@gmod/tabix 1.5.5 → 1.5.7

package/dist/tabixIndexedFile.js

@@ -19,10 +19,9 @@ const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const util_1 = require("./util");
 const tbi_1 = __importDefault(require("./tbi"));
 const csi_1 = __importDefault(require("./csi"));
+const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8') : undefined;
 function timeout(time) {
-    return new Promise(resolve => {
-        setTimeout(resolve, time);
-    });
+    return new Promise(resolve => setTimeout(resolve, time));
 }
 class TabixIndexedFile {
     /**
@@ -33,14 +32,12 @@ class TabixIndexedFile {
      * @param {filehandle} [args.tbiFilehandle]
      * @param {string} [args.csiPath]
      * @param {filehandle} [args.csiFilehandle]
-     * @param {chunkSizeLimit} default 50MiB
+     * @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.chunkCacheSize] maximum size in bytes of the chunk cache. default 5MB
-     * @param {number} [args.blockCacheSize] maximum size in bytes of the block cache. default 5MB
      */
-    constructor({ path, filehandle, tbiPath, tbiFilehandle, csiPath, csiFilehandle, chunkSizeLimit = 50000000, renameRefSeqs = n => n, chunkCacheSize = 5 * Math.pow(2, 20), }) {
+    constructor({ path, filehandle, tbiPath, tbiFilehandle, csiPath, csiFilehandle, yieldTime = 500, chunkSizeLimit = 50000000, renameRefSeqs = n => n, chunkCacheSize = 5 * Math.pow(2, 20), }) {
         if (filehandle) {
             this.filehandle = filehandle;
         }
@@ -85,19 +82,18 @@ class TabixIndexedFile {
         }
         this.chunkSizeLimit = chunkSizeLimit;
         this.renameRefSeq = renameRefSeqs;
+        this.yieldTime = yieldTime;
         this.chunkCache = new abortable_promise_cache_1.default({
-            cache: new quick_lru_1.default({
-                maxSize: Math.floor(chunkCacheSize / (1 << 16)),
-            }),
-            fill: this.readChunk.bind(this),
+            cache: new quick_lru_1.default({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),
+            fill: (args, signal) => this.readChunk(args, { signal }),
         });
     }
     /**
-     * @param {string} refName name of the reference sequence
-     * @param {number} start start of the region (in 0-based half-open coordinates)
-     * @param {number} end end of the region (in 0-based half-open coordinates)
-     * @param {function|object} lineCallback callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
-     * @returns {Promise} resolved when the whole read is finished, rejected on error
+     * @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
      */
     getLines(refName, start, end, opts) {
         return __awaiter(this, void 0, void 0, function* () {
@@ -149,20 +145,25 @@ class TabixIndexedFile {
             for (let chunkNum = 0; chunkNum < chunks.length; chunkNum += 1) {
                 let previousStartCoordinate;
                 const c = chunks[chunkNum];
-                const { buffer, cpositions, dpositions } = yield this.chunkCache.get(c.toString(), c, signal);
-                const lines = (typeof TextDecoder !== 'undefined'
-                    ? new TextDecoder('utf-8').decode(buffer)
-                    : buffer.toString()).split('\n');
-                lines.pop();
+                const { buffer, cpositions, dpositions } = yield this.chunkCache.get(c.toString(), c);
                 (0, util_1.checkAbortSignal)(signal);
-                let blockStart = c.minv.dataPosition;
-                let pos;
-                for (let i = 0; i < lines.length; i += 1) {
-                    const line = lines[i];
-                    for (pos = 0; blockStart >= dpositions[pos]; pos += 1) { }
+                let blockStart = 0;
+                let pos = 0;
+                while (blockStart < buffer.length) {
+                    const n = buffer.indexOf('\n', blockStart);
+                    if (n === -1) {
+                        break;
+                    }
+                    const b = buffer.subarray(blockStart, n);
+                    const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString();
+                    if (dpositions) {
+                        while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
+                        pos--;
+                    }
                     // filter the line for whether it is within the requested range
                     const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
-                    // do a small check just to make sure that the lines are really sorted by start coordinate
+                    // do a small check just to make sure that the lines are really sorted
+                    // by start coordinate
                     if (previousStartCoordinate !== undefined &&
                         startCoordinate !== undefined &&
                         previousStartCoordinate > startCoordinate) {
@@ -179,7 +180,10 @@ class TabixIndexedFile {
                         // then the blockStart-dpositions is an uncompressed file offset from
                         // that bgzip block boundary, and since the cpositions are multiplied by
                         // (1 << 8) these uncompressed offsets get a unique space
-                        cpositions[pos] * (1 << 8) + (blockStart - dpositions[pos]));
