Begin typescriptifying codecs

Eslint

Updates

src/cramFile/file.ts

@@ -4,11 +4,12 @@ import QuickLRU from 'quick-lru'
 import { XzReadableStream } from 'xz-decompress'
 
 import { CramMalformedError, CramUnimplementedError } from '../errors'
-import htscodecs from '../htscodecs'
+import * as htscodecs from '../htscodecs'
 import { open } from '../io'
 import ransuncompress from '../rans'
 import { parseHeaderText } from '../sam'
 import { unzip } from '../unzip'
+import { concatUint8Array } from '../util'
 import CramContainer from './container'
 import CramRecord from './record'
 import {
@@ -17,7 +18,7 @@ import {
   cramFileDefinition,
   getSectionParsers,
 } from './sectionParsers'
-import { concatUint8Array, parseItem, tinyMemoize } from './util'
+import { parseItem, tinyMemoize } from './util'
 
 import type { GenericFilehandle } from 'generic-filehandle2'
 

src/cramFile/slice/decodeRecord.ts

@@ -141,16 +141,14 @@ function decodeReadFeatures(
     const data = decodeDataSeries(dataSeriesName)
     if (type === 'character') {
       return String.fromCharCode(data)
-    }
-    if (type === 'string') {
+    } else if (type === 'string') {
       let r = ''
       for (let i = 0; i < data.byteLength; i++) {
         r += String.fromCharCode(data[i])
       }
       return r
-    }
-    if (type === 'numArray') {
-      return data.toArray()
+    } else if (type === 'numArray') {
+      return Array.from(data)
     }
     // else if (type === 'number') {
     //   return data[0]

src/cramFile/util.ts

@@ -179,20 +179,3 @@ export function tinyMemoize(_class: any, methodName: any) {
 export function sequenceMD5(seq: string) {
   return md5(seq.toUpperCase().replaceAll(/[^\u0021-\u007e]/g, ''))
 }
-
-export function sum(array: Uint8Array[]) {
-  let sum = 0
-  for (const entry of array) {
-    sum += entry.length
-  }
-  return sum
-}
-export function concatUint8Array(args: Uint8Array[]) {
-  const mergedArray = new Uint8Array(sum(args))
-  let offset = 0
-  for (const entry of args) {
-    mergedArray.set(entry, offset)
-    offset += entry.length
-  }
-  return mergedArray
-}