@gmod/tabix 1.5.13 → 1.5.15

package/dist/tabixIndexedFile.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
 import { GenericFilehandle } from 'generic-filehandle';
 import { Options, IndexData } from './indexFile';
@@ -12,41 +11,58 @@ interface GetLinesOpts {
 export default class TabixIndexedFile {
     private filehandle;
     private index;
-    private chunkSizeLimit;
     private yieldTime;
     private renameRefSeq;
     private chunkCache;
     /**
      * @param {object} args
+     *
      * @param {string} [args.path]
+     *
      * @param {filehandle} [args.filehandle]
+     *
      * @param {string} [args.tbiPath]
+     *
      * @param {filehandle} [args.tbiFilehandle]
+     *
      * @param {string} [args.csiPath]
+     *
      * @param {filehandle} [args.csiFilehandle]
-     * @param {number} [args.yieldTime] yield to main thread after N milliseconds if reading features is taking a long time to avoid hanging main thread
-     * @param {function} [args.renameRefSeqs] optional function with sig `string => string` to transform
-     * reference sequence names for the purpose of indexing and querying. note that the data that is returned is
-     * not altered, just the names of the reference sequences that are used for querying.
+     *
+     * @param {number} [args.yieldTime] yield to main thread after N milliseconds
+     * if reading features is taking a long time to avoid hanging main thread
+     *
+     * @param {function} [args.renameRefSeqs] optional function with sig `string
+     * => string` to transform reference sequence names for the purpose of
+     * indexing and querying. note that the data that is returned is not altered,
+     * just the names of the reference sequences that are used for querying.
      */
-    constructor({ path, filehandle, tbiPath, tbiFilehandle, csiPath, csiFilehandle, yieldTime, chunkSizeLimit, renameRefSeqs, chunkCacheSize, }: {
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, yieldTime, renameRefSeqs, chunkCacheSize, }: {
         path?: string;
         filehandle?: GenericFilehandle;
+        url?: string;
         tbiPath?: string;
+        tbiUrl?: string;
         tbiFilehandle?: GenericFilehandle;
         csiPath?: string;
+        csiUrl?: string;
         csiFilehandle?: GenericFilehandle;
         yieldTime?: number;
-        chunkSizeLimit?: number;
         renameRefSeqs?: (n: string) => string;
         chunkCacheSize?: number;
     });
     /**
      * @param refName name of the reference sequence
+     *
      * @param start start of the region (in 0-based half-open coordinates)
+     *
      * @param end end of the region (in 0-based half-open coordinates)
-     * @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
-     * @returns promise that is resolved when the whole read is finished, rejected on error
+     *
+     * @param opts callback called for each line in the region. can also pass a
+     * object param containing obj.lineCallback, obj.signal, etc
+     *
+     * @returns promise that is resolved when the whole read is finished,
+     * rejected on error
      */
     getLines(refName: string, s: number | undefined, e: number | undefined, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
     getMetadata(opts?: Options): Promise<{
@@ -63,31 +79,34 @@ export default class TabixIndexedFile {
         format: string;
     }>;
     /**
-     * get a buffer containing the "header" region of
-     * the file, which are the bytes up to the first
-     * non-meta line
+     * get a buffer containing the "header" region of the file, which are the
+     * bytes up to the first non-meta line
      */
     getHeaderBuffer(opts?: Options): Promise<Buffer>;
     /**
-     * get a string containing the "header" region of the
-     * file, is the portion up to the first non-meta line
+     * get a string containing the "header" region of the file, is the portion up
+     * to the first non-meta line
      *
      * @returns {Promise} for a string
      */
     getHeader(opts?: Options): Promise<string>;
     /**
-     * get an array of reference sequence names, in the order in which
-     * they occur in the file. reference sequence renaming is not applied
-     * to these names.
+     * get an array of reference sequence names, in the order in which they occur
+     * in the file. reference sequence renaming is not applied to these names.
      */
     getReferenceSequenceNames(opts?: Options): Promise<string[]>;
     /**
-     * @param {object} metadata metadata object from the parsed index,
-     * containing columnNumbers, metaChar, and format
+     * @param {object} metadata metadata object from the parsed index, containing
+     * columnNumbers, metaChar, and format
+     *
      * @param {string} regionRefName
+     *
      * @param {number} regionStart region start coordinate (0-based-half-open)
+     *
      * @param {number} regionEnd region end coordinate (0-based-half-open)
+     *
      * @param {array[string]} line
+     *
      * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,
      * true if line is a data line that overlaps the given region
      */
@@ -100,8 +119,11 @@ export default class TabixIndexedFile {
     };
     _getVcfEnd(startCoordinate: number, refSeq: string, info: any): number;
     /**
-     * return the approximate number of data lines in the given reference sequence
+     * return the approximate number of data lines in the given reference
+     * sequence
+     *
      * @param refSeq reference sequence name
+     *
      * @returns number of data lines present on that reference sequence
      */
     lineCount(refName: string, opts?: Options): Promise<number>;

