@gmod/bam - npm Package Compare versions

Comparing version 2.0.1 to 2.0.2

CHANGELOG.md

@@ -0,1 +1,5 @@
+## [2.0.2](https://github.com/GMOD/bam-js/compare/v2.0.1...v2.0.2) (2024-02-21)
+
+
+
 ## [2.0.1](https://github.com/GMOD/bam-js/compare/v2.0.0...v2.0.1) (2024-2-20)
@@ -2,0 +6,0 @@

dist/bai.d.ts

@@ -13,5 +13,3 @@ import VirtualOffset from './virtualOffset';
         indices: {
-            binIndex: {
-                [key: string]: Chunk[];
-            };
+            binIndex: Record<string, Chunk[]>;
             linearIndex: VirtualOffset[];
@@ -35,5 +33,3 @@ stats?: {
         indices: {
-            binIndex: {
-                [key: string]: Chunk[];
-            };
+            binIndex: Record<string, Chunk[]>;
             linearIndex: VirtualOffset[];
@@ -40,0 +36,0 @@ stats?: {

dist/bamFile.d.ts

@@ -54,5 +54,3 @@ /// <reference types="node" />
     _readRefSeqs(start: number, refSeqBytes: number, opts?: BaseOpts): Promise<{
-        chrToIndex: {
-            [key: string]: number;
-        };
+        chrToIndex: Record<string, number>;
         indexToChr: {
@@ -59,0 +57,0 @@ refName: string;

dist/bamFile.js

@@ -177,3 +177,3 @@ "use strict";
             else {
-                buffer = (yield this.bam.readFile(opts));
+                buffer = yield this.bam.readFile(opts);
             }
@@ -180,0 +180,0 @@ const uncba = yield (0, bgzf_filehandle_1.unzip)(buffer);

dist/chunk.js

@@ -12,3 +12,3 @@ "use strict";
     toUniqueString() {
-        return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
+        return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
     }
@@ -15,0 +15,0 @@ toString() {

dist/csi.d.ts

@@ -14,5 +14,3 @@ /// <reference types="node" />
     parseAuxData(bytes: Buffer, offset: number): {
-        refNameToId: {
-            [key: string]: number;
-        };
+        refNameToId: Record<string, number>;
         refIdToName: string[];
@@ -34,5 +32,3 @@ columnNumbers: {
     }): Promise<{
-        refNameToId?: {
-            [key: string]: number;
-        } | undefined;
+        refNameToId?: Record<string, number> | undefined;
         refIdToName?: string[] | undefined;
@@ -53,5 +49,3 @@ columnNumbers?: {
         indices: {
-            binIndex: {
-                [key: string]: Chunk[];
-            };
+            binIndex: Record<string, Chunk[]>;
             stats?: {
@@ -72,5 +66,3 @@ lineCount: number;
     parse(opts?: BaseOpts): Promise<{
-        refNameToId?: {
-            [key: string]: number;
-        } | undefined;
+        refNameToId?: Record<string, number> | undefined;
         refIdToName?: string[] | undefined;
@@ -91,5 +83,3 @@ columnNumbers?: {
         indices: {
-            binIndex: {
-                [key: string]: Chunk[];
-            };
+            binIndex: Record<string, Chunk[]>;
             stats?: {
@@ -96,0 +86,0 @@ lineCount: number;

dist/htsget.js

@@ -85,3 +85,2 @@ "use strict";
                 // @ts-expect-error
-                //eslint-disable-next-line @typescript-eslint/no-unused-vars
                 const { referer } = headers, rest = __rest(headers, ["referer"]);
@@ -88,0 +87,0 @@ const res = yield fetch(url, Object.assign(Object.assign({}, opts), { headers: Object.assign(Object.assign({}, opts === null || opts === void 0 ? void 0 : opts.headers), rest) }));

