@gmod/bam - npm Package Compare versions

Comparing version 2.0.2 to 2.0.3

CHANGELOG.md

@@ -1,9 +0,17 @@
-## [2.0.2](https://github.com/GMOD/bam-js/compare/v2.0.1...v2.0.2) (2024-02-21)
+## [2.0.3](https://github.com/GMOD/bam-js/compare/v2.0.2...v2.0.3) (2024-07-23)
 
 
+### Reverts
 
-## [2.0.1](https://github.com/GMOD/bam-js/compare/v2.0.0...v2.0.1) (2024-2-20)
+* Revert "Migrate to eslint9" ([65adcbb](https://github.com/GMOD/bam-js/commit/65adcbb2793243659682d30694f8604d241a5337))
+* Revert "Run format" ([2a02535](https://github.com/GMOD/bam-js/commit/2a02535db4df80f245232522cdba771cbf5ea214))
 
 
 
+## [2.0.2](https://github.com/GMOD/bam-js/compare/v2.0.1...v2.0.2) (2024-02-21)
+
+- Update typescript-eslint config and related fixes
+
+## [2.0.1](https://github.com/GMOD/bam-js/compare/v2.0.0...v2.0.1) (2024-2-20)
+
 - Update to buffer-crc32 1.0.0
@@ -10,0 +18,0 @@ - Fix BAM header parsing of refNames containing a :

dist/bai.d.ts

@@ -17,3 +17,3 @@ import VirtualOffset from './virtualOffset';
                 lineCount: number;
-            } | undefined;
+            };
         }[];
@@ -20,0 +20,0 @@ refCount: number;

dist/bai.js

@@ -39,4 +39,4 @@ "use strict";
     lineCount(refId, opts) {
-        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             const indexData = yield this.parse(opts);
@@ -116,4 +116,4 @@ return ((_b = (_a = indexData.indices[refId]) === null || _a === void 0 ? void 0 : _a.stats) === null || _b === void 0 ? void 0 : _b.lineCount) || 0;
     }
-    indexCov(seqId, start, end, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    indexCov(seqId_1, start_1, end_1) {
+        return __awaiter(this, arguments, void 0, function* (seqId, start, end, opts = {}) {
             const v = 16384;
@@ -151,4 +151,4 @@ const range = start !== undefined;
     }
-    blocksForRange(refId, min, max, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    blocksForRange(refId_1, min_1, max_1) {
+        return __awaiter(this, arguments, void 0, function* (refId, min, max, opts = {}) {
             if (min < 0) {
@@ -194,4 +194,4 @@ min = 0;
     }
-    parse(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    parse() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             if (!this.setupP) {
@@ -206,5 +206,5 @@ this.setupP = this._parse(opts).catch(e => {
     }
-    hasRefSeq(seqId, opts = {}) {
-        var _a;
-        return __awaiter(this, void 0, void 0, function* () {
+    hasRefSeq(seqId_1) {
+        return __awaiter(this, arguments, void 0, function* (seqId, opts = {}) {
+            var _a;
             const header = yield this.parse(opts);
@@ -211,0 +211,0 @@ return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);

dist/bamFile.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
@@ -3,0 +2,0 @@ import { GenericFilehandle } from 'generic-filehandle';

