npm - @gmod/bam - Versions diffs - 7.2.0 → 7.2.1 - Mend

@gmod/bam 7.2.0 → 7.2.1

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 (32) hide show

package/README.md CHANGED Viewed

@@ -58,6 +58,10 @@ const records = await ti.getRecordsForRange('1', 2000000, 2000001)
 Let us know if it doesn't work for your use case.
+Caveat: htsget `getRecordsForRange` does not honor `viewAsPairs`,
+`pairAcrossChr`, `maxInsertSize`, or `filterBy`. The range is fetched from the
+server as-is.
 ## Documentation
 ### BAM constructor

package/dist/bai.js CHANGED Viewed

@@ -199,7 +199,7 @@ class BAI extends indexFile_ts_1.default {
         }
         return depths.map(d => ({
             ...d,
-            score: (d.score * (stats?.lineCount || 0)) / totalSize,
+            score: (d.score * (stats?.lineCount ?? 0)) / totalSize,
         }));
     }
     reg2bins(min, max) {

package/dist/bamFile.js CHANGED Viewed

@@ -51,11 +51,11 @@ class BamFile {
             this.bam = new nullFilehandle_ts_1.default();
         }
         else {
-            throw new Error('unable to initialize bam');
+            throw new Error('no bam source: pass bamFilehandle, bamPath, bamUrl, or htsget: true');
         }
         const csiFh = resolveFilehandle(csiFilehandle, csiPath, csiUrl);
         const baiFh = resolveFilehandle(baiFilehandle, baiPath, baiUrl) ??
-            resolveFilehandle(undefined, bamPath && `${bamPath}.bai`, bamUrl && `${bamUrl}.bai`);
+            resolveFilehandle(undefined, bamPath ? `${bamPath}.bai` : undefined, bamUrl ? `${bamUrl}.bai` : undefined);
         if (csiFh) {
             this.index = new csi_ts_1.default({ filehandle: csiFh });
         }
@@ -63,7 +63,7 @@ class BamFile {
             this.index = new bai_ts_1.default({ filehandle: baiFh });
         }
         else if (!htsget) {
-            throw new Error('unable to infer index format');
+            throw new Error('no index source: pass csi*/bai* options or a bamPath/bamUrl so the .bai sibling can be inferred');
         }
         // htsget mode operates without a parsed index
     }
@@ -170,12 +170,12 @@ class BamFile {
     async fetchPairs(chrId, records, opts) {
         const { pairAcrossChr, maxInsertSize = 200000 } = opts;
         const readNameCounts = {};
-        const readIds = {};
+        const readIds = new Set();
         for (let i = 0, l = records.length; i < l; i++) {
             const r = records[i];
             const name = r.name;
-            readNameCounts[name] = (readNameCounts[name] || 0) + 1;
-            readIds[r.fileOffset] = 1;
+            readNameCounts[name] = (readNameCounts[name] ?? 0) + 1;
+            readIds.add(r.fileOffset);
         }
         const matePromises = [];
         for (let i = 0, l = records.length; i < l; i++) {
@@ -198,19 +198,19 @@ class BamFile {
                 map.set(m.toString(), m);
             }
         }
-        const mateFeatPromises = await Promise.all([...map.values()].map(async (c) => {
+        const mateFeatLists = await Promise.all([...map.values()].map(async (c) => {
             const features = await this._readChunkFeatures(c, opts);
             const mateRecs = [];
             for (let i = 0, l = features.length; i < l; i++) {
                 const feature = features[i];
                 if (readNameCounts[feature.name] === 1 &&
-                    !readIds[feature.fileOffset]) {
+                    !readIds.has(feature.fileOffset)) {
                     mateRecs.push(feature);
                 }
             }
             return mateRecs;
         }));
-        return mateFeatPromises.flat();
+        return mateFeatLists.flat();
     }
     async _readChunkFeatures(chunk, opts) {
         const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
@@ -228,8 +228,10 @@ class BamFile {
             const blockSize = dataView.getInt32(blockStart, true);
             const blockEnd = blockStart + 4 + blockSize - 1;
             if (hasDpositions) {
-                while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]) { }
-                pos--;
+                const target = blockStart + chunk.minv.dataPosition;
+                while (pos < dpositions.length && target >= dpositions[pos]) {
+                    pos++;
+                }
             }
             if (blockEnd < ba.length) {
                 const feature = new this.RecordClass({
@@ -282,11 +284,12 @@ class BamFile {
             return 0;
         }
         await this.getHeader(opts);
-        if (!this.chrToIndex) {
+        const chrToIndex = this.chrToIndex;
+        if (!chrToIndex) {
             throw new Error('Header not yet parsed');
         }
         const mapped = regions.flatMap(r => {
-            const refId = this.chrToIndex[r.refName];
+            const refId = chrToIndex[r.refName];
             if (refId === undefined) {
                 return [];
             }

package/dist/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/csi.js CHANGED Viewed