+                        cpositions[pos] * (1 << 8) +
+                            (blockStart - dpositions[pos]) +
+                            c.minv.dataPosition +
+                            1);
                     }
                     else if (startCoordinate !== undefined && startCoordinate >= end) {
                         // the lines were overlapping the region, but now have stopped, so
@@ -187,13 +191,13 @@ class TabixIndexedFile {
                         // processing data now
                         return;
                     }
-                    blockStart += line.length + 1;
                     // yield if we have emitted beyond the yield limit
-                    if (last - Date.now() > 500) {
+                    if (this.yieldTime && last - Date.now() > this.yieldTime) {
                         last = Date.now();
                         (0, util_1.checkAbortSignal)(signal);
                         yield timeout(1);
                     }
+                    blockStart = n + 1;
                 }
             }
         });
@@ -207,16 +211,12 @@ class TabixIndexedFile {
      * get a buffer containing the "header" region of
      * the file, which are the bytes up to the first
      * non-meta line
-     *
-     * @returns {Promise} for a buffer
      */
     getHeaderBuffer(opts = {}) {
         return __awaiter(this, void 0, void 0, function* () {
             const { firstDataLine, metaChar, maxBlockSize } = yield this.getMetadata(opts);
             (0, util_1.checkAbortSignal)(opts.signal);
-            const maxFetch = firstDataLine && firstDataLine.blockPosition
-                ? firstDataLine.blockPosition + maxBlockSize
-                : maxBlockSize;
+            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
             let bytes = yield this._readRegion(0, maxFetch, opts);
@@ -244,7 +244,7 @@ class TabixIndexedFile {
                         lastNewline = i;
                     }
                 }
-                bytes = bytes.slice(0, lastNewline + 1);
+                bytes = bytes.subarray(0, lastNewline + 1);
             }
             return bytes;
         });
@@ -258,17 +258,13 @@ class TabixIndexedFile {
     getHeader(opts = {}) {
         return __awaiter(this, void 0, void 0, function* () {
             const bytes = yield this.getHeaderBuffer(opts);
-            (0, util_1.checkAbortSignal)(opts.signal);
             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.
-     *
-     * @returns {Promise} for an array of string sequence names
+     * they occur in the file. reference sequence renaming is not applied
+     * to these names.
      */
     getReferenceSequenceNames(opts = {}) {
         return __awaiter(this, void 0, void 0, function* () {
@@ -286,7 +282,8 @@ class TabixIndexedFile {
      * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,
      * true if line is a data line that overlaps the given region
      */
-    checkLine({ columnNumbers, metaChar, coordinateType, format, }, regionRefName, regionStart, regionEnd, line) {
+    checkLine(metadata, regionRefName, regionStart, regionEnd, line) {
+        const { columnNumbers, metaChar, coordinateType, format } = metadata;
         // skip meta lines
         if (line.charAt(0) === metaChar) {
             return { overlaps: false };
@@ -391,36 +388,35 @@ class TabixIndexedFile {
     }
     /**
      * return the approximate number of data lines in the given reference sequence
-     * @param {string} refSeq reference sequence name
-     * @returns {Promise} for number of data lines present on that 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* () {
             return this.index.lineCount(refName, opts);
         });
     }
-    _readRegion(position, compressedSize, opts = {}) {
+    _readRegion(pos, size, opts = {}) {
         return __awaiter(this, void 0, void 0, function* () {
-            const { bytesRead, buffer } = yield this.filehandle.read(Buffer.alloc(compressedSize), 0, compressedSize, position, opts);
-            return bytesRead < compressedSize ? buffer.slice(0, bytesRead) : buffer;
+            const b = Buffer.alloc(size);
+            const { bytesRead, buffer } = yield this.filehandle.read(b, 0, size, pos, opts);
+            return buffer.subarray(0, bytesRead);
         });
     }
     /**
      * read and uncompress the data in a chunk (composed of one or more
      * contiguous bgzip blocks) of the file
-     * @param {Chunk} chunk
-     * @returns {Promise} for a string chunk of the file
      */
-    readChunk(chunk, opts = {}) {
+    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
-            const compressedData = yield this._readRegion(chunk.minv.blockPosition, chunk.fetchedSize(), opts);
+            const data = yield this._readRegion(c.minv.blockPosition, c.fetchedSize(), opts);
             try {
-                return (0, bgzf_filehandle_1.unzipChunkSlice)(compressedData, chunk);
+                return (0, bgzf_filehandle_1.unzipChunkSlice)(data, c);
             }
             catch (e) {
-                throw new Error(`error decompressing chunk ${chunk.toString()} ${e}`);
+                throw new Error(`error decompressing c ${c.toString()} ${e}`);
             }
         });
     }

