@gmod/tabix 1.6.1 → 2.0.0

package/CHANGELOG.md

@@ -1,10 +1,10 @@
-## [1.6.1](https://github.com/GMOD/tabix-js/compare/v1.6.0...v1.6.1) (2024-12-07)
-
+# [2.0.0](https://github.com/GMOD/tabix-js/compare/v1.6.1...v2.0.0) (2024-12-12)
 
 
-# [1.6.0](https://github.com/GMOD/tabix-js/compare/v1.5.15...v1.6.0) (2024-11-30)
 
+## [1.6.1](https://github.com/GMOD/tabix-js/compare/v1.6.0...v1.6.1) (2024-12-07)
 
+# [1.6.0](https://github.com/GMOD/tabix-js/compare/v1.5.15...v1.6.0) (2024-11-30)
 
 ## [1.5.15](https://github.com/GMOD/tabix-js/compare/v1.5.14...v1.5.15) (2024-08-30)
 

package/dist/csi.d.ts

@@ -1,4 +1,3 @@
-import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import IndexFile, { Options } from './indexFile';
@@ -9,7 +8,7 @@ export default class CSI extends IndexFile {
     constructor(args: any);
     lineCount(refName: string, opts?: Options): Promise<number>;
     indexCov(): void;
-    parseAuxData(bytes: Buffer, offset: number): {
+    parseAuxData(bytes: Uint8Array, offset: number): {
         refIdToName: string[];
         refNameToId: Record<string, number>;
         skipLines: number;
@@ -22,7 +21,7 @@ export default class CSI extends IndexFile {
         format: string;
         coordinateType: string;
     };
-    _parseNameBytes(namesBytes: Buffer): {
+    _parseNameBytes(namesBytes: Uint8Array): {
         refNameToId: Record<string, number>;
         refIdToName: string[];
     };
@@ -78,7 +77,7 @@ export default class CSI extends IndexFile {
         coordinateType: string;
         format: string;
     }>;
-    parsePseudoBin(bytes: Buffer, offset: number): {
+    parsePseudoBin(bytes: Uint8Array, offset: number): {
         lineCount: number;
     };
     blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;