@@ -111,6 +111,7 @@ class CSI extends indexFile_ts_1.default {
         const auxLength = dataView.getInt32(12, true);
         const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
         const refCount = dataView.getInt32(16 + auxLength, true);
+        // SYNC: ~/src/gmod/tabix-js/src/csi.ts _parse — two-pass structure
         // read the indexes for each reference sequence
         let curr = 16 + auxLength + 4;
         let firstDataLine;
@@ -194,6 +195,7 @@ class CSI extends indexFile_ts_1.default {
      * (zero-based half-open). Follows the reference implementation in hts-specs
      * CSIv1.tex.
      */
+    // SYNC: ~/src/gmod/tabix-js/src/csi.ts reg2bins
     reg2bins(beg, end) {
         // Clamp end to the maximum coordinate the index can address. With minShift
         // and depth, the index covers positions in [0, 2^(minShift + depth*3)).

package/dist/csi.js.map CHANGED Viewed

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

@@ -11,7 +11,7 @@ export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends Bam
         recordClass?: BamRecordClass<T>;
     });
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
-    getHeader(opts?: BaseOpts): Promise<{
+    getHeaderPre(opts?: BaseOpts): Promise<{
         tag: string;
         data: {
             tag: string;

package/dist/htsget.js CHANGED Viewed

@@ -87,7 +87,7 @@ class HtsgetFile extends bamFile_ts_1.default {
         const allRecords = await this.readBamFeatures(uncba, [], [], new chunk_ts_1.default(zero, zero, 0));
         return (0, util_ts_1.appendInRange)(allRecords, chrId, min, max);
     }
-    async getHeader(opts = {}) {
+    async getHeaderPre(opts = {}) {
         const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
         const result = await fetchOk(url, opts);
         const data = await result.json();

package/dist/htsget.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/indexFile.js CHANGED Viewed

@@ -6,6 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.memoizeByRefId = memoizeByRefId;
 const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
 const util_ts_1 = require("./util.js");
+// SYNC: ~/src/gmod/tabix-js/src/util.ts memoizeByRefId
 // LRU-cache the result of getIndices(refId) so repeated lookups for the same
 // reference don't re-walk the index bytes.
 function memoizeByRefId(getIndices, maxSize = 5) {
@@ -67,7 +68,7 @@ class IndexFile {
     }
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);
-        return indexData.indices(refId)?.stats?.lineCount || 0;
+        return indexData.indices(refId)?.stats?.lineCount ?? 0;
     }
     async hasRefSeq(seqId, opts) {
         const indexData = await this.parse(opts);

package/dist/indexFile.js.map CHANGED Viewed

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package/dist/util.js CHANGED Viewed

@@ -116,6 +116,7 @@ function findFirstData(firstDataLine, virtualOffset) {
             : firstDataLine
         : virtualOffset;
 }
+// SYNC: ~/src/gmod/tabix-js/src/util.ts parseNameBytes uses indexOf(0) instead of byte scan
 function parseNameBytes(namesBytes, renameRefSeq = s => s) {
     const decoder = new TextDecoder();
     let currRefId = 0;

package/dist/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/esm/bai.js CHANGED Viewed

@@ -161,7 +161,7 @@ export default class BAI extends IndexFile {
         }
         return depths.map(d => ({
             ...d,
-            score: (d.score * (stats?.lineCount || 0)) / totalSize,
+            score: (d.score * (stats?.lineCount ?? 0)) / totalSize,
         }));
     }
     reg2bins(min, max) {