package/dist/tabixIndexedFile.js.map

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package/dist/tbi.d.ts

@@ -17,12 +17,12 @@ export default class TabixIndex extends IndexFile {
         metaChar: string | null;
         maxBinNumber: number;
         maxRefLength: number;
-        skipLines: any;
+        skipLines: number;
         firstDataLine: VirtualOffset | undefined;
         columnNumbers: {
-            ref: any;
-            start: any;
-            end: any;
+            ref: number;
+            start: number;
+            end: number;
         };
         coordinateType: string;
         format: string;

package/dist/tbi.js

@@ -77,11 +77,11 @@ class TabixIndex extends indexFile_1.default {
             return -1;
         });
     }
-    // memoize
     // fetch and parse the index
     _parse(opts = {}) {
         return __awaiter(this, void 0, void 0, function* () {
-            const bytes = yield (0, bgzf_filehandle_1.unzip)((yield this.filehandle.readFile(opts)));
+            const buf = yield this.filehandle.readFile(opts);
+            const bytes = yield (0, bgzf_filehandle_1.unzip)(buf);
             (0, util_1.checkAbortSignal)(opts.signal);
             // check TBI magic numbers
             if (bytes.readUInt32LE(0) !== TBI_MAGIC /* "TBI\1" */) {
@@ -114,7 +114,7 @@ class TabixIndex extends indexFile_1.default {
             const skipLines = bytes.readInt32LE(28);
             // read sequence dictionary
             const nameSectionLength = bytes.readInt32LE(32);
-            const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
+            const { refNameToId, refIdToName } = this._parseNameBytes(bytes.subarray(36, 36 + nameSectionLength));
             // read the indexes for each reference sequence
             let currOffset = 36 + nameSectionLength;
             let firstDataLine;
@@ -180,7 +180,7 @@ class TabixIndex extends indexFile_1.default {
         });
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
+        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.subarray(offset + 16, offset + 24), true));
         return { lineCount };
     }
     _parseNameBytes(namesBytes) {

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;AACvB,iEAA0D;AAC1D,oDAA2B;AAC3B,2DAA6C;AAC7C,iCAAuE;AACvE,4DAAgD;AAEhD,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;GAEG;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;KACzC,CAAA;AACH,CAAC;AAED,MAAqB,UAAW,SAAQ,mBAAS;IACzC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;;YACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,IAAI,CAAC,SAAS,EAAE;gBACd,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACpC,IAAI,CAAC,GAAG,EAAE;gBACR,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YAC1C,IAAI,KAAK,EAAE;gBACT,OAAO,KAAK,CAAC,SAAS,CAAA;aACvB;YACD,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;KAAA;IAED,4BAA4B;IACtB,MAAM,CAAC,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;gBACrD,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;aACrD;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,GAA8B;gBAC5C,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;gBACX,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;aACpE;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,QAAQ,CAAC,EAAE,EAAE,EAAE,GAAG,iBAAiB,CAAC,CAC3C,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,GAA+B,EAAE,CAAA;gBAC/C,IAAI,KAAK,CAAA;gBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;oBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;oBAC1C,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE;wBAC1B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;qBACF;yBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE;wBACnC,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAChD,UAAU,IAAI,CAAC,CAAA;wBACf,IAAI,UAAU,KAAK,CAAC,EAAE;4BACpB,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;yBAC/C;wBACD,UAAU,IAAI,EAAE,GAAG,UAAU,CAAA;qBAC9B;yBAAM;wBACL,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;4BACtC,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;yBACjC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;qBACvB;iBACF;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;oBACvC,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;iBACnE;gBACD,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;YACzC,CAAC,CAAC,CAAA;YAEF,OAAO;gBACL,OAAO;gBACP,QAAQ;gBACR,YAAY;gBACZ,YAAY;g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package/esm/csi.d.ts

