@gmod/bam 2.0.0 → 2.0.2

package/src/htsget.ts

@@ -18,7 +18,7 @@ async function concat(arr: HtsgetChunk[], opts?: Record<string, any>) {
       } else {
         //remove referer header, it is not even allowed to be specified
         // @ts-expect-error
-        //eslint-disable-next-line @typescript-eslint/no-unused-vars
+
         const { referer, ...rest } = headers
         const res = await fetch(url, {
           ...opts,

package/src/record.ts

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-empty-function */
 import Constants from './constants'
 
 const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('')
@@ -8,7 +7,7 @@ const CIGAR_DECODER = 'MIDNSHP=X???????'.split('')
  * Class of each BAM record returned by this API.
  */
 export default class BamRecord {
-  private data = {} as { [key: string]: any }
+  private data = {} as Record<string, any>
   private bytes: { start: number; end: number; byteArray: Buffer }
   private _id: number
   private _tagOffset: number | undefined
@@ -84,12 +83,12 @@ export default class BamRecord {
     tags = tags.concat(this._tagList || [])
 
     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)
       }
     }
 
-    const seen: { [key: string]: boolean } = {}
+    const seen: Record<string, boolean> = {}
     return tags.filter(t => {
       if (
         (t in this.data && this.data[t] === undefined) ||
@@ -494,8 +493,6 @@ export default class BamRecord {
     }
   }
 
-  _flags() {}
-
   length_on_ref() {
     if (this.data.length_on_ref) {
       return this.data.length_on_ref
@@ -606,9 +603,9 @@ export default class BamRecord {
   }
 
   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
       }
       //@ts-ignore

package/src/sam.ts

@@ -7,7 +7,9 @@ export function parseHeaderText(text: string) {
       data.push({
         tag: tag.slice(1),
         data: fields.map(f => {
-          const [fieldTag, value] = f.split(':', 2)
+          const r = f.indexOf(':')
+          const fieldTag = f.slice(0, r)
+          const value = f.slice(r + 1)
           return { tag: fieldTag, value }
         }),
       })

package/src/util.ts

@@ -75,7 +75,7 @@ export interface BaseOpts {
 }
 
 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
 }
 
 export function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset) {
@@ -140,7 +140,7 @@ export function parseNameBytes(
   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) {