@gmod/tabix 3.0.5 → 3.1.0

package/esm/csi.js.map

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

@@ -7,7 +7,7 @@ export interface Options {
 export interface IndexData {
     refNameToId: Record<string, number>;
     refIdToName: string[];
-    metaChar: string | null;
+    metaChar: string | undefined;
     columnNumbers: {
         ref: number;
         start: number;
@@ -31,7 +31,7 @@ export default abstract class IndexFile {
         [key: string]: any;
         refNameToId: Record<string, number>;
         refIdToName: string[];
-        metaChar: string | null;
+        metaChar: string | undefined;
         columnNumbers: {
             ref: number;
             start: number;

package/esm/indexFile.js

@@ -19,9 +19,9 @@ export default class IndexFile {
     }
     async parse(opts = {}) {
         if (!this.parseP) {
-            this.parseP = this._parse(opts).catch((e) => {
+            this.parseP = this._parse(opts).catch((error) => {
                 this.parseP = undefined;
-                throw e;
+                throw error;
             });
         }
         return this.parseP;

package/esm/indexFile.js.map

@@ -1 +1 @@
-{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAmBA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IACvC,CAAC;CACF"}
+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAmBA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;gBACvD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,KAAK,CAAA;YACb,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IACvC,CAAC;CACF"}

package/esm/tabixIndexedFile.d.ts

@@ -1,3 +1,4 @@
+import LRU from 'quick-lru';
 import Chunk from './chunk.ts';
 import { IndexData, Options } from './indexFile.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
@@ -12,6 +13,10 @@ export default class TabixIndexedFile {
     private index;
     private renameRefSeq;
     private chunkCache;
+    cache: LRU<string, {
+        buffer: Uint8Array;
+        nextIn: number;
+    }>;
     /**
      * @param {object} args
      *
@@ -69,7 +74,7 @@ export default class TabixIndexedFile {
         [key: string]: any;
         refNameToId: Record<string, number>;
         refIdToName: string[];
-        metaChar: string | null;
+        metaChar: string | undefined;
         columnNumbers: {
             ref: number;
             start: number;

package/esm/tabixIndexedFile.js

@@ -37,6 +37,9 @@ export default class TabixIndexedFile {
      * just the names of the reference sequences that are used for querying.
      */
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, renameRefSeqs = n => n, chunkCacheSize = 5 * 2 ** 20, }) {
+        this.cache = new LRU({
+            maxSize: 1000,
+        });
         if (filehandle) {
             this.filehandle = filehandle;
         }
@@ -226,11 +229,12 @@ export default class TabixIndexedFile {
             let lastNewline = -1;
             const newlineByte = '\n'.charCodeAt(0);
             const metaByte = metaChar.charCodeAt(0);
-            for (let i = 0; i < bytes.length; i += 1) {
-                if (i === lastNewline + 1 && bytes[i] !== metaByte) {
+            for (let i = 0, l = bytes.length; i < l; i++) {
+                const byte = bytes[i];
+                if (i === lastNewline + 1 && byte !== metaByte) {
                     break;
                 }
-                if (bytes[i] === newlineByte) {
+                if (byte === newlineByte) {
                     lastNewline = i;
                 }
             }
@@ -312,7 +316,7 @@ export default class TabixIndexedFile {
                     }
                 }
                 else if (currentColumnNumber === start) {
-                    startCoordinate = parseInt(line.slice(currentColumnStart, i), 10);
+                    startCoordinate = Number.parseInt(line.slice(currentColumnStart, i), 10);
                     // we convert to 0-based-half-open
                     if (coordinateType === '1-based-closed') {
                         startCoordinate -= 1;
@@ -323,14 +327,12 @@ export default class TabixIndexedFile {
                             overlaps: false,
                         };
                     }
-                    if (end === 0 || end === start) {
-                        // if we have no end, we assume the feature is 1 bp long
-                        if (startCoordinate + 1 <= regionStart) {
-                            return {
-                                startCoordinate,
-                                overlaps: false,
-                            };
-                        }
+                    if ((end === 0 || end === start) && // if we have no end, we assume the feature is 1 bp long
+                        startCoordinate + 1 <= regionStart) {
+                        return {
+                            startCoordinate,
+                            overlaps: false,
+                        };
                     }
                 }
                 else if (format === 'VCF' && currentColumnNumber === 4) {
@@ -375,7 +377,7 @@ export default class TabixIndexedFile {
                     if (valueEnd === -1) {
                         valueEnd = info.length;
                     }
-                    endCoordinate = parseInt(info.slice(j + 4, valueEnd), 10);
+                    endCoordinate = Number.parseInt(info.slice(j + 4, valueEnd), 10);
                     break;
                 }
                 prevChar = info[j];
@@ -403,7 +405,7 @@ export default class TabixIndexedFile {
      */
     async readChunk(c, opts = {}) {
         const ret = await this.filehandle.read(c.fetchedSize(), c.minv.blockPosition, opts);
-        return unzipChunkSlice(ret, c);
+        return unzipChunkSlice(ret, c, this.cache);
     }
 }
 //# sourceMappingURL=tabixIndexedFile.js.map

