@gmod/tabix 1.5.11 → 1.5.12

package/esm/util.js.map

@@ -1 +1 @@
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package/esm/virtualOffset.js.map

@@ -1 +1 @@
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+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AACA,MAAM,CAAC,OAAO,OAAO,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;AACD,MAAM,UAAU,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"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.11",
+  "version": "1.5.12",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",
@@ -22,7 +22,7 @@
   "scripts": {
     "test": "jest",
     "coverage": "npm test -- --coverage",
-    "lint": "eslint --ext .js,.ts src test",
+    "lint": "eslint --ext .js,.ts src",
     "clean": "rimraf dist esm",
     "prebuild": "npm run clean && npm run lint",
     "build:esm": "tsc --target es2018 --outDir esm",
@@ -46,22 +46,23 @@
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@types/jest": "^29.5.0",
+    "@types/jest": "^29.5.11",
     "@types/long": "^4.0.0",
-    "@types/node": "^18.15.5",
-    "@typescript-eslint/eslint-plugin": "^5.59.6",
-    "@typescript-eslint/parser": "^5.59.6",
+    "@types/node": "^20.10.5",
+    "@typescript-eslint/eslint-plugin": "^6.15.0",
+    "@typescript-eslint/parser": "^6.15.0",
     "eslint": "^8.40.0",
-    "eslint-config-prettier": "^8.8.0",
+    "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-import": "^2.27.5",
-    "eslint-plugin-prettier": "^4.2.1",
-    "jest": "^29.5.0",
+    "eslint-plugin-prettier": "^5.0.1",
+    "eslint-plugin-unicorn": "^49.0.0",
+    "jest": "^29.7.0",
     "jest-environment-jsdom": "^29.5.0",
-    "prettier": "^2.8.8",
+    "prettier": "^3.1.1",
     "rimraf": "^5.0.1",
-    "standard-changelog": "^2.0.27",
-    "ts-jest": "^29.1.0",
-    "typescript": "^5.0.4"
+    "standard-changelog": "^5.0.0",
+    "ts-jest": "^29.1.1",
+    "typescript": "^5.3.3"
   },
   "publishConfig": {
     "access": "public"

package/src/chunk.ts

@@ -7,12 +7,6 @@ export default class Chunk {
   public bin: number
   public _fetchedSize?: number
 
-  /**
-   * @param {VirtualOffset} minv
-   * @param {VirtualOffset} maxv
-   * @param {number} bin
-   * @param {number} [fetchedSize]
-   */
   constructor(
     minv: VirtualOffset,
     maxv: VirtualOffset,
@@ -26,6 +20,7 @@ export default class Chunk {
   }
 
   toUniqueString() {
+    // eslint-disable-next-line @typescript-eslint/restrict-template-expressions
     return `${this.minv}..${this.maxv} (bin ${
       this.bin
     }, fetchedSize ${this.fetchedSize()})`

package/src/csi.ts

@@ -44,7 +44,7 @@ export default class CSI extends IndexFile {
     }
     return -1
   }
-  async indexCov() {
+  indexCov() {
     throw new Error('CSI indexes do not support indexcov')
   }
 
@@ -85,7 +85,7 @@ export default class CSI extends IndexFile {
     let currRefId = 0
     let currNameStart = 0
     const refIdToName = []
-    const refNameToId: { [key: string]: number } = {}
+    const refNameToId: Record<string, number> = {}
     for (let i = 0; i < namesBytes.length; i += 1) {
       if (!namesBytes[i]) {
         if (currNameStart < i) {
@@ -104,7 +104,7 @@ export default class CSI extends IndexFile {
   // fetch and parse the index
 
   async _parse(opts: Options = {}) {
-    const bytes = await unzip((await this.filehandle.readFile(opts)) as Buffer)
+    const bytes = await unzip(await this.filehandle.readFile(opts))
 
     // check TBI magic numbers
     let csiVersion
@@ -142,7 +142,7 @@ export default class CSI extends IndexFile {
       // the binning index
       const binCount = bytes.readInt32LE(currOffset)
       currOffset += 4
-      const binIndex: { [key: string]: Chunk[] } = {}
+      const binIndex: Record<string, Chunk[]> = {}
       let stats // < provided by parsing a pseudo-bin, if present
       for (let j = 0; j < binCount; j += 1) {
         const bin = bytes.readUInt32LE(currOffset)
@@ -224,9 +224,8 @@ export default class CSI extends IndexFile {
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
         if (ba.binIndex[bin]) {
-          const binChunks = ba.binIndex[bin]
-          for (let c = 0; c < binChunks.length; ++c) {
-            chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin))
+          for (const c of ba.binIndex[bin]) {
+            chunks.push(new Chunk(c.minv, c.maxv, bin))
           }
         }
       }