dist/bamFile.js

@@ -45,3 +45,3 @@ "use strict";
 const generic_filehandle_1 = require("generic-filehandle");
-const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
+const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
@@ -57,5 +57,5 @@ // locals
 function gen2array(gen) {
-    var _a, gen_1, gen_1_1;
-    var _b, e_1, _c, _d;
     return __awaiter(this, void 0, void 0, function* () {
+        var _a, gen_1, gen_1_1;
+        var _b, e_1, _c, _d;
         let out = [];
@@ -202,4 +202,4 @@ try {
     }
-    getHeaderText(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getHeaderText() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             yield this.getHeader(opts);
@@ -247,4 +247,4 @@ return this.header;
     streamRecordsForRange(chr, min, max, opts) {
-        var _a;
         return __asyncGenerator(this, arguments, function* streamRecordsForRange_1() {
+            var _a;
             yield __await(this.getHeader(opts));
@@ -261,4 +261,4 @@ const chrId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[chr];
     }
-    _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
-        return __asyncGenerator(this, arguments, function* _fetchChunkFeatures_1() {
+    _fetchChunkFeatures(chunks_1, chrId_1, min_1, max_1) {
+        return __asyncGenerator(this, arguments, function* _fetchChunkFeatures_1(chunks, chrId, min, max, opts = {}) {
             const { viewAsPairs } = opts;
@@ -357,4 +357,4 @@ const feats = [];
     }
-    _readRegion(position, size, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    _readRegion(position_1, size_1) {
+        return __awaiter(this, arguments, void 0, function* (position, size, opts = {}) {
             const { bytesRead, buffer } = yield this.bam.read(buffer_1.Buffer.alloc(size), 0, size, position, opts);
@@ -364,4 +364,4 @@ return buffer.subarray(0, Math.min(bytesRead, size));
     }
-    _readChunk({ chunk, opts }) {
-        return __awaiter(this, void 0, void 0, function* () {
+    _readChunk(_a) {
+        return __awaiter(this, arguments, void 0, function* ({ chunk, opts }) {
             const buffer = yield this._readRegion(chunk.minv.blockPosition, chunk.fetchedSize(), opts);
@@ -434,4 +434,4 @@ const { buffer: data, cpositions, dpositions, } = yield (0, bgzf_filehandle_1.unzipChunkSlice)(buffer, chunk);
     hasRefSeq(seqName) {
-        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
@@ -442,4 +442,4 @@ return seqId === undefined ? false : (_b = this.index) === null || _b === void 0 ? void 0 : _b.hasRefSeq(seqId);
     lineCount(seqName) {
-        var _a;
         return __awaiter(this, void 0, void 0, function* () {
+            var _a;
             const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
@@ -450,4 +450,4 @@ return seqId === undefined || !this.index ? 0 : this.index.lineCount(seqId);
     indexCov(seqName, start, end) {
-        var _a;
         return __awaiter(this, void 0, void 0, function* () {
+            var _a;
             if (!this.index) {
@@ -462,4 +462,4 @@ return [];
     blocksForRange(seqName, start, end, opts) {
-        var _a;
         return __awaiter(this, void 0, void 0, function* () {
+            var _a;
             if (!this.index) {
@@ -466,0 +466,0 @@ return [];

dist/chunk.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 import VirtualOffset from './virtualOffset';
@@ -3,0 +2,0 @@ export default class Chunk {

dist/csi.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 import VirtualOffset from './virtualOffset';
@@ -50,3 +49,3 @@ import Chunk from './chunk';
                 lineCount: number;
-            } | undefined;
+            };
         }[];
@@ -53,0 +52,0 @@ refCount: number;

dist/csi.js

@@ -59,4 +59,4 @@ "use strict";
     lineCount(refId, opts) {
-        var _a, _b;
         return __awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             const indexData = yield this.parse(opts);
@@ -160,4 +160,4 @@ return ((_b = (_a = indexData.indices[refId]) === null || _a === void 0 ? void 0 : _a.stats) === null || _b === void 0 ? void 0 : _b.lineCount) || 0;
     }
-    blocksForRange(refId, min, max, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    blocksForRange(refId_1, min_1, max_1) {
+        return __awaiter(this, arguments, void 0, function* (refId, min, max, opts = {}) {
             if (min < 0) {
@@ -217,4 +217,4 @@ min = 0;
     }
-    parse(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    parse() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             if (!this.setupP) {
@@ -229,5 +229,5 @@ this.setupP = this._parse(opts).catch(e => {
     }
-    hasRefSeq(seqId, opts = {}) {
-        var _a;
-        return __awaiter(this, void 0, void 0, function* () {
+    hasRefSeq(seqId_1) {
+        return __awaiter(this, arguments, void 0, function* (seqId, opts = {}) {
+            var _a;
             const header = yield this.parse(opts);
@@ -234,0 +234,0 @@ return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);

dist/htsget.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
@@ -3,0 +2,0 @@ import { BaseOpts, BamOpts } from './util';