dist/record.d.ts

@@ -68,3 +68,2 @@ /// <reference types="node" />
     cigar(): any;
-    _flags(): void;
     length_on_ref(): any;
@@ -86,5 +85,3 @@ _n_cigar_op(): number;
     template_length(): number;
-    toJSON(): {
-        [key: string]: any;
-    };
+    toJSON(): Record<string, any>;
 }

dist/record.js

@@ -65,3 +65,3 @@ "use strict";
         for (const k of Object.keys(this.data)) {
-            if (k[0] !== '_' && k !== 'next_seq_id') {
+            if (!k.startsWith('_') && k !== 'next_seq_id') {
                 tags.push(k);
@@ -434,3 +434,2 @@ }
     }
-    _flags() { }
     length_on_ref() {
@@ -534,3 +533,3 @@ if (this.data.length_on_ref) {
         for (const k of Object.keys(this)) {
-            if (k.charAt(0) === '_' || k === 'bytes') {
+            if (k.startsWith('_') || k === 'bytes') {
                 continue;
@@ -537,0 +536,0 @@ }

dist/util.d.ts

@@ -43,6 +43,4 @@ /// <reference types="node" />
 export declare function parseNameBytes(namesBytes: Buffer, renameRefSeq?: (arg: string) => string): {
-    refNameToId: {
-        [key: string]: number;
-    };
+    refNameToId: Record<string, number>;
     refIdToName: string[];
 };

esm/bai.d.ts

@@ -13,5 +13,3 @@ import VirtualOffset from './virtualOffset';
         indices: {
-            binIndex: {
-                [key: string]: Chunk[];
-            };
+            binIndex: Record<string, Chunk[]>;
             linearIndex: VirtualOffset[];
@@ -35,5 +33,3 @@ stats?: {
         indices: {
-            binIndex: {
-                [key: string]: Chunk[];
-            };
+            binIndex: Record<string, Chunk[]>;
             linearIndex: VirtualOffset[];
@@ -40,0 +36,0 @@ stats?: {

esm/bamFile.d.ts

@@ -54,5 +54,3 @@ /// <reference types="node" />
     _readRefSeqs(start: number, refSeqBytes: number, opts?: BaseOpts): Promise<{
-        chrToIndex: {
-            [key: string]: number;
-        };
+        chrToIndex: Record<string, number>;
         indexToChr: {
@@ -59,0 +57,0 @@ refName: string;

esm/bamFile.js

@@ -120,3 +120,3 @@ import { Buffer } from 'buffer';
         else {
-            buffer = (await this.bam.readFile(opts));
+            buffer = await this.bam.readFile(opts);
         }
@@ -123,0 +123,0 @@ const uncba = await unzip(buffer);

esm/chunk.js

@@ -10,3 +10,3 @@ // little class representing a chunk in the index
     toUniqueString() {
-        return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
+        return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
     }
@@ -13,0 +13,0 @@ toString() {

esm/csi.d.ts

@@ -14,5 +14,3 @@ /// <reference types="node" />
     parseAuxData(bytes: Buffer, offset: number): {
-        refNameToId: {
-            [key: string]: number;
-        };
+        refNameToId: Record<string, number>;
         refIdToName: string[];
@@ -34,5 +32,3 @@ columnNumbers: {
     }): Promise<{
-        refNameToId?: {
-            [key: string]: number;
-        } | undefined;
+        refNameToId?: Record<string, number> | undefined;
         refIdToName?: string[] | undefined;
@@ -53,5 +49,3 @@ columnNumbers?: {
         indices: {
-            binIndex: {
-                [key: string]: Chunk[];
-            };
+            binIndex: Record<string, Chunk[]>;
             stats?: {
@@ -72,5 +66,3 @@ lineCount: number;
     parse(opts?: BaseOpts): Promise<{
-        refNameToId?: {
-            [key: string]: number;
-        } | undefined;
+        refNameToId?: Record<string, number> | undefined;
         refIdToName?: string[] | undefined;
@@ -91,5 +83,3 @@ columnNumbers?: {
         indices: {
-            binIndex: {
-                [key: string]: Chunk[];
-            };
+            binIndex: Record<string, Chunk[]>;
             stats?: {
@@ -96,0 +86,0 @@ lineCount: number;

