@gmod/tabix 1.5.14 → 1.6.0

package/dist/tbi.js

@@ -15,22 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -44,7 +45,8 @@ 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
@@ -59,125 +61,121 @@ function reg2bins(beg, end) {
     ];
 }
 class TabixIndex extends indexFile_1.default {
-    lineCount(refName_1) {
-        return __awaiter(this, arguments, void 0, function* (refName, opts = {}) {
-            const indexData = yield this.parse(opts);
-            if (!indexData) {
-                return -1;
-            }
-            const refId = indexData.refNameToId[refName];
-            const idx = indexData.indices[refId];
-            if (!idx) {
-                return -1;
-            }
-            const { stats } = indexData.indices[refId];
-            if (stats) {
-                return stats.lineCount;
-            }
+    async lineCount(refName, opts = {}) {
+        const indexData = await this.parse(opts);
+        const refId = indexData.refNameToId[refName];
+        if (refId === undefined) {
             return -1;
-        });
+        }
+        const idx = indexData.indices[refId];
+        if (!idx) {
+            return -1;
+        }
+        const { stats } = indexData.indices[refId];
+        if (stats) {
+            return stats.lineCount;
+        }
+        return -1;
     }
     // fetch and parse the index
-    _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);
-            // check TBI magic numbers
-            if (bytes.readUInt32LE(0) !== TBI_MAGIC /* "TBI\1" */) {
-                throw new Error('Not a TBI file');
-                // TODO: do we need to support big-endian TBI files?
-            }
-            // number of reference sequences in the index
-            const refCount = bytes.readInt32LE(4);
-            const formatFlags = bytes.readInt32LE(8);
-            const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
-            const formatOpts = {
-                0: 'generic',
-                1: 'SAM',
-                2: 'VCF',
-            };
-            const format = formatOpts[formatFlags & 0xf];
-            if (!format) {
-                throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
-            }
-            const columnNumbers = {
-                ref: bytes.readInt32LE(12),
-                start: bytes.readInt32LE(16),
-                end: bytes.readInt32LE(20),
-            };
-            const metaValue = bytes.readInt32LE(24);
-            const depth = 5;
-            const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
-            const maxRefLength = Math.pow(2, (14 + depth * 3));
-            const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
-            const skipLines = bytes.readInt32LE(28);
-            // read sequence dictionary
-            const nameSectionLength = bytes.readInt32LE(32);
-            const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
-            // read the indexes for each reference sequence
-            let currOffset = 36 + nameSectionLength;
-            let firstDataLine;
-            const indices = new Array(refCount).fill(0).map(() => {
-                // the binning index
-                const binCount = bytes.readInt32LE(currOffset);
+    async _parse(opts = {}) {
+        const buf = await this.filehandle.readFile(opts);
+        const bytes = await (0, bgzf_filehandle_1.unzip)(buf);
+        (0, util_1.checkAbortSignal)(opts.signal);
+        // check TBI magic numbers
+        if (bytes.readUInt32LE(0) !== TBI_MAGIC /* "TBI\1" */) {
+            throw new Error('Not a TBI file');
+            // TODO: do we need to support big-endian TBI files?
+        }
+        // number of reference sequences in the index
+        const refCount = bytes.readInt32LE(4);
+        const formatFlags = bytes.readInt32LE(8);
+        const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
+        const formatOpts = {
+            0: 'generic',
+            1: 'SAM',
+            2: 'VCF',
+        };
+        const format = formatOpts[formatFlags & 0xf];
+        if (!format) {
+            throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
+        }
+        const columnNumbers = {
+            ref: bytes.readInt32LE(12),
+            start: bytes.readInt32LE(16),
+            end: bytes.readInt32LE(20),
+        };
+        const metaValue = bytes.readInt32LE(24);
+        const depth = 5;
+        const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
+        const maxRefLength = 2 ** (14 + depth * 3);
+        const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
+        const skipLines = bytes.readInt32LE(28);
+        // read sequence dictionary
+        const nameSectionLength = bytes.readInt32LE(32);
+        const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
+        // read the indexes for each reference sequence
+        let currOffset = 36 + nameSectionLength;
+        let firstDataLine;
+        const indices = new Array(refCount).fill(0).map(() => {
+            // the binning index
+            const binCount = bytes.readInt32LE(currOffset);
+            currOffset += 4;
+            const binIndex = {};
+            let stats;
+            for (let j = 0; j < binCount; j += 1) {
+                const bin = bytes.readUInt32LE(currOffset);
                 currOffset += 4;
-                const binIndex = {};
-                let stats;
-                for (let j = 0; j < binCount; j += 1) {
-                    const bin = bytes.readUInt32LE(currOffset);
+                if (bin > maxBinNumber + 1) {
+                    throw new Error('tabix index contains too many bins, please use a CSI index');
+                }
+                else if (bin === maxBinNumber + 1) {
+                    const chunkCount = bytes.readInt32LE(currOffset);
                     currOffset += 4;
-                    if (bin > maxBinNumber + 1) {
-                        throw new Error('tabix index contains too many bins, please use a CSI index');
-                    }
-                    else if (bin === maxBinNumber + 1) {
-                        const chunkCount = bytes.readInt32LE(currOffset);
-                        currOffset += 4;
-                        if (chunkCount === 2) {
-                            stats = this.parsePseudoBin(bytes, currOffset);
-                        }
-                        currOffset += 16 * chunkCount;
-                    }
-                    else {
-                        const chunkCount = bytes.readInt32LE(currOffset);
-                        currOffset += 4;
-                        const chunks = new Array(chunkCount);
-                        for (let k = 0; k < chunkCount; k += 1) {
-                            const u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
-                            const v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
-                            currOffset += 16;
-                            firstDataLine = this._findFirstData(firstDataLine, u);
-                            chunks[k] = new chunk_1.default(u, v, bin);
