Updates

eslint.config.mjs

@@ -5,7 +5,14 @@ import tseslint from 'typescript-eslint'
 
 export default tseslint.config(
   {
-    ignores: ['esm/**/*', 'dist/**/*', '*.js', '*.mjs', 'example/*'],
+    ignores: [
+      'esm/**/*',
+      'dist/**/*',
+      '*.js',
+      '*.mjs',
+      'example/*',
+      'src/htscodecs',
+    ],
   },
   {
     languageOptions: {

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/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
-}

src/htscodecs/arith_gen.ts

@@ -1,3 +1,6 @@
+/* eslint-disable no-var */
+// @ts-nocheck
+
 /*
  * Copyright (c) 2019,2020 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -36,23 +39,7 @@ import bzip2 from 'bzip2'
 import RangeCoder from './arith_sh'
 import ByteModel from './byte_model'
 import IOStream from './iostream'
-
-function sum(array) {
-  let sum = 0
-  for (const entry of array) {
-    sum += entry.length
-  }
-  return sum
-}
-function concatUint8Array(args) {
-  const mergedArray = new Uint8Array(sum(args))
-  let offset = 0
-  for (const entry of args) {
-    mergedArray.set(entry, offset)
-    offset += entry.length
-  }
-  return mergedArray
-}
+import { concatUint8Array } from '../util'
 
 const ARITH_ORDER = 1
 const ARITH_EXT = 4
@@ -63,12 +50,13 @@ const ARITH_RLE = 64
 const ARITH_PACK = 128
 
 export default class RangeCoderGen {
-  decode(src) {
+  stream: IOStream
+  decode(src: Uint8Array) {
     this.stream = new IOStream(src)
     return this.decodeStream(this.stream)
   }
 
-  decodeStream(stream, n_out = 0) {
+  decodeStream(stream: IOStream, n_out = 0) {
     const flags = this.stream.ReadByte()
     if (!(flags & ARITH_NOSIZE)) {
       n_out = this.stream.ReadUint7()

src/htscodecs/arith_sh.ts

@@ -1,3 +1,5 @@
+// @ts-nocheck
+
 /*
  * Copyright (c) 2019 Genome Research Ltd.
  * Author(s): James Bonfield

src/htscodecs/byte_model.ts

@@ -1,3 +1,6 @@
+/* eslint-disable no-var */
+// @ts-nocheck
+
 /*
  * Copyright (c) 2019 Genome Research Ltd.
  * Author(s): James Bonfield

src/htscodecs/fqzcomp.ts

@@ -1,3 +1,6 @@
+/* eslint-disable no-var */
+// @ts-nocheck
+
 /*
  * Copyright (c) 2019 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -293,7 +296,7 @@ function decode_fqz_new_record(src, rc, gparams, model, state, rev) {
   state.rec++
 }
 
-function decode_fqz(src, q_lens) {
+function decode_fqz(src: IOStream, q_lens: number) {
   // Decode parameter block
   const n_out = src.ReadUint7()
   const gparams = decode_fqz_params(src)
@@ -384,10 +387,8 @@ function reverse_qualities(qual, qual_len, rev, len) {
   }
 }
 
-export function decode(src, q_lens) {
+export function decode(src: Uint8Array, q_lens) {
   const stream = new IOStream(src)
 
-  // var n_out = stream.ReadUint32(); stream.ReadUint32(); // move to main
-
   return decode_fqz(stream, q_lens)
 }

src/htscodecs/index.ts

@@ -1,3 +1,5 @@
+// @ts-nocheck
+//
 /*
  * Copyright (c) 2020 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -43,35 +45,27 @@ import * as r4x8 from './rans'
 import * as r4x16 from './rans4x16'
 import * as tok3 from './tok3'
 
-function r4x8_uncompress(inputBuffer, outputBuffer) {
+export function r4x8_uncompress(inputBuffer: Uint8Array) {
   return r4x8.decode(inputBuffer)
 }
 
-function r4x16_uncompress(inputBuffer) {
+export function r4x16_uncompress(inputBuffer: Uint8Array) {
   return r4x16.decode(inputBuffer)
 }
 
-function arith_uncompress(inputBuffer) {
+export function arith_uncompress(inputBuffer: Uint8Array) {
   // fix by @cmdcolin for CRAM 3.1
   // xref https://github.com/jkbonfield/htscodecs/pull/1/files
   return new arith().decode(inputBuffer)
 }
 
-function fqzcomp_uncompress(inputBuffer) {
+export function fqzcomp_uncompress(inputBuffer: Uint8Array) {
   const q_lens = []
   return fqzcomp.decode(inputBuffer, q_lens)
 }
 
-function tok3_uncompress(inputBuffer) {
+export function tok3_uncompress(inputBuffer: Uint8Array) {
   // Returns in string form instead of buffer
   const out = tok3.decode(inputBuffer, 0, '\0')
   return Uint8Array.from(Array.from(out).map(letter => letter.charCodeAt(0)))
 }
-
-module.exports = {
-  arith_uncompress: arith_uncompress,
-  fqzcomp_uncompress: fqzcomp_uncompress,
-  r4x16_uncompress: r4x16_uncompress,
-  r4x8_uncompress: r4x8_uncompress,
-  tok3_uncompress: tok3_uncompress,
-}