@@ -8,22 +8,14 @@ export default class CSI extends IndexFile {
     private minShift;
     constructor(args: any);
     lineCount(refName: string, opts?: Options): Promise<number>;
-    indexCov(): Promise<never[]>;
-    parseAuxData(bytes: Buffer, offset: number, auxLength: number): {
-        refIdToName: never[];
-        refNameToId: {};
-        skipLines?: undefined;
-        metaChar?: undefined;
-        columnNumbers?: undefined;
-        format?: undefined;
-        coordinateType?: undefined;
-    } | {
+    indexCov(): Promise<void>;
+    parseAuxData(bytes: Buffer, offset: number): {
         refIdToName: string[];
         refNameToId: {
             [key: string]: number;
         };
         skipLines: number;
-        metaChar: string;
+        metaChar: string | null;
         columnNumbers: {
             ref: number;
             start: number;
@@ -40,7 +32,7 @@ export default class CSI extends IndexFile {
     };
     _parse(opts?: Options): Promise<{
         csi: boolean;
-        refCount: any;
+        refCount: number;
         maxBlockSize: number;
         firstDataLine: VirtualOffset | undefined;
         csiVersion: number;
@@ -59,6 +51,42 @@ export default class CSI extends IndexFile {
         refNameToId: {
             [key: string]: number;
         };
+        skipLines: number;
+        metaChar: string | null;
+        columnNumbers: {
+            ref: number;
+            start: number;
+            end: number;
+        };
+        format: string;
+        coordinateType: string;
+    } | {
+        csi: boolean;
+        refCount: number;
+        maxBlockSize: number;
+        firstDataLine: VirtualOffset | undefined;
+        csiVersion: number;
+        indices: {
+            binIndex: {
+                [key: string]: Chunk[];
+            };
+            stats: {
+                lineCount: number;
+            } | undefined;
+        }[];
+        depth: number;
+        maxBinNumber: number;
+        maxRefLength: number;
+        refIdToName: never[];
+        refNameToId: {};
+        metaChar: null;
+        columnNumbers: {
+            ref: number;
+            start: number;
+            end: number;
+        };
+        coordinateType: string;
+        format: string;
     }>;
     parsePseudoBin(bytes: Buffer, offset: number): {
         lineCount: number;