package/esm/tabixIndexedFile.js.map

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

@@ -11,7 +11,7 @@ export default class TabixIndex extends IndexFile {
                 lineCount: number;
             } | undefined;
         }[];
-        metaChar: string | null;
+        metaChar: string | undefined;
         maxBinNumber: number;
         maxRefLength: number;
         skipLines: number;

package/esm/tbi.js

@@ -54,7 +54,7 @@ export default class TabixIndex extends IndexFile {
             1: 'SAM',
             2: 'VCF',
         };
-        const format = formatOpts[formatFlags & 0xf];
+        const format = formatOpts[formatFlags & 0xF];
         if (!format) {
             throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
         }
@@ -67,7 +67,7 @@ export default class TabixIndex extends IndexFile {
         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 metaChar = metaValue ? String.fromCharCode(metaValue) : undefined;
         const skipLines = dataView.getInt32(28, true);
         // read sequence dictionary
         const nameSectionLength = dataView.getInt32(32, true);
@@ -179,7 +179,7 @@ export default class TabixIndex extends IndexFile {
         if (!ba) {
             return [];
         }
-        const minOffset = ba.linearIndex.length
+        const minOffset = ba.linearIndex.length > 0
             ? ba.linearIndex[min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
                 ? ba.linearIndex.length - 1
                 : min >> TAD_LIDX_SHIFT]
@@ -203,15 +203,13 @@ export default class TabixIndex extends IndexFile {
         // 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;
+        let lowest;
         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;
-                }
+            if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
+                lowest = vp;
             }
         }
         return optimizeChunks(chunks, lowest);

package/esm/tbi.js.map

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

@@ -17,14 +17,14 @@ export function checkAbortSignal(signal) {
         return;
     }
     if (signal.aborted) {
-        if (typeof DOMException !== 'undefined') {
-            throw new DOMException('aborted', 'AbortError');
-        }
-        else {
+        if (typeof DOMException === 'undefined') {
             const e = new AbortError('aborted');
             e.code = 'ERR_ABORTED';
             throw e;
         }
+        else {
+            throw new DOMException('aborted', 'AbortError');
+        }
     }
 }
 /**
@@ -43,17 +43,17 @@ export function canMergeBlocks(chunk1, chunk2) {
 }
 export function optimizeChunks(chunks, lowest) {
     const mergedChunks = [];
-    let lastChunk = null;
+    let lastChunk;
     if (chunks.length === 0) {
         return chunks;
     }
     chunks.sort(function (c0, c1) {
         const dif = c0.minv.blockPosition - c1.minv.blockPosition;
-        return dif !== 0 ? dif : c0.minv.dataPosition - c1.minv.dataPosition;
+        return dif === 0 ? c0.minv.dataPosition - c1.minv.dataPosition : dif;
     });
-    chunks.forEach(chunk => {
+    for (const chunk of chunks) {
         if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
-            if (lastChunk === null) {
+            if (lastChunk === undefined) {
                 mergedChunks.push(chunk);
                 lastChunk = chunk;
             }
@@ -69,7 +69,7 @@ export function optimizeChunks(chunks, lowest) {
                 }
             }
         }
-    });
+    }
     return mergedChunks;
 }
 //# sourceMappingURL=util.js.map