package/src/index.ts

@@ -1,5 +1,3 @@
-import TabixIndexedFile from './tabixIndexedFile'
-import TBI from './tbi'
-import CSI from './csi'
-
-export { TabixIndexedFile, TBI, CSI }
+export { default as TabixIndexedFile } from './tabixIndexedFile'
+export { default as CSI } from './csi'
+export { default as TBI } from './tbi'

package/src/indexFile.ts

@@ -9,7 +9,7 @@ export interface Options {
 }
 
 export interface IndexData {
-  refNameToId: { [key: string]: number }
+  refNameToId: Record<string, number>
   refIdToName: string[]
   metaChar: string | null
   columnNumbers: { ref: number; start: number; end: number }
@@ -39,8 +39,7 @@ export default abstract class IndexFile {
   protected abstract _parse(opts: Options): Promise<IndexData>
 
   public async getMetadata(opts: Options = {}) {
-    // eslint-disable-next-line @typescript-eslint/no-unused-vars
-    const { indices, ...rest } = await this.parse(opts)
+    const { indices: _indices, ...rest } = await this.parse(opts)
     return rest
   }
 
@@ -75,6 +74,7 @@ export default abstract class IndexFile {
   }
 
   async hasRefSeq(seqId: number, opts: Options = {}) {
-    return !!((await this.parse(opts)).indices[seqId] || {}).binIndex
+    const idx = await this.parse(opts)
+    return !!idx.indices[seqId]?.binIndex
   }
 }

package/src/tabixIndexedFile.ts

@@ -13,7 +13,7 @@ import CSI from './csi'
 type GetLinesCallback = (line: string, fileOffset: number) => void
 
 const decoder =
-  typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8') : undefined
+  typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined
 
 interface GetLinesOpts {
   [key: string]: unknown
@@ -132,14 +132,14 @@ export default class TabixIndexedFile {
    */
   async getLines(
     refName: string,
-    start: number,
-    end: number,
+    s: number | undefined,
+    e: number | undefined,
     opts: GetLinesOpts | GetLinesCallback,
   ) {
     let signal: AbortSignal | undefined
     let options: Options = {}
     let callback: (line: string, lineOffset: number) => void
-    if (typeof opts === 'undefined') {
+    if (opts === undefined) {
       throw new TypeError('line callback must be provided')
     }
     if (typeof opts === 'function') {
@@ -157,12 +157,8 @@ export default class TabixIndexedFile {
 
     const metadata = await this.index.getMetadata(options)
     checkAbortSignal(signal)
-    if (!start) {
-      start = 0
-    }
-    if (!end) {
-      end = metadata.maxRefLength
-    }
+    const start = s ?? 0
+    const end = e ?? metadata.maxRefLength
     if (!(start <= end)) {
       throw new TypeError(
         'invalid start and end coordinates. start must be less than or equal to end',
@@ -177,8 +173,8 @@ export default class TabixIndexedFile {
 
     // check the chunks for any that are over the size limit.  if
     // any are, don't fetch any of them
-    for (let i = 0; i < chunks.length; i += 1) {
-      const size = chunks[i].fetchedSize()
+    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()}.`,
@@ -188,12 +184,12 @@ export default class TabixIndexedFile {
 
     // now go through each chunk and parse and filter the lines out of it
     let last = Date.now()
-    for (let chunkNum = 0; chunkNum < chunks.length; chunkNum += 1) {
+    for (const c of chunks) {
       let previousStartCoordinate: number | undefined
-      const c = chunks[chunkNum]
       const { buffer, cpositions, dpositions } = await this.chunkCache.get(
         c.toString(),
         c,
+        signal,
       )
 
       checkAbortSignal(signal)
@@ -205,7 +201,7 @@ export default class TabixIndexedFile {
           break
         }
         const b = buffer.slice(blockStart, n)
-        const line = decoder?.decode(b) || b.toString()
+        const line = decoder?.decode(b) ?? b.toString()
 
         if (dpositions) {
           while (blockStart + c.minv.dataPosition >= dpositions[pos++]) {}
@@ -278,25 +274,15 @@ export default class TabixIndexedFile {
    * non-meta line
    */
   async getHeaderBuffer(opts: Options = {}) {
-    const { firstDataLine, metaChar, maxBlockSize } = await this.getMetadata(
-      opts,
-    )
+    const { firstDataLine, metaChar, maxBlockSize } =
+      await this.getMetadata(opts)
     checkAbortSignal(opts.signal)
     const maxFetch = (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 = await this._readRegion(0, maxFetch, opts)
-    checkAbortSignal(opts.signal)
-    try {
-      bytes = await unzip(bytes)
-    } catch (e) {
-      console.error(e)
-      throw new Error(
-        //@ts-ignore
-        `error decompressing block ${e.code} at 0 (length ${maxFetch}) ${e}`,
-      )
-    }
+    const buf = await this._readRegion(0, maxFetch, opts)
+    const bytes = await unzip(buf)
 