package/dist/tabixIndexedFile.js

@@ -12,7 +12,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
+const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
 const buffer_1 = require("buffer");
 const generic_filehandle_1 = require("generic-filehandle");
@@ -27,24 +27,37 @@ function timeout(time) {
 class TabixIndexedFile {
     /**
      * @param {object} args
+     *
      * @param {string} [args.path]
+     *
      * @param {filehandle} [args.filehandle]
+     *
      * @param {string} [args.tbiPath]
+     *
      * @param {filehandle} [args.tbiFilehandle]
+     *
      * @param {string} [args.csiPath]
+     *
      * @param {filehandle} [args.csiFilehandle]
-     * @param {number} [args.yieldTime] yield to main thread after N milliseconds if reading features is taking a long time to avoid hanging main thread
-     * @param {function} [args.renameRefSeqs] optional function with sig `string => string` to transform
-     * reference sequence names for the purpose of indexing and querying. note that the data that is returned is
-     * not altered, just the names of the reference sequences that are used for querying.
+     *
+     * @param {number} [args.yieldTime] yield to main thread after N milliseconds
+     * if reading features is taking a long time to avoid hanging main thread
+     *
+     * @param {function} [args.renameRefSeqs] optional function with sig `string
+     * => string` to transform reference sequence names for the purpose of
+     * indexing and querying. note that the data that is returned is not altered,
+     * just the names of the reference sequences that are used for querying.
      */
-    constructor({ path, filehandle, tbiPath, tbiFilehandle, csiPath, csiFilehandle, yieldTime = 500, chunkSizeLimit = 50000000, renameRefSeqs = n => n, chunkCacheSize = 5 * Math.pow(2, 20), }) {
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, yieldTime = 500, renameRefSeqs = n => n, chunkCacheSize = 5 * Math.pow(2, 20), }) {
         if (filehandle) {
             this.filehandle = filehandle;
         }
         else if (path) {
             this.filehandle = new generic_filehandle_1.LocalFile(path);
         }
+        else if (url) {
+            this.filehandle = new generic_filehandle_1.RemoteFile(url);
+        }
         else {
             throw new TypeError('must provide either filehandle or path');
         }
@@ -78,10 +91,24 @@ class TabixIndexedFile {
                 renameRefSeqs,
             });
         }
+        else if (csiUrl) {
+            this.index = new csi_1.default({
+                filehandle: new generic_filehandle_1.RemoteFile(csiUrl),
+            });
+        }
+        else if (tbiUrl) {
+            this.index = new tbi_1.default({
+                filehandle: new generic_filehandle_1.RemoteFile(tbiUrl),
+            });
+        }
+        else if (url) {
+            this.index = new tbi_1.default({
+                filehandle: new generic_filehandle_1.RemoteFile(`${url}.tbi`),
+            });
+        }
         else {
-            throw new TypeError('must provide one of tbiFilehandle, tbiPath, csiFilehandle, or csiPath');
+            throw new TypeError('must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl');
         }
-        this.chunkSizeLimit = chunkSizeLimit;
         this.renameRefSeq = renameRefSeqs;
         this.yieldTime = yieldTime;
         this.chunkCache = new abortable_promise_cache_1.default({
@@ -91,20 +118,23 @@ class TabixIndexedFile {
     }
     /**
      * @param refName name of the reference sequence
+     *
      * @param start start of the region (in 0-based half-open coordinates)
+     *
      * @param end end of the region (in 0-based half-open coordinates)
-     * @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
-     * @returns promise that is resolved when the whole read is finished, rejected on error
+     *
+     * @param opts callback called for each line in the region. can also pass a
+     * object param containing obj.lineCallback, obj.signal, etc
+     *
+     * @returns promise that is resolved when the whole read is finished,
+     * rejected on error
      */
     getLines(refName, s, e, opts) {
-        var _a;
         return __awaiter(this, void 0, void 0, function* () {
+            var _a;
             let signal;
             let options = {};
             let callback;
-            if (opts === undefined) {
-                throw new TypeError('line callback must be provided');
-            }
             if (typeof opts === 'function') {
                 callback = opts;
             }
@@ -113,12 +143,6 @@ class TabixIndexedFile {
                 callback = opts.lineCallback;
                 signal = opts.signal;
             }
-            if (refName === undefined) {
-                throw new TypeError('must provide a reference sequence name');
-            }
-            if (!callback) {
-                throw new TypeError('line callback must be provided');
-            }
             const metadata = yield this.index.getMetadata(options);
             (0, util_1.checkAbortSignal)(signal);
             const start = s !== null && s !== void 0 ? s : 0;
@@ -131,14 +155,6 @@ class TabixIndexedFile {
             }
             const chunks = yield this.index.blocksForRange(refName, start, end, options);
             (0, util_1.checkAbortSignal)(signal);
-            // check the chunks for any that are over the size limit.  if
-            // any are, don't fetch any of them
-            for (const chunk of chunks) {
-                const size = chunk.fetchedSize();
-                if (size > this.chunkSizeLimit) {
-                    throw new Error(`Too much data. Chunk size ${size.toLocaleString()} bytes exceeds chunkSizeLimit of ${this.chunkSizeLimit.toLocaleString()}.`);
-                }
-            }
             // now go through each chunk and parse and filter the lines out of it
             let last = Date.now();
             for (const c of chunks) {
@@ -154,6 +170,7 @@ class TabixIndexedFile {
                     }
                     const b = buffer.slice(blockStart, n);
