Lazy load alternative methods

GMOD · Nov 12, 2023 · 84b13c2 · 84b13c2
1 parent 8db6cac
commit 84b13c2
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Showing 6 changed files with 11 additions and 20,834 deletions.
diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml
@@ -4,14 +4,14 @@ on: push
 
 jobs:
   test:
-    name: Lint, build, and test on node 16.x and ubuntu-latest
+    name: Lint, build, and test on node 20.x and ubuntu-latest
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Use Node.js 16.x
+      - name: Use Node.js 20.x
         uses: actions/setup-node@v3
         with:
-          node-version: 16.x
+          node-version: 20.x
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Lint codebase

diff --git a/src/cramFile/file.ts b/src/cramFile/file.ts
@@ -1,12 +1,11 @@
 import { unzip } from '../unzip'
 import crc32 from 'buffer-crc32'
 import QuickLRU from 'quick-lru'
+import htscodecs from '@jkbonfield/htscodecs'
+import { Parser } from '@gmod/binary-parser'
 // @ts-expect-error
 import bzip2 from 'bzip2'
 import { XzReadableStream } from 'xz-decompress'
-import htscodecs from '@jkbonfield/htscodecs'
-import { Parser } from '@gmod/binary-parser'
-
 import { CramMalformedError, CramUnimplementedError } from '../errors'
 import ransuncompress from '../rans'
 import {
@@ -110,17 +109,6 @@ export default class CramFile {
     }
   }
 
-  // toString() {
-  //   if (this.file.filename) {
-  //     return this.file.filename
-  //   }
-  //   if (this.file.url) {
-  //     return this.file.url
-  //   }
-  //
-  //   return '(cram file)'
-  // }
-
   // can just read this object like a filehandle
   read(
     buffer: Buffer,

diff --git a/test/compressions.test.ts b/test/compressions.test.ts
@@ -5,7 +5,7 @@ import { CramFile } from '../src/index'
 import { FetchableSmallFasta } from './lib/fasta'
 
 test('lzma', async () => {
-  const fasta = new FetchableSmallFasta(testDataFile('hts-specs/ce.fa'))
+  const fasta = new FetchableSmallFasta(testDataFile('ce.fa'))
   const seqFetch = fasta.fetch.bind(fasta)
   const file = new CramFile({
     filehandle: testDataFile('hts-specs/0903_comp_lzma.cram'),
@@ -18,7 +18,7 @@ test('lzma', async () => {
 })
 
 test('bzip2', async () => {
-  const fasta = new FetchableSmallFasta(testDataFile('hts-specs/ce.fa'))
+  const fasta = new FetchableSmallFasta(testDataFile('ce.fa'))
   const seqFetch = fasta.fetch.bind(fasta)
   const file = new CramFile({
     filehandle: testDataFile('hts-specs/0902_comp_bz2.cram'),