-                        }
-                        binIndex[bin] = chunks;
+                    if (chunkCount === 2) {
+                        stats = this.parsePseudoBin(bytes, currOffset);
                     }
+                    currOffset += 16 * chunkCount;
                 }
-                // the linear index
-                const linearCount = bytes.readInt32LE(currOffset);
-                currOffset += 4;
-                const linearIndex = new Array(linearCount);
-                for (let k = 0; k < linearCount; k += 1) {
-                    linearIndex[k] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
-                    currOffset += 8;
-                    firstDataLine = this._findFirstData(firstDataLine, linearIndex[k]);
+                else {
+                    const chunkCount = bytes.readInt32LE(currOffset);
+                    currOffset += 4;
+                    const chunks = new Array(chunkCount);
+                    for (let k = 0; k < chunkCount; k += 1) {
+                        const u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
+                        const v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
+                        currOffset += 16;
+                        firstDataLine = this._findFirstData(firstDataLine, u);
+                        chunks[k] = new chunk_1.default(u, v, bin);
+                    }
+                    binIndex[bin] = chunks;
                 }
-                return { binIndex, linearIndex, stats };
-            });
-            return {
-                indices,
-                metaChar,
-                maxBinNumber,
-                maxRefLength,
-                skipLines,
-                firstDataLine,
-                columnNumbers,
-                coordinateType,
-                format,
-                refIdToName,
-                refNameToId,
-                maxBlockSize: 1 << 16,
-            };
+            }
+            // the linear index
+            const linearCount = bytes.readInt32LE(currOffset);
+            currOffset += 4;
+            const linearIndex = new Array(linearCount);
+            for (let k = 0; k < linearCount; k += 1) {
+                linearIndex[k] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
+                currOffset += 8;
+                firstDataLine = this._findFirstData(firstDataLine, linearIndex[k]);
+            }
+            return { binIndex, linearIndex, stats };
         });
+        return {
+            indices,
+            metaChar,
+            maxBinNumber,
+            maxRefLength,
+            skipLines,
+            firstDataLine,
+            columnNumbers,
+            coordinateType,
+            format,
+            refIdToName,
+            refNameToId,
+            maxBlockSize: 1 << 16,
+        };
     }
     parsePseudoBin(bytes, offset) {
         const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
@@ -202,57 +200,55 @@ class TabixIndex extends indexFile_1.default {
         }
         return { refNameToId, refIdToName };
     }
-    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) {
-                return [];
-            }
-            const refId = indexData.refNameToId[refName];
-            const ba = indexData.indices[refId];
-            if (!ba) {
-                return [];
-            }
-            const minOffset = ba.linearIndex.length
-                ? ba.linearIndex[min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
-                    ? ba.linearIndex.length - 1
-                    : min >> TAD_LIDX_SHIFT]
-                : new virtualOffset_1.default(0, 0);
-            if (!minOffset) {
-                console.warn('querying outside of possible tabix range');
-            }
-            // const { linearIndex, binIndex } = indexes
-            const overlappingBins = reg2bins(min, max); // List of bin #s that overlap min, max
-            const chunks = [];
-            // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
-            for (const [start, end] of overlappingBins) {
-                for (let bin = start; bin <= end; bin++) {
-                    if (ba.binIndex[bin]) {
-                        for (const c of ba.binIndex[bin]) {
-                            chunks.push(new chunk_1.default(c.minv, c.maxv, bin));
-                        }
+    async blocksForRange(refName, min, max, opts = {}) {
+        if (min < 0) {
+            min = 0;
+        }
+        const indexData = await this.parse(opts);
+        const refId = indexData.refNameToId[refName];
+        if (refId === undefined) {
+            return [];
+        }
+        const ba = indexData.indices[refId];
+        if (!ba) {
+            return [];
+        }
+        const minOffset = ba.linearIndex.length
+            ? ba.linearIndex[min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
+                ? ba.linearIndex.length - 1
+                : min >> TAD_LIDX_SHIFT]
+            : new virtualOffset_1.default(0, 0);
+        if (!minOffset) {
+            console.warn('querying outside of possible tabix range');
+        }
+        // const { linearIndex, binIndex } = indexes
+        const overlappingBins = reg2bins(min, max); // List of bin #s that overlap min, max
+        const chunks = [];
+        // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+        for (const [start, end] of overlappingBins) {
+            for (let bin = start; bin <= end; bin++) {
+                if (ba.binIndex[bin]) {
+                    for (const c of ba.binIndex[bin]) {
+                        chunks.push(new chunk_1.default(c.minv, c.maxv, bin));
                     }
                 }
             }
-            // Use the linear index to find minimum file position of chunks that could
-            // contain alignments in the region
-            const nintv = ba.linearIndex.length;
-            let lowest = null;
-            const minLin = Math.min(min >> 14, nintv - 1);
-            const maxLin = Math.min(max >> 14, nintv - 1);
-            for (let i = minLin; i <= maxLin; ++i) {
-                const vp = ba.linearIndex[i];
-                if (vp) {
-                    if (!lowest || vp.compareTo(lowest) < 0) {
-                        lowest = vp;
-                    }
+        }
+        // Use the linear index to find minimum file position of chunks that could
+        // contain alignments in the region
+        const nintv = ba.linearIndex.length;
+        let lowest = null;
+        const minLin = Math.min(min >> 14, nintv - 1);
+        const maxLin = Math.min(max >> 14, nintv - 1);
+        for (let i = minLin; i <= maxLin; ++i) {
+            const vp = ba.linearIndex[i];
+            if (vp) {
+                if (!lowest || vp.compareTo(lowest) < 0) {
+                    lowest = vp;
                 }
             }
-            return (0, util_1.optimizeChunks)(chunks, lowest);
-        });
+        }
+        return (0, util_1.optimizeChunks)(chunks, lowest);
     }
 }
 exports.default = TabixIndex;