dist/htsget.js

@@ -103,4 +103,4 @@ "use strict";
     streamRecordsForRange(chr, min, max, opts) {
-        var _a;
         return __asyncGenerator(this, arguments, function* streamRecordsForRange_1() {
+            var _a;
             const base = `${this.baseUrl}/${this.trackId}`;
@@ -152,4 +152,4 @@ const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
     }
-    _readChunk({ chunk }) {
-        return __awaiter(this, void 0, void 0, function* () {
+    _readChunk(_a) {
+        return __awaiter(this, arguments, void 0, function* ({ chunk }) {
             if (!chunk.buffer) {
@@ -161,4 +161,4 @@ throw new Error('expected chunk.buffer in htsget');
     }
-    getHeader(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getHeader() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
@@ -165,0 +165,0 @@ const result = yield fetch(url, opts);

dist/record.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 /**
@@ -3,0 +2,0 @@ * Class of each BAM record returned by this API.

dist/sam.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseHeaderText = void 0;
+exports.parseHeaderText = parseHeaderText;
 function parseHeaderText(text) {
@@ -23,3 +23,2 @@ const lines = text.split(/\r?\n/);
 }
-exports.parseHeaderText = parseHeaderText;
 //# sourceMappingURL=sam.js.map

dist/util.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 import Long from 'long';
@@ -3,0 +2,0 @@ import Chunk from './chunk';

dist/util.js

@@ -15,3 +15,12 @@ "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseNameBytes = exports.findFirstData = exports.parsePseudoBin = exports.optimizeChunks = exports.makeOpts = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = exports.timeout = void 0;
+exports.timeout = timeout;
+exports.longToNumber = longToNumber;
+exports.checkAbortSignal = checkAbortSignal;
+exports.abortBreakPoint = abortBreakPoint;
+exports.canMergeBlocks = canMergeBlocks;
+exports.makeOpts = makeOpts;
+exports.optimizeChunks = optimizeChunks;
+exports.parsePseudoBin = parsePseudoBin;
+exports.findFirstData = findFirstData;
+exports.parseNameBytes = parseNameBytes;
 const long_1 = __importDefault(require("long"));
@@ -21,3 +30,2 @@ function timeout(ms) {
 }
-exports.timeout = timeout;
 function longToNumber(long) {
@@ -30,3 +38,2 @@ if (long.greaterThan(Number.MAX_SAFE_INTEGER) ||
 }
-exports.longToNumber = longToNumber;
 /**
@@ -60,3 +67,2 @@ * Properly check if the given AbortSignal is aborted.
 }
-exports.checkAbortSignal = checkAbortSignal;
 /**
@@ -74,3 +80,2 @@ * Skips to the next tick, then runs `checkAbortSignal`.
 }
-exports.abortBreakPoint = abortBreakPoint;
 function canMergeBlocks(chunk1, chunk2) {
@@ -80,7 +85,5 @@ return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
 }
-exports.canMergeBlocks = canMergeBlocks;
 function makeOpts(obj = {}) {
     return 'aborted' in obj ? { signal: obj } : obj;
 }
-exports.makeOpts = makeOpts;
 function optimizeChunks(chunks, lowest) {
@@ -117,3 +120,2 @@ const mergedChunks = [];
 }
-exports.optimizeChunks = optimizeChunks;
 function parsePseudoBin(bytes, offset) {
@@ -123,3 +125,2 @@ const lineCount = longToNumber(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset, offset + 8), true));
 }
-exports.parsePseudoBin = parsePseudoBin;
 function findFirstData(firstDataLine, virtualOffset) {
@@ -132,3 +133,2 @@ return firstDataLine
 }
-exports.findFirstData = findFirstData;
 function parseNameBytes(namesBytes, renameRefSeq = s => s) {
@@ -153,3 +153,2 @@ let currRefId = 0;
 }
-exports.parseNameBytes = parseNameBytes;
 //# sourceMappingURL=util.js.map

dist/virtualOffset.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 export default class VirtualOffset {
@@ -3,0 +2,0 @@ blockPosition: number;

dist/virtualOffset.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.fromBytes = void 0;
+exports.fromBytes = fromBytes;
 class VirtualOffset {
@@ -41,3 +41,2 @@ constructor(blockPosition, dataPosition) {
 }
-exports.fromBytes = fromBytes;
 //# sourceMappingURL=virtualOffset.js.map