                     const line = (_a = decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) !== null && _a !== void 0 ? _a : b.toString();
+                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                     if (dpositions) {
                         while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
                         pos--;
@@ -200,20 +217,20 @@ class TabixIndexedFile {
             }
         });
     }
-    getMetadata(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getMetadata() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             return this.index.getMetadata(opts);
         });
     }
     /**
-     * get a buffer containing the "header" region of
-     * the file, which are the bytes up to the first
-     * non-meta line
+     * get a buffer containing the "header" region of the file, which are the
+     * bytes up to the first non-meta line
      */
-    getHeaderBuffer(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getHeaderBuffer() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const { firstDataLine, metaChar, maxBlockSize } = yield this.getMetadata(opts);
             (0, util_1.checkAbortSignal)(opts.signal);
+            // eslint-disable-next-line @typescript-eslint/restrict-plus-operands
             const maxFetch = ((firstDataLine === null || firstDataLine === void 0 ? void 0 : firstDataLine.blockPosition) || 0) + maxBlockSize;
             // TODO: what if we don't have a firstDataLine, and the header
             // actually takes up more than one block? this case is not covered here
@@ -239,35 +256,39 @@ class TabixIndexedFile {
         });
     }
     /**
-     * get a string containing the "header" region of the
-     * file, is the portion up to the first non-meta line
+     * get a string containing the "header" region of the file, is the portion up
+     * to the first non-meta line
      *
      * @returns {Promise} for a string
      */
-    getHeader(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getHeader() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const bytes = yield this.getHeaderBuffer(opts);
             return bytes.toString('utf8');
         });
     }
     /**
-     * get an array of reference sequence names, in the order in which
-     * they occur in the file. reference sequence renaming is not applied
-     * to these names.
+     * get an array of reference sequence names, in the order in which they occur
+     * in the file. reference sequence renaming is not applied to these names.
      */
-    getReferenceSequenceNames(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getReferenceSequenceNames() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const metadata = yield this.getMetadata(opts);
             return metadata.refIdToName;
         });
     }
     /**
-     * @param {object} metadata metadata object from the parsed index,
-     * containing columnNumbers, metaChar, and format
+     * @param {object} metadata metadata object from the parsed index, containing
+     * columnNumbers, metaChar, and format
+     *
      * @param {string} regionRefName
+     *
      * @param {number} regionStart region start coordinate (0-based-half-open)
+     *
      * @param {number} regionEnd region end coordinate (0-based-half-open)
+     *
      * @param {array[string]} line
+     *
      * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,
      * true if line is a data line that overlaps the given region
      */
@@ -292,9 +313,9 @@ class TabixIndexedFile {
             end = 8;
         }
         const maxColumn = Math.max(ref, start, end);
-        // this code is kind of complex, but it is fairly fast.
-        // basically, we want to avoid doing a split, because if the lines are really long
-        // that could lead to us allocating a bunch of extra memory, which is slow
+        // this code is kind of complex, but it is fairly fast. basically, we want
+        // to avoid doing a split, because if the lines are really long that could
+        // lead to us allocating a bunch of extra memory, which is slow
         let currentColumnNumber = 1; // cols are numbered starting at 1 in the index metadata
         let currentColumnStart = 0;
         let refSeq = '';
@@ -372,17 +393,20 @@ class TabixIndexedFile {
         return endCoordinate;
     }
     /**
-     * return the approximate number of data lines in the given reference sequence
+     * return the approximate number of data lines in the given reference
+     * sequence
+     *
      * @param refSeq reference sequence name
+     *
      * @returns number of data lines present on that reference sequence
      */
-    lineCount(refName, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    lineCount(refName_1) {
+        return __awaiter(this, arguments, void 0, function* (refName, opts = {}) {
             return this.index.lineCount(refName, opts);
         });
     }
-    _readRegion(pos, size, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    _readRegion(pos_1, size_1) {
+        return __awaiter(this, arguments, void 0, function* (pos, size, opts = {}) {
             const b = buffer_1.Buffer.alloc(size);
             const { bytesRead, buffer } = yield this.filehandle.read(b, 0, size, pos, opts);
             return buffer.slice(0, bytesRead);
@@ -392,10 +416,10 @@ class TabixIndexedFile {
      * read and uncompress the data in a chunk (composed of one or more
      * contiguous bgzip blocks) of the file
      */
-    readChunk(c, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
-            // fetch the uncompressed data, uncompress carefully a block at a time,
-            // and stop when done
+    readChunk(c_1) {
+        return __awaiter(this, arguments, void 0, function* (c, opts = {}) {
+            // fetch the uncompressed data, uncompress carefully a block at a time, and
+            // stop when done
             const data = yield this._readRegion(c.minv.blockPosition, c.fetchedSize(), opts);
             return (0, bgzf_filehandle_1.unzipChunkSlice)(data, c);
         });