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;IAC/C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE,CAAC;YACV,OAAO,KAAK,CAAC,SAAS,CAAA;QACxB,CAAC;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAA;QAC9B,IAAA,uBAAgB,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAE7B,0BAA0B;QAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,aAAa,EAAE,CAAC;YACtD,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACjC,oDAAoD;QACtD,CAAC;QAED,6CAA6C;QAC7C,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACrC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACxC,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,UAAU,GAA2B;YACzC,CAAC,EAAE,SAAS;YACZ,CAAC,EAAE,KAAK;YACR,CAAC,EAAE,KAAK;SACT,CAAA;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC5C,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;YAC1B,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;YAC5B,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;SAC3B,CAAA;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QACvC,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACvD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QAEvC,2BAA2B;QAC3B,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QAC/C,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,GAAG,iBAAiB,CAAC,CACxC,CAAA;QAED,+CAA+C;QAC/C,IAAI,UAAU,GAAG,EAAE,GAAG,iBAAiB,CAAA;QACvC,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;YACnD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YAC9C,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;gBAC1C,UAAU,IAAI,CAAC,CAAA;gBACf,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;oBAChD,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;wBACrB,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAChD,CAAC;oBACD,UAAU,IAAI,EAAE,GAAG,UAAU,CAAA;gBAC/B,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;oBAChD,UAAU,IAAI,CAAC,CAAA;oBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAC1C,UAAU,IAAI,EAAE,CAAA;wBAChB,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBACrD,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,mBAAmB;YACnB,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YACjD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;YAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACxC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gBAC7C,UAAU,IAAI,CAAC,CAAA;gBACf,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;YACpE,CAAC;YACD,OAAO,EAAE,QAAQ,E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package/dist/util.d.ts