package/esm/csi.js

@@ -37,15 +37,8 @@ export default class CSI extends IndexFile {
     }
     async indexCov() {
         throw new Error('CSI indexes do not support indexcov');
-        return [];
     }
-    parseAuxData(bytes, offset, auxLength) {
-        if (auxLength < 30) {
-            return {
-                refIdToName: [],
-                refNameToId: {},
-            };
-        }
+    parseAuxData(bytes, offset) {
         const formatFlags = bytes.readInt32LE(offset);
         const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
         const format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[formatFlags & 0xf];
@@ -58,10 +51,10 @@ export default class CSI extends IndexFile {
             end: bytes.readInt32LE(offset + 12),
         };
         const metaValue = bytes.readInt32LE(offset + 16);
-        const metaChar = metaValue ? String.fromCharCode(metaValue) : '';
+        const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
         const skipLines = bytes.readInt32LE(offset + 20);
         const nameSectionLength = bytes.readInt32LE(offset + 24);
-        const { refIdToName, refNameToId } = this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength));
+        const { refIdToName, refNameToId } = this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength));
         return {
             refIdToName,
             refNameToId,
@@ -111,13 +104,16 @@ export default class CSI extends IndexFile {
         this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
         const maxRefLength = 2 ** (this.minShift + this.depth * 3);
         const auxLength = bytes.readInt32LE(12);
-        let aux = {
-            refIdToName: [],
-            refNameToId: {},
-        };
-        if (auxLength) {
-            aux = this.parseAuxData(bytes, 16, auxLength);
-        }
+        const aux = auxLength && auxLength >= 30
+            ? this.parseAuxData(bytes, 16)
+            : {
+                refIdToName: [],
+                refNameToId: {},
+                metaChar: null,
+                columnNumbers: { ref: 0, start: 1, end: 2 },
+                coordinateType: 'zero-based-half-open',
+                format: 'generic',
+            };
         const refCount = bytes.readInt32LE(16 + auxLength);
         // read the indexes for each reference sequence
         let firstDataLine;
@@ -168,7 +164,7 @@ export default class CSI extends IndexFile {
         };
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = longToNumber(Long.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
+        const lineCount = longToNumber(Long.fromBytesLE(bytes.subarray(offset + 28, offset + 36), true));
         return { lineCount };
     }
     async blocksForRange(refName, min, max, opts = {}) {

package/esm/csi.js.map

@@ -1 +1 @@
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package/esm/indexFile.d.ts

@@ -5,28 +5,48 @@ export interface Options {
     [key: string]: unknown;
     signal?: AbortSignal;
 }
+export interface IndexData {
+    refNameToId: {
+        [key: string]: number;
+    };
+    refIdToName: string[];
+    metaChar: string | null;
+    columnNumbers: {
+        ref: number;
+        start: number;
+        end: number;
+    };
+    coordinateType: string;
+    format: string;
+    [key: string]: any;
+}
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
     renameRefSeq: (arg0: string) => string;
-    private _parseCache;
-    /**
-     * @param {filehandle} filehandle
-     * @param {function} [renameRefSeqs]
-     */
+    private parseP?;
     constructor({ filehandle, renameRefSeqs, }: {
         filehandle: GenericFilehandle;
         renameRefSeqs?: (a: string) => string;
     });
     abstract lineCount(refName: string, args: Options): Promise<number>;
-    protected abstract _parse(opts: Options): Promise<{
+    protected abstract _parse(opts: Options): Promise<IndexData>;
+    getMetadata(opts?: Options): Promise<{
+        [key: string]: any;
         refNameToId: {
             [key: string]: number;
         };
         refIdToName: string[];
+        metaChar: string | null;
+        columnNumbers: {
+            ref: number;
+            start: number;
+            end: number;
+        };
+        coordinateType: string;
+        format: string;
     }>;
-    getMetadata(opts?: Options): Promise<any>;
     abstract blocksForRange(refName: string, start: number, end: number, opts: Options): Promise<Chunk[]>;
     _findFirstData(currentFdl: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
-    parse(opts?: Options): Promise<any>;
+    parse(opts?: Options): Promise<IndexData>;
     hasRefSeq(seqId: number, opts?: Options): Promise<boolean>;
 }

package/esm/indexFile.js

@@ -1,10 +1,4 @@
-import AbortablePromiseCache from 'abortable-promise-cache';
-import QuickLRU from 'quick-lru';
 export default class IndexFile {
-    /**
-     * @param {filehandle} filehandle
-     * @param {function} [renameRefSeqs]
-     */
     constructor({ filehandle, renameRefSeqs = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeqs;
@@ -25,13 +19,13 @@ export default class IndexFile {
         }
     }
     async parse(opts = {}) {
-        if (!this._parseCache) {
-            this._parseCache = new AbortablePromiseCache({
-                cache: new QuickLRU({ maxSize: 1 }),
-                fill: () => this._parse(opts),
+        if (!this.parseP) {
+            this.parseP = this._parse(opts).catch(e => {
+                this.parseP = undefined;
+                throw e;
             });
         }
-        return this._parseCache.get('index', null, undefined);
+        return this.parseP;
     }
     async hasRefSeq(seqId, opts = {}) {
         return !!((await this.parse(opts)).indices[seqId] || {}).binIndex;