package/dist/tabixIndexedFile.js.map

@@ -1 +1 @@
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package/dist/tbi.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';

package/dist/tbi.js

@@ -44,7 +44,8 @@ const indexFile_1 = __importDefault(require("./indexFile"));
 const TBI_MAGIC = 21578324; // TBI\1
 const TAD_LIDX_SHIFT = 14;
 /**
- * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
+ * calculate the list of bins that may overlap with region [beg,end)
+ * (zero-based half-open)
  */
 function reg2bins(beg, end) {
     beg += 1; // < convert to 1-based closed
@@ -59,13 +60,13 @@ function reg2bins(beg, end) {
     ];
 }
 class TabixIndex extends indexFile_1.default {
-    lineCount(refName, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    lineCount(refName_1) {
+        return __awaiter(this, arguments, void 0, function* (refName, opts = {}) {
             const indexData = yield this.parse(opts);
-            if (!indexData) {
+            const refId = indexData.refNameToId[refName];
+            if (refId === undefined) {
                 return -1;
             }
-            const refId = indexData.refNameToId[refName];
             const idx = indexData.indices[refId];
             if (!idx) {
                 return -1;
@@ -78,8 +79,8 @@ class TabixIndex extends indexFile_1.default {
         });
     }
     // fetch and parse the index
-    _parse(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    _parse() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const buf = yield this.filehandle.readFile(opts);
             const bytes = yield (0, bgzf_filehandle_1.unzip)(buf);
             (0, util_1.checkAbortSignal)(opts.signal);
@@ -202,16 +203,16 @@ class TabixIndex extends indexFile_1.default {
         }
         return { refNameToId, refIdToName };
     }
-    blocksForRange(refName, min, max, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    blocksForRange(refName_1, min_1, max_1) {
+        return __awaiter(this, arguments, void 0, function* (refName, min, max, opts = {}) {
             if (min < 0) {
                 min = 0;
             }
             const indexData = yield this.parse(opts);
-            if (!indexData) {
+            const refId = indexData.refNameToId[refName];
+            if (refId === undefined) {
                 return [];
             }
-            const refId = indexData.refNameToId[refName];
             const ba = indexData.indices[refId];
             if (!ba) {
                 return [];