esm/htsget.js

@@ -14,3 +14,2 @@ import { unzip } from '@gmod/bgzf-filehandle';
             // @ts-expect-error
-            //eslint-disable-next-line @typescript-eslint/no-unused-vars
             const { referer, ...rest } = headers;
@@ -17,0 +16,0 @@ const res = await fetch(url, {

esm/record.d.ts

@@ -68,3 +68,2 @@ /// <reference types="node" />
     cigar(): any;
-    _flags(): void;
     length_on_ref(): any;
@@ -86,5 +85,3 @@ _n_cigar_op(): number;
     template_length(): number;
-    toJSON(): {
-        [key: string]: any;
-    };
+    toJSON(): Record<string, any>;
 }

esm/record.js

@@ -60,3 +60,3 @@ import Constants from './constants';
         for (const k of Object.keys(this.data)) {
-            if (k[0] !== '_' && k !== 'next_seq_id') {
+            if (!k.startsWith('_') && k !== 'next_seq_id') {
                 tags.push(k);
@@ -429,3 +429,2 @@ }
     }
-    _flags() { }
     length_on_ref() {
@@ -529,3 +528,3 @@ if (this.data.length_on_ref) {
         for (const k of Object.keys(this)) {
-            if (k.charAt(0) === '_' || k === 'bytes') {
+            if (k.startsWith('_') || k === 'bytes') {
                 continue;
@@ -532,0 +531,0 @@ }

esm/util.d.ts

@@ -43,6 +43,4 @@ /// <reference types="node" />
 export declare function parseNameBytes(namesBytes: Buffer, renameRefSeq?: (arg: string) => string): {
-    refNameToId: {
-        [key: string]: number;
-    };
+    refNameToId: Record<string, number>;
     refIdToName: string[];
 };

package.json

 {
   "name": "@gmod/bam",
-  "version": "2.0.1",
+  "version": "2.0.2",
   "description": "Parser for BAM and BAM index (bai) files",
@@ -5,0 +5,0 @@ "license": "MIT",

src/bai.ts

@@ -53,3 +53,3 @@ import VirtualOffset, { fromBytes } from './virtualOffset'
 
-    type BinIndex = { [key: string]: Chunk[] }
+    type BinIndex = Record<string, Chunk[]>
     type LinearIndex = VirtualOffset[]
@@ -67,3 +67,3 @@ const indices = new Array<{
       curr += 4
-      const binIndex: { [key: number]: Chunk[] } = {}
+      const binIndex: Record<number, Chunk[]> = {}
 
@@ -70,0 +70,0 @@ for (let j = 0; j < binCount; j += 1) {

src/bamFile.ts

@@ -157,3 +157,3 @@ import { Buffer } from 'buffer'
     } else {
-      buffer = (await this.bam.readFile(opts)) as Buffer
+      buffer = await this.bam.readFile(opts)
     }
@@ -202,3 +202,3 @@
   ): Promise<{
-    chrToIndex: { [key: string]: number }
+    chrToIndex: Record<string, number>
     indexToChr: { refName: string; length: number }[]
@@ -225,3 +225,3 @@ }> {
     let p = start + 4
-    const chrToIndex: { [key: string]: number } = {}
+    const chrToIndex: Record<string, number> = {}
     const indexToChr: { refName: string; length: number }[] = []
@@ -320,6 +320,6 @@ for (let i = 0; i < nRef; i += 1) {
     const { pairAcrossChr, maxInsertSize = 200000 } = opts
-    const unmatedPairs: { [key: string]: boolean } = {}
-    const readIds: { [key: string]: number } = {}
+    const unmatedPairs: Record<string, boolean> = {}
+    const readIds: Record<string, number> = {}
     feats.map(ret => {
-      const readNames: { [key: string]: number } = {}
+      const readNames: Record<string, number> = {}
       for (const element of ret) {
@@ -326,0 +326,0 @@ const name = element.name()