package/esm/util.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.0.5",
+  "version": "3.1.0",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",
   "types": "./dist/index.d.ts",
@@ -63,7 +63,7 @@
     "documentation": "^14.0.3",
     "eslint": "^9.9.0",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^59.0.0",
+    "eslint-plugin-unicorn": "^60.0.0",
     "prettier": "^3.3.3",
     "rimraf": "^6.0.1",
     "standard-changelog": "^7.0.1",

package/src/chunk.ts

@@ -11,7 +11,7 @@ export default class Chunk {
     minv: VirtualOffset,
     maxv: VirtualOffset,
     bin: number,
-    fetchedSize = undefined,
+    fetchedSize?: number,
   ) {
     this.minv = minv
     this.maxv = maxv

package/src/csi.ts

@@ -58,7 +58,7 @@ export default class CSI extends IndexFile {
     const formatFlags = dataView.getInt32(offset, true)
     const coordinateType =
       formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed'
-    const format = formats[(formatFlags & 0xf) as 0 | 1 | 2]
+    const format = formats[(formatFlags & 0xF) as 0 | 1 | 2]
     if (!format) {
       throw new Error(`invalid Tabix preset format flags ${formatFlags}`)
     }
@@ -68,7 +68,7 @@ export default class CSI extends IndexFile {
       end: dataView.getInt32(offset + 12, true),
     }
     const metaValue = dataView.getInt32(offset + 16, true)
-    const metaChar = metaValue ? String.fromCharCode(metaValue) : null
+    const metaChar = metaValue ? String.fromCharCode(metaValue) : undefined
     const skipLines = dataView.getInt32(offset + 20, true)
     const nameSectionLength = dataView.getInt32(offset + 24, true)
 
@@ -112,8 +112,6 @@ export default class CSI extends IndexFile {
     }
   }
 
-  // fetch and parse the index
-
   async _parse(opts: Options = {}) {
     const bytes = await unzip(await this.filehandle.readFile(opts))
     const dataView = new DataView(bytes.buffer)
@@ -139,7 +137,7 @@ export default class CSI extends IndexFile {
         : {
             refIdToName: [],
             refNameToId: {},
-            metaChar: null,
+            metaChar: undefined,
             columnNumbers: { ref: 0, start: 1, end: 2 },
             coordinateType: 'zero-based-half-open',
             format: 'generic',

package/src/indexFile.ts

@@ -10,7 +10,7 @@ export interface Options {
 export interface IndexData {
   refNameToId: Record<string, number>
   refIdToName: string[]
-  metaChar: string | null
+  metaChar: string | undefined
   columnNumbers: { ref: number; start: number; end: number }
   coordinateType: string
   format: string
@@ -64,9 +64,9 @@ export default abstract class IndexFile {
 
   async parse(opts: Options = {}) {
     if (!this.parseP) {
-      this.parseP = this._parse(opts).catch((e: unknown) => {
+      this.parseP = this._parse(opts).catch((error: unknown) => {
         this.parseP = undefined
-        throw e
+        throw error
       })
     }
     return this.parseP

package/src/tabixIndexedFile.ts

@@ -35,6 +35,9 @@ export default class TabixIndexedFile {
   private index: IndexFile
   private renameRefSeq: (n: string) => string
   private chunkCache: AbortablePromiseCache<Chunk, ReadChunk>
+  public cache = new LRU<string, { buffer: Uint8Array; nextIn: number }>({
+    maxSize: 1000,
+  })
 
