seqMd5}`);
                     }

package/dist/cramFile/slice/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/cramFile/util.d.ts CHANGED Viewed

@@ -1,12 +1,12 @@
-/// <reference path="../../src/typings/binary-parser.d.ts" />
-/// <reference types="node" />
-import { Parser } from '@gmod/binary-parser';
 export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
-export declare function parseItf8(buffer: Uint8Array, initialOffset: number): [number, number];
-export type ParsedItem<T> = T & {
+export declare function parseItf8(buffer: Uint8Array, initialOffset: number): readonly [number, number];
+export declare function parseLtf8(buffer: Buffer, initialOffset: number): readonly [number, number];
+export declare function parseItem<T>(buffer: Buffer, parser: (buffer: Buffer, offset: number) => {
+    offset: number;
+    value: T;
+}, startBufferPosition?: number, startFilePosition?: number): T & {
     _endPosition: number;
     _size: number;
 };
-export declare function parseItem<T>(buffer: Buffer, parser: Parser<T>, startBufferPosition?: number, startFilePosition?: number): ParsedItem<T>;
 export declare function tinyMemoize(_class: any, methodName: any): void;
 export declare function sequenceMD5(seq: string): string;

package/dist/cramFile/util.js CHANGED Viewed

@@ -3,8 +3,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.sequenceMD5 = exports.tinyMemoize = exports.parseItem = exports.parseItf8 = exports.itf8Size = void 0;
+exports.itf8Size = itf8Size;
+exports.parseItf8 = parseItf8;
+exports.parseLtf8 = parseLtf8;
+exports.parseItem = parseItem;
+exports.tinyMemoize = tinyMemoize;
+exports.sequenceMD5 = sequenceMD5;
 const md5_1 = __importDefault(require("md5"));
+const long_1 = __importDefault(require("long"));
 const getBits_1 = require("./codecs/getBits");
 function itf8Size(v) {
     if (!(v & ~0x7f)) {
@@ -21,7 +27,6 @@ function itf8Size(v) {
     }
     return 5;
 }
-exports.itf8Size = itf8Size;
 function parseItf8(buffer, initialOffset) {
     let offset = initialOffset;
     const countFlags = buffer[offset];
@@ -65,16 +70,94 @@ function parseItf8(buffer, initialOffset) {
     }
     return [result, offset - initialOffset];
 }
-exports.parseItf8 = parseItf8;
+function parseLtf8(buffer, initialOffset) {
+    let offset = initialOffset;
+    const countFlags = buffer[offset];
+    let n;
+    if (countFlags < 0x80) {
+        n = countFlags;
+        offset += 1;
+    }
+    else if (countFlags < 0xc0) {
+        n = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff;
+        offset += 2;
+    }
+    else if (countFlags < 0xe0) {
+        n =
+            ((buffer[offset] << 16) |
+                (buffer[offset + 1] << 8) |
+                buffer[offset + 2]) &
+                0x1fffff;
+        n = ((countFlags & 63) << 16) | buffer.readUInt16LE(offset + 1);
+        offset += 3;
+    }
+    else if (countFlags < 0xf0) {
+        n =
+            ((buffer[offset] << 24) |
+                (buffer[offset + 1] << 16) |
+                (buffer[offset + 2] << 8) |
+                buffer[offset + 3]) &
+                0x0fffffff;
+        offset += 4;
+    }
+    else if (countFlags < 0xf8) {
+        n =
+            ((buffer[offset] & 15) * Math.pow(2, 32) + (buffer[offset + 1] << 24)) |
+                ((buffer[offset + 2] << 16) |
+                    (buffer[offset + 3] << 8) |
+                    buffer[offset + 4]);
+        // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
+        offset += 5;
+    }
+    else if (countFlags < 0xfc) {
+        n =
+            ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2, 32) +
+                (buffer[offset + 2] << 24)) |
+                ((buffer[offset + 3] << 16) |
+                    (buffer[offset + 4] << 8) |
+                    buffer[offset + 5]);
+        offset += 6;
+    }
+    else if (countFlags < 0xfe) {
+        n =
+            ((((buffer[offset] & 3) << 16) |
+                (buffer[offset + 1] << 8) |
+                buffer[offset + 2]) *
+                Math.pow(2, 32) +
+                (buffer[offset + 3] << 24)) |
+                ((buffer[offset + 4] << 16) |
+                    (buffer[offset + 5] << 8) |
+                    buffer[offset + 6]);
+        offset += 7;
+    }
+    else if (countFlags < 0xff) {
+        n = long_1.default.fromBytesBE(buffer.slice(offset + 1, offset + 8));
+        if (n.greaterThan(Number.MAX_SAFE_INTEGER) ||
+            n.lessThan(Number.MIN_SAFE_INTEGER)) {
+            throw new Error('integer overflow');
+        }
+        n = n.toNumber();
+        offset += 8;
+    }
+    else {
+        n = long_1.default.fromBytesBE(buffer.slice(offset + 1, offset + 9));
+        if (n.greaterThan(Number.MAX_SAFE_INTEGER) ||
+            n.lessThan(Number.MIN_SAFE_INTEGER)) {
+            throw new Error('integer overflow');
+        }
+        n = n.toNumber();
+        offset += 9;
+    }
+    return [n, offset - initialOffset];
+}
 function parseItem(buffer, parser, startBufferPosition = 0, startFilePosition = 0) {
-    const { offset, result } = parser.parse(buffer);
-    return Object.assign(Object.assign({}, result), { _endPosition: offset + startFilePosition, _size: offset - startBufferPosition });
+    const { offset, value } = parser(buffer, startBufferPosition);
+    return Object.assign(Object.assign({}, value), { _endPosition: offset + startFilePosition, _size: offset - startBufferPosition });
 }
-exports.parseItem = parseItem;
-// this would be nice as a decorator, but i'm a little worried about
-// babel support for it going away or changing.
-// memoizes a method in the stupidest possible way, with no regard for the
-// arguments.  actually, this only works on methods that take no arguments
+// this would be nice as a decorator, but i'm a little worried about babel
+// support for it going away or changing. memoizes a method in the stupidest
+// possible way, with no regard for the arguments.  actually, this only works
+// on methods that take no arguments
 function tinyMemoize(_class, methodName) {
     const method = _class.prototype[methodName];
     const memoAttrName = `_memo_${methodName}`;
@@ -89,9 +172,7 @@ function tinyMemoize(_class, methodName) {
         return this[memoAttrName];
     };
 }
-exports.tinyMemoize = tinyMemoize;
 function sequenceMD5(seq) {
     return (0, md5_1.default)(seq.toUpperCase().replaceAll(/[^\u0021-\u007e]/g, ''));
 }
-exports.sequenceMD5 = sequenceMD5;
 //# sourceMappingURL=util.js.map