package/esm/bamFile.js CHANGED Viewed

@@ -45,11 +45,11 @@ export default class BamFile {
             this.bam = new NullFilehandle();
         }
         else {
-            throw new Error('unable to initialize bam');
+            throw new Error('no bam source: pass bamFilehandle, bamPath, bamUrl, or htsget: true');
         }
         const csiFh = resolveFilehandle(csiFilehandle, csiPath, csiUrl);
         const baiFh = resolveFilehandle(baiFilehandle, baiPath, baiUrl) ??
-            resolveFilehandle(undefined, bamPath && `${bamPath}.bai`, bamUrl && `${bamUrl}.bai`);
+            resolveFilehandle(undefined, bamPath ? `${bamPath}.bai` : undefined, bamUrl ? `${bamUrl}.bai` : undefined);
         if (csiFh) {
             this.index = new CSI({ filehandle: csiFh });
         }
@@ -57,7 +57,7 @@ export default class BamFile {
             this.index = new BAI({ filehandle: baiFh });
         }
         else if (!htsget) {
-            throw new Error('unable to infer index format');
+            throw new Error('no index source: pass csi*/bai* options or a bamPath/bamUrl so the .bai sibling can be inferred');
         }
         // htsget mode operates without a parsed index
     }
@@ -164,12 +164,12 @@ export default class BamFile {
     async fetchPairs(chrId, records, opts) {
         const { pairAcrossChr, maxInsertSize = 200000 } = opts;
         const readNameCounts = {};
-        const readIds = {};
+        const readIds = new Set();
         for (let i = 0, l = records.length; i < l; i++) {
             const r = records[i];
             const name = r.name;
-            readNameCounts[name] = (readNameCounts[name] || 0) + 1;
-            readIds[r.fileOffset] = 1;
+            readNameCounts[name] = (readNameCounts[name] ?? 0) + 1;
+            readIds.add(r.fileOffset);
         }
         const matePromises = [];
         for (let i = 0, l = records.length; i < l; i++) {
@@ -192,19 +192,19 @@ export default class BamFile {
                 map.set(m.toString(), m);
             }
         }
-        const mateFeatPromises = await Promise.all([...map.values()].map(async (c) => {
+        const mateFeatLists = await Promise.all([...map.values()].map(async (c) => {
             const features = await this._readChunkFeatures(c, opts);
             const mateRecs = [];
             for (let i = 0, l = features.length; i < l; i++) {
                 const feature = features[i];
                 if (readNameCounts[feature.name] === 1 &&
-                    !readIds[feature.fileOffset]) {
+                    !readIds.has(feature.fileOffset)) {
                     mateRecs.push(feature);
                 }
             }
             return mateRecs;
         }));
-        return mateFeatPromises.flat();
+        return mateFeatLists.flat();
     }
     async _readChunkFeatures(chunk, opts) {
         const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
@@ -222,8 +222,10 @@ export default class BamFile {
             const blockSize = dataView.getInt32(blockStart, true);
             const blockEnd = blockStart + 4 + blockSize - 1;
             if (hasDpositions) {
-                while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]) { }
-                pos--;
+                const target = blockStart + chunk.minv.dataPosition;
+                while (pos < dpositions.length && target >= dpositions[pos]) {
+                    pos++;
+                }
             }
             if (blockEnd < ba.length) {
                 const feature = new this.RecordClass({
@@ -276,11 +278,12 @@ export default class BamFile {
             return 0;
         }
         await this.getHeader(opts);
-        if (!this.chrToIndex) {
+        const chrToIndex = this.chrToIndex;
+        if (!chrToIndex) {
             throw new Error('Header not yet parsed');
         }
         const mapped = regions.flatMap(r => {
-            const refId = this.chrToIndex[r.refName];
+            const refId = chrToIndex[r.refName];
             if (refId === undefined) {
                 return [];
             }

package/esm/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/csi.js CHANGED Viewed

@@ -73,6 +73,7 @@ export default class CSI extends IndexFile {
         const auxLength = dataView.getInt32(12, true);
         const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
         const refCount = dataView.getInt32(16 + auxLength, true);
+        // SYNC: ~/src/gmod/tabix-js/src/csi.ts _parse — two-pass structure
         // read the indexes for each reference sequence
         let curr = 16 + auxLength + 4;
         let firstDataLine;
@@ -156,6 +157,7 @@ export default class CSI extends IndexFile {
      * (zero-based half-open). Follows the reference implementation in hts-specs
      * CSIv1.tex.
      */
+    // SYNC: ~/src/gmod/tabix-js/src/csi.ts reg2bins
     reg2bins(beg, end) {
         // Clamp end to the maximum coordinate the index can address. With minShift
         // and depth, the index covers positions in [0, 2^(minShift + depth*3)).