   /**
    * @param {object} args
@@ -303,11 +306,13 @@ export default class TabixIndexedFile {
       let lastNewline = -1
       const newlineByte = '\n'.charCodeAt(0)
       const metaByte = metaChar.charCodeAt(0)
-      for (let i = 0; i < bytes.length; i += 1) {
-        if (i === lastNewline + 1 && bytes[i] !== metaByte) {
+
+      for (let i = 0, l = bytes.length; i < l; i++) {
+        const byte = bytes[i]
+        if (i === lastNewline + 1 && byte !== metaByte) {
           break
         }
-        if (bytes[i] === newlineByte) {
+        if (byte === newlineByte) {
           lastNewline = i
         }
       }
@@ -402,7 +407,10 @@ export default class TabixIndexedFile {
             }
           }
         } else if (currentColumnNumber === start) {
-          startCoordinate = parseInt(line.slice(currentColumnStart, i), 10)
+          startCoordinate = Number.parseInt(
+            line.slice(currentColumnStart, i),
+            10,
+          )
           // we convert to 0-based-half-open
           if (coordinateType === '1-based-closed') {
             startCoordinate -= 1
@@ -413,13 +421,13 @@ export default class TabixIndexedFile {
               overlaps: false,
             }
           }
-          if (end === 0 || end === start) {
-            // if we have no end, we assume the feature is 1 bp long
-            if (startCoordinate + 1 <= regionStart) {
-              return {
-                startCoordinate,
-                overlaps: false,
-              }
+          if (
+            (end === 0 || end === start) && // if we have no end, we assume the feature is 1 bp long
+            startCoordinate + 1 <= regionStart
+          ) {
+            return {
+              startCoordinate,
+              overlaps: false,
             }
           }
         } else if (format === 'VCF' && currentColumnNumber === 4) {
@@ -469,7 +477,7 @@ export default class TabixIndexedFile {
           if (valueEnd === -1) {
             valueEnd = info.length
           }
-          endCoordinate = parseInt(info.slice(j + 4, valueEnd), 10)
+          endCoordinate = Number.parseInt(info.slice(j + 4, valueEnd), 10)
           break
         }
         prevChar = info[j]
@@ -502,6 +510,6 @@ export default class TabixIndexedFile {
       c.minv.blockPosition,
       opts,
     )
-    return unzipChunkSlice(ret, c)
+    return unzipChunkSlice(ret, c, this.cache)
   }
 }

package/src/tbi.ts

@@ -62,7 +62,7 @@ export default class TabixIndex extends IndexFile {
       1: 'SAM',
       2: 'VCF',
     }
-    const format = formatOpts[formatFlags & 0xf]
+    const format = formatOpts[formatFlags & 0xF]
     if (!format) {
       throw new Error(`invalid Tabix preset format flags ${formatFlags}`)
     }
@@ -75,7 +75,7 @@ export default class TabixIndex extends IndexFile {
     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 metaChar = metaValue ? String.fromCharCode(metaValue) : undefined
     const skipLines = dataView.getInt32(28, true)
 
     // read sequence dictionary
@@ -205,13 +205,14 @@ export default class TabixIndex extends IndexFile {
       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(0, 0)
+    const minOffset =
+      ba.linearIndex.length > 0
+        ? ba.linearIndex[
+            min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
+              ? ba.linearIndex.length - 1
+              : min >> TAD_LIDX_SHIFT
+          ]
+        : new VirtualOffset(0, 0)
     if (!minOffset) {
       console.warn('querying outside of possible tabix range')
     }
@@ -235,15 +236,13 @@ export default class TabixIndex extends IndexFile {
     // 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
+    let lowest: VirtualOffset | undefined
     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
-        }
+      if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
+        lowest = vp
       }
     }