     // trim off lines after the last non-meta line
     if (metaChar) {
@@ -312,7 +298,7 @@ export default class TabixIndexedFile {
           lastNewline = i
         }
       }
-      bytes = bytes.slice(0, lastNewline + 1)
+      return bytes.slice(0, lastNewline + 1)
     }
     return bytes
   }
@@ -357,7 +343,7 @@ export default class TabixIndexedFile {
   ) {
     const { columnNumbers, metaChar, coordinateType, format } = metadata
     // skip meta lines
-    if (line.charAt(0) === metaChar) {
+    if (metaChar && line.startsWith(metaChar)) {
       return { overlaps: false }
     }
 
@@ -412,17 +398,15 @@ export default class TabixIndexedFile {
         } else if (format === 'VCF' && currentColumnNumber === 4) {
           refSeq = line.slice(currentColumnStart, i)
         } else if (currentColumnNumber === end) {
-          let endCoordinate
           // this will never match if there is no end column
-          if (format === 'VCF') {
-            endCoordinate = this._getVcfEnd(
-              startCoordinate,
-              refSeq,
-              line.slice(currentColumnStart, i),
-            )
-          } else {
-            endCoordinate = parseInt(line.slice(currentColumnStart, i), 10)
-          }
+          const endCoordinate =
+            format === 'VCF'
+              ? this._getVcfEnd(
+                  startCoordinate,
+                  refSeq,
+                  line.slice(currentColumnStart, i),
+                )
+              : parseInt(line.slice(currentColumnStart, i), 10)
           if (endCoordinate <= regionStart) {
             return { overlaps: false }
           }
@@ -439,12 +423,12 @@ export default class TabixIndexedFile {
 
   _getVcfEnd(startCoordinate: number, refSeq: string, info: any) {
     let endCoordinate = startCoordinate + refSeq.length
-    // ignore TRA features as they specify CHR2 and END
-    // as being on a different chromosome
-    // if CHR2 is on the same chromosome, still ignore it
-    // because there should be another pairwise feature
-    // at the end of this one
-    const isTRA = info.indexOf('SVTYPE=TRA') !== -1
+    // ignore TRA features as they specify CHR2 and END as being on a different
+    // chromosome
+    //
+    // if CHR2 is on the same chromosome, still ignore it because there should
+    // be another pairwise feature at the end of this one
+    const isTRA = info.includes('SVTYPE=TRA')
     if (info[0] !== '.' && !isTRA) {
       let prevChar = ';'
       for (let j = 0; j < info.length; j += 1) {
@@ -499,10 +483,6 @@ export default class TabixIndexedFile {
       c.fetchedSize(),
       opts,
     )
-    try {
-      return unzipChunkSlice(data, c)
-    } catch (e) {
-      throw new Error(`error decompressing c ${c.toString()} ${e}`)
-    }
+    return unzipChunkSlice(data, c)
   }
 }

package/src/tbi.ts

@@ -60,7 +60,7 @@ export default class TabixIndex extends IndexFile {
     const formatFlags = bytes.readInt32LE(8)
     const coordinateType =
       formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed'
-    const formatOpts: { [key: number]: string } = {
+    const formatOpts: Record<number, string> = {
       0: 'generic',
       1: 'SAM',
       2: 'VCF',
@@ -94,7 +94,7 @@ export default class TabixIndex extends IndexFile {
       // the binning index
       const binCount = bytes.readInt32LE(currOffset)
       currOffset += 4
-      const binIndex: { [key: number]: Chunk[] } = {}
+      const binIndex: Record<number, Chunk[]> = {}
       let stats
       for (let j = 0; j < binCount; j += 1) {
         const bin = bytes.readUInt32LE(currOffset)
@@ -167,7 +167,7 @@ export default class TabixIndex extends IndexFile {
     let currRefId = 0
     let currNameStart = 0
     const refIdToName: string[] = []
-    const refNameToId: { [key: string]: number } = {}
+    const refNameToId: Record<string, number> = {}
     for (let i = 0; i < namesBytes.length; i += 1) {
       if (!namesBytes[i]) {
         if (currNameStart < i) {
@@ -223,9 +223,8 @@ export default class TabixIndex extends IndexFile {
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
         if (ba.binIndex[bin]) {
-          const binChunks = ba.binIndex[bin]
-          for (let c = 0; c < binChunks.length; ++c) {
-            chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin))
+          for (const c of ba.binIndex[bin]) {
+            chunks.push(new Chunk(c.minv, c.maxv, bin))
           }
         }
       }

package/src/util.ts

@@ -70,11 +70,7 @@ export function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset) {
 
   chunks.sort(function (c0, c1) {
     const dif = c0.minv.blockPosition - c1.minv.blockPosition
-    if (dif !== 0) {
-      return dif
-    } else {
-      return c0.minv.dataPosition - c1.minv.dataPosition
-    }
+    return dif !== 0 ? dif : c0.minv.dataPosition - c1.minv.dataPosition
   })
 
   chunks.forEach(chunk => {