package/dist/csi.js

@@ -15,13 +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 __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 };
 };
@@ -34,6 +44,11 @@ const util_1 = require("./util");
 const indexFile_1 = __importDefault(require("./indexFile"));
 const CSI1_MAGIC = 21582659; // CSI\1
 const CSI2_MAGIC = 38359875; // CSI\2
+const formats = {
+    0: 'generic',
+    1: 'SAM',
+    2: 'VCF',
+};
 function lshift(num, bits) {
     return num * 2 ** bits;
 }
@@ -67,22 +82,23 @@ class CSI extends indexFile_1.default {
         throw new Error('CSI indexes do not support indexcov');
     }
     parseAuxData(bytes, offset) {
-        const formatFlags = bytes.readInt32LE(offset);
+        const dataView = new DataView(bytes.buffer);
+        const formatFlags = dataView.getInt32(offset, true);
         const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
-        const format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[formatFlags & 0xf];
+        const format = formats[(formatFlags & 0xf)];
         if (!format) {
             throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
         }
         const columnNumbers = {
-            ref: bytes.readInt32LE(offset + 4),
-            start: bytes.readInt32LE(offset + 8),
-            end: bytes.readInt32LE(offset + 12),
+            ref: dataView.getInt32(offset + 4, true),
+            start: dataView.getInt32(offset + 8, true),
+            end: dataView.getInt32(offset + 12, true),
         };
-        const metaValue = bytes.readInt32LE(offset + 16);
+        const metaValue = dataView.getInt32(offset + 16, true);
         const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
-        const skipLines = bytes.readInt32LE(offset + 20);
-        const nameSectionLength = bytes.readInt32LE(offset + 24);
-        const { refIdToName, refNameToId } = this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength));
+        const skipLines = dataView.getInt32(offset + 20, true);
+        const nameSectionLength = dataView.getInt32(offset + 24, true);
+        const { refIdToName, refNameToId } = this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength));
         return {
             refIdToName,
             refNameToId,
@@ -98,11 +114,11 @@ class CSI extends indexFile_1.default {
         let currNameStart = 0;
         const refIdToName = [];
         const refNameToId = {};
+        const decoder = new TextDecoder('utf8');
         for (let i = 0; i < namesBytes.length; i += 1) {
             if (!namesBytes[i]) {
                 if (currNameStart < i) {
-                    let refName = namesBytes.toString('utf8', currNameStart, i);
-                    refName = this.renameRefSeq(refName);
+                    const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
                     refIdToName[currRefId] = refName;
                     refNameToId[refName] = currRefId;
                 }
@@ -110,28 +126,31 @@ class CSI extends indexFile_1.default {
                 currRefId += 1;
             }
         }
-        return { refNameToId, refIdToName };
+        return {
+            refNameToId,
+            refIdToName,
+        };
     }
     // fetch and parse the index
     async _parse(opts = {}) {
         const bytes = await (0, bgzf_filehandle_1.unzip)(await this.filehandle.readFile(opts));
+        const dataView = new DataView(bytes.buffer);
         // check TBI magic numbers
         let csiVersion;
-        if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
+        if (dataView.getUint32(0, true) === CSI1_MAGIC) {
             csiVersion = 1;
         }
-        else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
+        else if (dataView.getUint32(0, true) === CSI2_MAGIC) {
             csiVersion = 2;
         }
         else {
             throw new Error('Not a CSI file');
-            // TODO: do we need to support big-endian CSI files?
         }
-        this.minShift = bytes.readInt32LE(4);
-        this.depth = bytes.readInt32LE(8);
+        this.minShift = dataView.getInt32(4, true);
+        this.depth = dataView.getInt32(8, true);
         this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
         const maxRefLength = 2 ** (this.minShift + this.depth * 3);
-        const auxLength = bytes.readInt32LE(12);
+        const auxLength = dataView.getInt32(12, true);
         const aux = auxLength && auxLength >= 30
             ? this.parseAuxData(bytes, 16)
             : {
@@ -142,35 +161,33 @@ class CSI extends indexFile_1.default {
                 coordinateType: 'zero-based-half-open',
                 format: 'generic',
             };
-        const refCount = bytes.readInt32LE(16 + auxLength);
+        const refCount = dataView.getInt32(16 + auxLength, true);
         // read the indexes for each reference sequence
         let firstDataLine;
         let currOffset = 16 + auxLength + 4;
         const indices = new Array(refCount).fill(0).map(() => {
-            // the binning index
-            const binCount = bytes.readInt32LE(currOffset);
+            const binCount = dataView.getInt32(currOffset, true);
             currOffset += 4;
             const binIndex = {};
-            let stats; // < provided by parsing a pseudo-bin, if present
+            let stats;
             for (let j = 0; j < binCount; j += 1) {
-                const bin = bytes.readUInt32LE(currOffset);
+                const bin = dataView.getUint32(currOffset, true);
                 if (bin > this.maxBinNumber) {
-                    // this is a fake bin that actually has stats information
-                    // about the reference sequence in it
+                    // this is a fake bin that actually has stats information about the
+                    // reference sequence in it
                     stats = this.parsePseudoBin(bytes, currOffset + 4);
                     currOffset += 4 + 8 + 4 + 16 + 16;
                 }
                 else {
                     const loffset = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 4);
                     firstDataLine = this._findFirstData(firstDataLine, loffset);
-                    const chunkCount = bytes.readInt32LE(currOffset + 12);
+                    const chunkCount = dataView.getInt32(currOffset + 12, true);
                     currOffset += 16;
                     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;
-                        // this._findFirstData(data, u)
                         chunks[k] = new chunk_1.default(u, v, bin);
                     }
                     binIndex[bin] = chunks;
@@ -192,8 +209,9 @@ class CSI extends indexFile_1.default {
         };
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
-        return { lineCount };
+        return {
+            lineCount: (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.subarray(offset + 28, offset + 36), true)),
+        };
     }
     async blocksForRange(refName, min, max, opts = {}) {
         if (min < 0) {
@@ -208,8 +226,8 @@ class CSI extends indexFile_1.default {
         if (!ba) {
             return [];
         }
-        // const { linearIndex, binIndex } = indexes
-        const overlappingBins = this.reg2bins(min, max); // List of bin #s that overlap min, max
+        // List of bin #s that overlap min, max
+        const overlappingBins = this.reg2bins(min, max);
         const chunks = [];
         // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
         for (const [start, end] of overlappingBins) {

package/dist/csi.js.map

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

@@ -1,4 +1,4 @@
-import { GenericFilehandle } from 'generic-filehandle';
+import { GenericFilehandle } from 'generic-filehandle2';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 export interface Options {

package/dist/indexFile.js

@@ -29,9 +29,8 @@ class IndexFile {
         return this.parseP;
     }
     async hasRefSeq(seqId, opts = {}) {
-        var _a;
         const idx = await this.parse(opts);
-        return !!((_a = idx.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
+        return !!idx.indices[seqId]?.binIndex;
     }
 }
 exports.default = IndexFile;

package/dist/indexFile.js.map

@@ -1 +1 @@
-{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAoBA,MAA8B,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,CAAA,MAAA,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAA,CAAA;IACvC,CAAC;CACF;AA3DD,4BA2DC"}
+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAoBA,MAA8B,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;AA3DD,4BA2DC"}