package/dist/cramFile/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/indexedCramFile.d.ts CHANGED Viewed

@@ -15,20 +15,17 @@ export interface CramIndexLike {
 export default class IndexedCramFile {
     cram: CramFile;
     index: CramIndexLike;
-    private fetchSizeLimit;
     /**
      *
      * @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: {
         index: CramIndexLike;
-        fetchSizeLimit?: number;
     } & ({
         cram: CramFile;
     } | ({

package/dist/indexedCramFile.js CHANGED Viewed

@@ -21,7 +21,6 @@ class IndexedCramFile {
      * @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.
      */
@@ -44,7 +43,6 @@ class IndexedCramFile {
         if (!this.index.getEntriesForRange) {
             throw new Error('invalid arguments: not an index');
         }
-        this.fetchSizeLimit = args.fetchSizeLimit || 3000000;
     }
     /**
      *
@@ -53,8 +51,8 @@ class IndexedCramFile {
      * @param {number} end end of the range of interest. 1-based closed coordinates.
      * @returns {Promise[Array[CramRecord]]}
      */
-    getRecordsForRange(seq, start, end, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    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;
@@ -64,10 +62,6 @@ class IndexedCramFile {
             }
             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 &&
@@ -123,13 +117,7 @@ class IndexedCramFile {
                     .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 => {
+                for (const c of mateChunks) {
                     let recordPromise = this.cram.featureCache.get(c.toString());
                     if (!recordPromise) {
                         recordPromise = this.getRecordsInSlice(c, () => true);
@@ -149,7 +137,7 @@ class IndexedCramFile {
                         return mateRecs;
                     });
                     mateFeatPromises.push(featPromise);
-                });
+                }
                 const newMateFeats = yield Promise.all(mateFeatPromises);
                 if (newMateFeats.length) {
                     const newMates = newMateFeats.reduce((result, current) => result.concat(current));

package/dist/indexedCramFile.js.map CHANGED Viewed

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

@@ -1,6 +1,4 @@
 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 { fromUrl, open };
+export { open };
 export { LocalFile, RemoteFile } from 'generic-filehandle';