src/chunk.ts

@@ -15,3 +15,3 @@ import VirtualOffset from './virtualOffset'
   toUniqueString() {
-    return `${this.minv}..${this.maxv} (bin ${
+    return `${this.minv.toString()}..${this.maxv.toString()} (bin ${
       this.bin
@@ -18,0 +18,0 @@ }, fetchedSize ${this.fetchedSize()})`

src/csi.ts

@@ -45,5 +45,3 @@ import { unzip } from '@gmod/bgzf-filehandle'
     const format = (
-      { 0: 'generic', 1: 'SAM', 2: 'VCF' } as {
-        [key: number]: string
-      }
+      { 0: 'generic', 1: 'SAM', 2: 'VCF' } as Record<number, string>
     )[formatFlags & 0xf]
@@ -101,3 +99,3 @@ if (!format) {
 
-    type BinIndex = { [key: string]: Chunk[] }
+    type BinIndex = Record<string, Chunk[]>
 
@@ -115,3 +113,3 @@ // read the indexes for each reference sequence
       curr += 4
-      const binIndex: { [key: string]: Chunk[] } = {}
+      const binIndex: Record<string, Chunk[]> = {}
       let stats // < provided by parsing a pseudo-bin, if present
@@ -118,0 +116,0 @@ for (let j = 0; j < binCount; j++) {

src/htsget.ts

@@ -21,3 +21,3 @@ import { unzip } from '@gmod/bgzf-filehandle'
         // @ts-expect-error
-        //eslint-disable-next-line @typescript-eslint/no-unused-vars
+
         const { referer, ...rest } = headers
@@ -24,0 +24,0 @@ const res = await fetch(url, {

src/record.ts

@@ -10,3 +10,3 @@ import Constants from './constants'
 export default class BamRecord {
-  private data = {} as { [key: string]: any }
+  private data = {} as Record<string, any>
   private bytes: { start: number; end: number; byteArray: Buffer }
@@ -87,3 +87,3 @@ private _id: number
     for (const k of Object.keys(this.data)) {
-      if (k[0] !== '_' && k !== 'next_seq_id') {
+      if (!k.startsWith('_') && k !== 'next_seq_id') {
         tags.push(k)
@@ -93,3 +93,3 @@ }
 
-    const seen: { [key: string]: boolean } = {}
+    const seen: Record<string, boolean> = {}
     return tags.filter(t => {
@@ -499,4 +499,2 @@ if (
 
-  _flags() {}
-
   length_on_ref() {
@@ -612,5 +610,5 @@ if (this.data.length_on_ref) {
   toJSON() {
-    const data: { [key: string]: any } = {}
+    const data: Record<string, any> = {}
     for (const k of Object.keys(this)) {
-      if (k.charAt(0) === '_' || k === 'bytes') {
+      if (k.startsWith('_') || k === 'bytes') {
         continue
@@ -617,0 +615,0 @@ }

src/util.ts

@@ -78,3 +78,3 @@ import Long from 'long'
 export function makeOpts(obj: AbortSignal | BaseOpts = {}): BaseOpts {
-  return 'aborted' in obj ? ({ signal: obj } as BaseOpts) : (obj as BaseOpts)
+  return 'aborted' in obj ? ({ signal: obj } as BaseOpts) : obj
 }
@@ -144,3 +144,3 @@
   const refIdToName = []
-  const refNameToId: { [key: string]: number } = {}
+  const refNameToId: Record<string, number> = {}
   for (let i = 0; i < namesBytes.length; i += 1) {
@@ -147,0 +147,0 @@ if (!namesBytes[i]) {

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Worsened metrics

Total package byte prevSize

373029

decreased by-0.21%

Lines of code

6559

decreased by-0.76%

No dependency changes