All ts files

jest.config.js

@@ -1,9 +1,6 @@
-/** @type {import("ts-jest/dist/types").InitialOptionsTsJest} */
+/** @type {import('ts-jest').JestConfigWithTsJest} */
 module.exports = {
   preset: 'ts-jest',
-  transform: {
-    '^.+\\.(ts|js)x?$': 'ts-jest',
-  },
+  testEnvironment: 'node',
   transformIgnorePatterns: ['[/\\\\]node_modules[/\\\\](?!quick-lru/).+\\.js$'],
-  testTimeout: 1000,
 }

package.json

@@ -56,7 +56,7 @@
   "devDependencies": {
     "@babel/plugin-transform-modules-commonjs": "^7.18.2",
     "@babel/preset-typescript": "^7.17.12",
-    "@gmod/indexedfasta": "^2.0.2",
+    "@gmod/indexedfasta": "^2.1.0",
     "@types/buffer-crc32": "^0.2.2",
     "@types/jest": "^29.2.4",
     "@types/long": "^4.0.2",

src/rans/d04.js → src/rans/d04.ts

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import { TF_SHIFT } from './constants'

src/rans/d14.js → src/rans/d14.ts

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { TF_SHIFT } from './constants'
 import Decoding from './decoding'
 

src/rans/decoding.js → src/rans/decoding.ts

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import { RANS_BYTE_L } from './constants'

src/rans/frequencies.js → src/rans/frequencies.ts

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import { TOTFREQ } from './constants'

src/rans/index.js → src/rans/index.ts

@@ -1,3 +1,4 @@
+//@ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import Decoding from './decoding'

test/__snapshots__/compressions.test.ts.snap

@@ -0,0 +1,23 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`bzip2 1`] = `
+{
+  "code": "X",
+  "data": 1,
+  "pos": 51,
+  "ref": "A",
+  "refPos": 1050,
+  "sub": "G",
+}
+`;
+
+exports[`lzma 1`] = `
+{
+  "code": "X",
+  "data": 1,
+  "pos": 51,
+  "ref": "A",
+  "refPos": 1050,
+  "sub": "G",
+}
+`;

test/compressions.test.ts

@@ -0,0 +1,31 @@
+//@ts-nocheck
+import { testDataFile } from './lib/util'
+import { dumpWholeFile } from './lib/dumpFile'
+import { CramFile } from '../src/index'
+import { FetchableSmallFasta } from './lib/fasta'
+
+test('lzma', async () => {
+  const fasta = new FetchableSmallFasta(testDataFile('hts-specs/ce.fa'))
+  const seqFetch = fasta.fetch.bind(fasta)
+  const file = new CramFile({
+    filehandle: testDataFile('hts-specs/0903_comp_lzma.cram'),
+    seqFetch,
+  })
+  const fileData = await dumpWholeFile(file)
+  const feat = fileData[2].data[1].features[0]
+  const hardClip = feat.readFeatures[0]
+  expect(hardClip).toMatchSnapshot()
+})
+
+test('bzip2', async () => {
+  const fasta = new FetchableSmallFasta(testDataFile('hts-specs/ce.fa'))
+  const seqFetch = fasta.fetch.bind(fasta)
+  const file = new CramFile({
+    filehandle: testDataFile('hts-specs/0902_comp_bz2.cram'),
+    seqFetch,
+  })
+  const fileData = await dumpWholeFile(file)
+  const feat = fileData[2].data[1].features[0]
+  const hardClip = feat.readFeatures[0]
+  expect(hardClip).toMatchSnapshot()
+})

test/dump.test.ts

@@ -79,42 +79,6 @@ test('works with hard clipping', async () => {
   expect(hardClip.data).toEqual(803)
 })
 
-test('lzma', async () => {
-  const fasta = new FetchableSmallFasta(testDataFile('hts-specs/ce.fa'))
-  const seqFetch = fasta.fetch.bind(fasta)
-  const file = new CramFile({
-    filehandle: testDataFile('hts-specs/0903_comp_lzma.cram'),
-    seqFetch,
-  })
-  const fileData = await dumpWholeFile(file)
-  const feat = fileData[2].data[1].features[0]
-  const hardClip = feat.readFeatures[0]
-  const nextReadFeature = feat.readFeatures[0]
-  expect(hardClip.refPos).toEqual(1050)
-  expect(nextReadFeature.refPos).toEqual(1050)
-  expect(hardClip.refPos).toEqual(1050)
-  expect(hardClip.pos).toEqual(51)
-  expect(hardClip.data).toEqual(1)
-})
-
-test('bzip2', async () => {
-  const fasta = new FetchableSmallFasta(testDataFile('hts-specs/ce.fa'))
-  const seqFetch = fasta.fetch.bind(fasta)
-  const file = new CramFile({
-    filehandle: testDataFile('hts-specs/0902_comp_bz2.cram'),
-    seqFetch,
-  })
-  const fileData = await dumpWholeFile(file)
-  const feat = fileData[2].data[1].features[0]
-  const hardClip = feat.readFeatures[0]
-  const nextReadFeature = feat.readFeatures[0]
-  expect(hardClip.refPos).toEqual(737)
-  expect(nextReadFeature.refPos).toEqual(737)
-  expect(hardClip.refPos).toEqual(feat.alignmentStart)
-  expect(hardClip.pos).toEqual(1)
-  expect(hardClip.data).toEqual(803)
-})
-
 function isIterable(input) {
   if (input === null || input === undefined) {
     return false

test/lib/dumpFile.js → test/lib/dumpFile.ts

@@ -1,3 +1,4 @@
+//@ts-nocheck
 async function dumpSlice(container, sliceOffset) {
   const slice = container.getSlice(sliceOffset)
   const header = await slice.getHeader()

test/lib/fasta/index.js → test/lib/fasta/index.ts

@@ -1,6 +1,5 @@
-import IndexedFasta from './indexedFasta'
-
-function parseSmallFasta(text) {
+//@ts-nocheck
+function parseSmallFasta(text: string) {
   return text
     .split('>')
     .filter(t => /\S/.test(t))
@@ -38,4 +37,4 @@ class FetchableSmallFasta {
   }
 }
 
-export { parseSmallFasta, FetchableSmallFasta, IndexedFasta }
+export { parseSmallFasta, FetchableSmallFasta }

test/lib/syncLocalFile.js → test/lib/syncLocalFile.ts

@@ -1,3 +1,4 @@
+//@ts-nocheck
 // don't load fs native module if running in webpacked code
 const fs = typeof __webpack_require__ !== 'function' ? require('fs') : null // eslint-disable-line camelcase
 

test/lib/util.js → test/lib/util.ts

@@ -1,3 +1,4 @@
+//@ts-nocheck
 const path = typeof __webpack_require__ !== 'function' ? require('path') : null // eslint-disable-line camelcase
 const fs = typeof __webpack_require__ !== 'function' ? require('fs') : null // eslint-disable-line camelcase
 import { fromUrl } from '../../src/io'