@@ -2,14 +2,15 @@ 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;
@@ -21,4 +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[];

package/dist/util.js

@@ -1,13 +1,4 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.longToNumber = longToNumber;
 exports.checkAbortSignal = checkAbortSignal;
@@ -24,14 +15,15 @@ function longToNumber(long) {
 class AbortError extends Error {
 }
 /**
- * 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
  */
 function checkAbortSignal(signal) {
@@ -55,11 +47,9 @@ function checkAbortSignal(signal) {
  * provide a place to break when an abort signal is received.
  * @param {AbortSignal} signal
  */
-function abortBreakPoint(signal) {
-    return __awaiter(this, void 0, void 0, function* () {
-        yield Promise.resolve();
-        checkAbortSignal(signal);
-    });
+async function abortBreakPoint(signal) {
+    await Promise.resolve();
+    checkAbortSignal(signal);
 }
 function canMergeBlocks(chunk1, chunk2) {
     return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAGA,oCAQC;AAiBD,4CAcC;AAQD,0CAGC;AAED,wCAKC;AAED,wCAgCC;AA3FD,SAAgB,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AAED,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD;;;;;;;;;;;GAWG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACI,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAAS,GAAiB,IAAI,CAAA;IAElC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,EAAE,EAAE;QAC1B,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QACrB,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,IAAI,EAAE,CAAC;gBACvB,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC,CAAC,CAAA;IAEF,OAAO,YAAY,CAAA;AACrB,CAAC"}

package/dist/virtualOffset.d.ts

@@ -5,6 +5,5 @@ export default class VirtualOffset {
     constructor(blockPosition: number, dataPosition: number);
     toString(): string;
     compareTo(b: VirtualOffset): number;
-    static min(...args: VirtualOffset[]): VirtualOffset;
 }
 export declare function fromBytes(bytes: Buffer, offset?: number, bigendian?: boolean): VirtualOffset;

package/dist/virtualOffset.js

@@ -12,19 +12,6 @@ class VirtualOffset {
     compareTo(b) {
         return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
     }
-    static min(...args) {
-        let min;
-        let i = 0;
-        for (; !min; i += 1) {
-            min = args[i];
-        }
-        for (; i < args.length; i += 1) {
-            if (min.compareTo(args[i]) > 0) {
-                min = args[i];
-            }
-        }
-        return min;
-    }
 }
 exports.default = VirtualOffset;
 function fromBytes(bytes, offset = 0, bigendian = false) {

package/dist/virtualOffset.js.map

@@ -1 +1 @@
-{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;AAiCA,8BAcC;AA9CD,MAAqB,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AA/BD,gCA+BC;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC"}
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;AAmBA,8BAcC;AAhCD,MAAqB,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;CACF;AAjBD,gCAiBC;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}

package/esm/chunk.js

@@ -7,7 +7,6 @@ export default class Chunk {
         this._fetchedSize = fetchedSize;
     }
     toUniqueString() {
-        // eslint-disable-next-line @typescript-eslint/restrict-template-expressions
         return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
     }
     toString() {

package/esm/chunk.js.map

@@ -1 +1 @@
-{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,4EAA4E;QAC5E,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
+{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}

package/esm/csi.d.ts

@@ -85,5 +85,5 @@ export default class CSI extends IndexFile {
     /**
      * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
      */
-    reg2bins(beg: number, end: number): number[][];
+    reg2bins(beg: number, end: number): (readonly [number, number])[];
 }

package/esm/csi.js

@@ -21,10 +21,10 @@ export default class CSI extends IndexFile {
     }
     async lineCount(refName, opts = {}) {
         const indexData = await 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;
@@ -172,10 +172,10 @@ export default class CSI extends IndexFile {
             min = 0;
         }
         const indexData = await 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 [];