package/esm/csi.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/htsget.d.ts CHANGED Viewed

@@ -11,7 +11,7 @@ export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends Bam
         recordClass?: BamRecordClass<T>;
     });
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
-    getHeader(opts?: BaseOpts): Promise<{
+    getHeaderPre(opts?: BaseOpts): Promise<{
         tag: string;
         data: {
             tag: string;

package/esm/htsget.js CHANGED Viewed

@@ -49,7 +49,7 @@ export default class HtsgetFile extends BamFile {
         const allRecords = await this.readBamFeatures(uncba, [], [], new Chunk(zero, zero, 0));
         return appendInRange(allRecords, chrId, min, max);
     }
-    async getHeader(opts = {}) {
+    async getHeaderPre(opts = {}) {
         const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
         const result = await fetchOk(url, opts);
         const data = await result.json();

package/esm/htsget.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/indexFile.js CHANGED Viewed

@@ -1,5 +1,6 @@
 import QuickLRU from '@jbrowse/quick-lru';
 import { optimizeChunks } from "./util.js";
+// SYNC: ~/src/gmod/tabix-js/src/util.ts memoizeByRefId
 // LRU-cache the result of getIndices(refId) so repeated lookups for the same
 // reference don't re-walk the index bytes.
 export function memoizeByRefId(getIndices, maxSize = 5) {
@@ -61,7 +62,7 @@ export default class IndexFile {
     }
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);
-        return indexData.indices(refId)?.stats?.lineCount || 0;
+        return indexData.indices(refId)?.stats?.lineCount ?? 0;
     }
     async hasRefSeq(seqId, opts) {
         const indexData = await this.parse(opts);

package/esm/indexFile.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/util.js CHANGED Viewed

@@ -100,6 +100,7 @@ export function findFirstData(firstDataLine, virtualOffset) {
             : firstDataLine
         : virtualOffset;
 }
+// SYNC: ~/src/gmod/tabix-js/src/util.ts parseNameBytes uses indexOf(0) instead of byte scan
 export function parseNameBytes(namesBytes, renameRefSeq = s => s) {
     const decoder = new TextDecoder();
     let currRefId = 0;

package/esm/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.2.0",
+  "version": "7.2.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": {

package/src/bai.ts CHANGED Viewed

@@ -200,7 +200,7 @@ export default class BAI extends IndexFile<BaiParsed> {
     }
     return depths.map(d => ({
       ...d,
-      score: (d.score * (stats?.lineCount || 0)) / totalSize,
+      score: (d.score * (stats?.lineCount ?? 0)) / totalSize,
     }))
   }