package/dist/tbi.js.map

@@ -1 +1 @@
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+{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gDAAuB;AAEvB,iEAA0D;AAC1D,oDAA2B;AAC3B,2DAA6C;AAC7C,iCAAuE;AACvE,4DAAgD;AAEhD,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;IACvC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAqB,UAAW,SAAQ,mBAAS;IACzC,SAAS;6DAAC,OAAe,EAAE,OAAgB,EAAE;YACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,CAAC,CAAC,CAAA;YACX,CAAC;YACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACpC,IAAI,CAAC,GAAG,EAAE,CAAC;gBACT,OAAO,CAAC,CAAC,CAAA;YACX,CAAC;YACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YAC1C,IAAI,KAAK,EAAE,CAAC;gBACV,OAAO,KAAK,CAAC,SAAS,CAAA;YACxB,CAAC;YACD,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;KAAA;IAED,4BAA4B;IACtB,MAAM;6DAAC,OAAgB,EAAE;YAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YAChD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAA;YAC9B,IAAA,uBAAgB,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YAE7B,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,aAAa,EAAE,CAAC;gBACtD,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;YACtD,CAAC;YAED,6CAA6C;YAC7C,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACrC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACxC,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;YACnE,MAAM,UAAU,GAA2B;gBACzC,CAAC,EAAE,SAAS;gBACZ,CAAC,EAAE,KAAK;gBACR,CAAC,EAAE,KAAK;aACT,CAAA;YACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;YACrE,CAAC;YACD,MAAM,aAAa,GAAG;gBACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC1B,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC5B,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;aAC3B,CAAA;YACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACvC,MAAM,KAAK,GAAG,CAAC,CAAA;YACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YACvD,MAAM,YAAY,GAAG,SAAA,CAAC,EAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA,CAAA;YAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;YAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YAEvC,2BAA2B;YAC3B,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YAC/C,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,GAAG,iBAAiB,CAAC,CACxC,CAAA;YAED,+CAA+C;YAC/C,IAAI,UAAU,GAAG,EAAE,GAAG,iBAAiB,CAAA;YACvC,IAAI,aAAwC,CAAA;YAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;gBACnD,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBAC9C,UAAU,IAAI,CAAC,CAAA;gBACf,MAAM,QAAQ,GAA4B,EAAE,CAAA;gBAC5C,IAAI,KAAK,CAAA;gBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;oBACrC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;oBAC1C,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;wBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;oBACH,CAAC;yBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;wBACpC,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAChD,UAAU,IAAI,CAAC,CAAA;wBACf,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;4BACrB,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBAChD,CAAC;wBACD,UAAU,IAAI,EAAE,GAAG,UAAU,CAAA;oBAC/B,CAAC;yBAAM,CAAC;wBACN,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAChD,UAAU,IAAI,CAAC,CAAA;wBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;wBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;4BACvC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;4BACtC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;4BAC1C,UAAU,IAAI,EAAE,CAAA;4BAChB,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;4BACrD,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;wBAClC,CAAC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;oBACxB,CAAC;gBACH,CAAC;gBAED,mBAAmB;gBACnB,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBACjD,UAAU,IAAI,CAAC,CAAA;gBACf,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;gBAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;oBACxC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAC7C,UAAU,IAAI,CAAC,CAAA;oBACf,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;gBACpE,CAAC;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package/dist/util.d.ts

@@ -1,16 +1,16 @@
-/// <reference types="long" />
 import Chunk from './chunk';
 import VirtualOffset from './virtualOffset';
 export declare function longToNumber(long: Long): number;
 /**
- * Properly check if the given AbortSignal is aborted.
- * Per the standard, if the signal reads as aborted,
- * this function throws either a DOMException AbortError, or a regular error
- * with a `code` attribute set to `ERR_ABORTED`.
+ * Properly check if the given AbortSignal is aborted. Per the standard, if the
+ * signal reads as aborted, this function throws either a DOMException
+ * AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
  *
  * For convenience, passing `undefined` is a no-op
  *
- * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted` attribute
+ * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted`
+ * attribute
+ *
  * @returns nothing
  */
 export declare function checkAbortSignal(signal?: AbortSignal): void;
@@ -22,4 +22,4 @@ export declare function checkAbortSignal(signal?: AbortSignal): void;
  */
 export declare function abortBreakPoint(signal?: AbortSignal): Promise<void>;
 export declare function canMergeBlocks(chunk1: Chunk, chunk2: Chunk): boolean;
-export declare function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset): Chunk[];
+export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];