esm/bai.d.ts

@@ -17,3 +17,3 @@ import VirtualOffset from './virtualOffset';
                 lineCount: number;
-            } | undefined;
+            };
         }[];
@@ -20,0 +20,0 @@ refCount: number;

esm/bamFile.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
@@ -3,0 +2,0 @@ import { GenericFilehandle } from 'generic-filehandle';

esm/bamFile.js

@@ -5,3 +5,3 @@ import { Buffer } from 'buffer';
 import { LocalFile, RemoteFile } from 'generic-filehandle';
-import AbortablePromiseCache from 'abortable-promise-cache';
+import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import QuickLRU from 'quick-lru';
@@ -8,0 +8,0 @@ // locals

esm/chunk.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 import VirtualOffset from './virtualOffset';
@@ -3,0 +2,0 @@ export default class Chunk {

esm/csi.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 import VirtualOffset from './virtualOffset';
@@ -50,3 +49,3 @@ import Chunk from './chunk';
                 lineCount: number;
-            } | undefined;
+            };
         }[];
@@ -53,0 +52,0 @@ refCount: number;

esm/htsget.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
@@ -3,0 +2,0 @@ import { BaseOpts, BamOpts } from './util';

esm/record.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 /**
@@ -3,0 +2,0 @@ * Class of each BAM record returned by this API.

esm/util.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 import Long from 'long';
@@ -3,0 +2,0 @@ import Chunk from './chunk';

esm/virtualOffset.d.ts

@@ -1,2 +0,1 @@
-/// <reference types="node" />
 export default class VirtualOffset {
@@ -3,0 +2,0 @@ blockPosition: number;

package.json

 {
   "name": "@gmod/bam",
-  "version": "2.0.2",
+  "version": "2.0.3",
   "description": "Parser for BAM and BAM index (bai) files",
@@ -25,3 +25,3 @@ "license": "MIT",
     "coverage": "npm test -- --coverage",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts src test",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
     "clean": "rimraf dist esm",
@@ -43,4 +43,4 @@ "build:esm": "tsc --target es2018 --outDir esm",
   "dependencies": {
+    "@gmod/abortable-promise-cache": "^2.0.0",
     "@gmod/bgzf-filehandle": "^1.4.4",
-    "abortable-promise-cache": "^1.5.0",
     "buffer-crc32": "^1.0.0",
@@ -57,12 +57,11 @@ "generic-filehandle": "^3.0.0",
     "@typescript-eslint/parser": "^7.0.2",
-    "eslint": "^8.40.0",
+    "eslint": "^9.0.0",
     "eslint-config-prettier": "^9.1.0",
-    "eslint-plugin-import": "^2.27.5",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^51.0.1",
+    "eslint-plugin-unicorn": "^54.0.0",
     "jest": "^29.5.0",
     "jest-fetch-mock": "^3.0.3",
     "prettier": "^3.2.5",
-    "rimraf": "^5.0.0",
-    "standard-changelog": "^5.0.0",
+    "rimraf": "^6.0.1",
+    "standard-changelog": "^6.0.0",
     "ts-jest": "^29.1.0",
@@ -69,0 +68,0 @@ "typescript": "^5.0.4"

src/bamFile.ts

@@ -5,3 +5,3 @@ import { Buffer } from 'buffer'
 import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle'
-import AbortablePromiseCache from 'abortable-promise-cache'
+import AbortablePromiseCache from '@gmod/abortable-promise-cache'
 import QuickLRU from 'quick-lru'
@@ -8,0 +8,0 @@

No alert changes

Improved metrics

Dev dependency count

16

decreased by-5.88%

Worsened metrics

Total package byte prevSize

372905

decreased by-0.03%

Lines of code

6542

decreased by-0.26%

Dependency changes

• + Added@gmod/abortable-promise-cache@^2.0.0

• + Added@gmod/abortable-promise-cache@2.0.1(transitive)

• - Removedabortable-promise-cache@^1.5.0

• - Removedabortable-promise-cache@1.5.0(transitive)

• - Removedabortcontroller-polyfill@1.7.8(transitive)