package/src/bamFile.ts CHANGED Viewed

@@ -119,7 +119,9 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       this.htsget = true
       this.bam = new NullFilehandle()
     } else {
-      throw new Error('unable to initialize bam')
+      throw new Error(
+        'no bam source: pass bamFilehandle, bamPath, bamUrl, or htsget: true',
+      )
     }
     const csiFh = resolveFilehandle(csiFilehandle, csiPath, csiUrl)
@@ -127,15 +129,17 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       resolveFilehandle(baiFilehandle, baiPath, baiUrl) ??
       resolveFilehandle(
         undefined,
-        bamPath && `${bamPath}.bai`,
-        bamUrl && `${bamUrl}.bai`,
+        bamPath ? `${bamPath}.bai` : undefined,
+        bamUrl ? `${bamUrl}.bai` : undefined,
       )
     if (csiFh) {
       this.index = new CSI({ filehandle: csiFh })
     } else if (baiFh) {
       this.index = new BAI({ filehandle: baiFh })
     } else if (!htsget) {
-      throw new Error('unable to infer index format')
+      throw new Error(
+        'no index source: pass csi*/bai* options or a bamPath/bamUrl so the .bai sibling can be inferred',
+      )
     }
     // htsget mode operates without a parsed index
   }
@@ -270,13 +274,13 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
   async fetchPairs(chrId: number, records: T[], opts: BamOpts) {
     const { pairAcrossChr, maxInsertSize = 200000 } = opts
     const readNameCounts: Record<string, number> = {}
-    const readIds: Record<number, number> = {}
+    const readIds = new Set<number>()
     for (let i = 0, l = records.length; i < l; i++) {
       const r = records[i]!
       const name = r.name
-      readNameCounts[name] = (readNameCounts[name] || 0) + 1
-      readIds[r.fileOffset] = 1
+      readNameCounts[name] = (readNameCounts[name] ?? 0) + 1
+      readIds.add(r.fileOffset)
     }
     const matePromises: Promise<Chunk[]>[] = []
@@ -311,7 +315,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       }
     }
-    const mateFeatPromises = await Promise.all(
+    const mateFeatLists = await Promise.all(
       [...map.values()].map(async c => {
         const features = await this._readChunkFeatures(c, opts)
         const mateRecs = [] as T[]
@@ -319,7 +323,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
           const feature = features[i]!
           if (
             readNameCounts[feature.name] === 1 &&
-            !readIds[feature.fileOffset]
+            !readIds.has(feature.fileOffset)
           ) {
             mateRecs.push(feature)
           }
@@ -327,7 +331,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         return mateRecs
       }),
     )
-    return mateFeatPromises.flat()
+    return mateFeatLists.flat()
   }
   async _readChunkFeatures(chunk: Chunk, opts: BaseOpts) {
@@ -363,8 +367,10 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       const blockEnd = blockStart + 4 + blockSize - 1
       if (hasDpositions) {
-        while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]!) {}
-        pos--
+        const target = blockStart + chunk.minv.dataPosition
+        while (pos < dpositions.length && target >= dpositions[pos]!) {
+          pos++
+        }
       }
       if (blockEnd < ba.length) {
@@ -434,11 +440,12 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
       return 0
     }
     await this.getHeader(opts)
-    if (!this.chrToIndex) {
+    const chrToIndex = this.chrToIndex
+    if (!chrToIndex) {
       throw new Error('Header not yet parsed')
     }
     const mapped = regions.flatMap(r => {
-      const refId = this.chrToIndex![r.refName]
+      const refId = chrToIndex[r.refName]
       if (refId === undefined) {
         return []
       }

package/src/csi.ts CHANGED Viewed

@@ -90,6 +90,7 @@ export default class CSI extends IndexFile {
     const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined
     const refCount = dataView.getInt32(16 + auxLength, true)
+    // SYNC: ~/src/gmod/tabix-js/src/csi.ts _parse — two-pass structure
     // read the indexes for each reference sequence
     let curr = 16 + auxLength + 4
     let firstDataLine: VirtualOffset | undefined
@@ -176,6 +177,7 @@ export default class CSI extends IndexFile {
    * (zero-based half-open). Follows the reference implementation in hts-specs
    * CSIv1.tex.
    */
+  // SYNC: ~/src/gmod/tabix-js/src/csi.ts reg2bins
   protected reg2bins(beg: number, end: number) {
     // Clamp end to the maximum coordinate the index can address. With minShift
     // and depth, the index covers positions in [0, 2^(minShift + depth*3)).

package/src/htsget.ts CHANGED Viewed

@@ -87,7 +87,7 @@ export default class HtsgetFile<
     return appendInRange(allRecords, chrId, min, max)
   }
-  async getHeader(opts: BaseOpts = {}) {
+  async getHeaderPre(opts: BaseOpts = {}) {
     const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`
     const result = await fetchOk(url, opts)
     const data = await result.json()

package/src/indexFile.ts CHANGED Viewed

@@ -25,6 +25,7 @@ export interface ParsedIndexBase<R extends RefIndex = RefIndex> {
   indices: (refId: number) => R | undefined
 }
+// SYNC: ~/src/gmod/tabix-js/src/util.ts memoizeByRefId
 // LRU-cache the result of getIndices(refId) so repeated lookups for the same
 // reference don't re-walk the index bytes.
 export function memoizeByRefId<T>(
@@ -130,7 +131,7 @@ export default abstract class IndexFile<
   async lineCount(refId: number, opts?: BaseOpts) {
     const indexData = await this.parse(opts)
-    return indexData.indices(refId)?.stats?.lineCount || 0
+    return indexData.indices(refId)?.stats?.lineCount ?? 0
   }
   async hasRefSeq(seqId: number, opts?: BaseOpts) {

package/src/util.ts CHANGED Viewed

@@ -151,6 +151,7 @@ export function findFirstData(
     : virtualOffset
 }
+// SYNC: ~/src/gmod/tabix-js/src/util.ts parseNameBytes uses indexOf(0) instead of byte scan
 export function parseNameBytes(
   namesBytes: Uint8Array,
   renameRefSeq: (arg: string) => string = s => s,