fix lint and type errors for TypeScript 6 compatibility

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: cmdcolin

src/csi.ts

@@ -91,9 +91,8 @@ export default class CSI extends IndexFile {
   }
 
   async _parse(opts: Options = {}) {
-    const bytes = (await unzip(
-      await this.filehandle.readFile(opts),
-    )) as Uint8Array
+    const buf = await this.filehandle.readFile({ signal: opts.signal })
+    const bytes = (await unzip(buf)) as Uint8Array
     const dataView = new DataView(bytes.buffer)
 
     // check TBI magic numbers

src/tbi.ts

@@ -44,7 +44,7 @@ export default class TabixIndex extends IndexFile {
 
   // fetch and parse the index
   async _parse(opts: Options = {}) {
-    const buf = await this.filehandle.readFile(opts)
+    const buf = await this.filehandle.readFile({ signal: opts.signal })
     const bytes = (await unzip(buf)) as Uint8Array
     const dataView = new DataView(bytes.buffer)
 
@@ -128,9 +128,10 @@ export default class TabixIndex extends IndexFile {
       currOffset += 4
       const linearIndex = Array.from<VirtualOffset>({ length: linearCount })
       for (let k = 0; k < linearCount; k += 1) {
-        linearIndex[k] = fromBytes(bytes, currOffset)
+        const lv = fromBytes(bytes, currOffset)
+        linearIndex[k] = lv
         currOffset += 8
-        firstDataLine = this._findFirstData(firstDataLine, linearIndex[k])
+        firstDataLine = this._findFirstData(firstDataLine, lv)
       }
       return {
         binIndex,

test/csi.test.ts

@@ -6,7 +6,9 @@ import VirtualOffset from '../src/virtualOffset.ts'
 
 test('loads test.gff3.gz.csi', async () => {
   const ti = new CSI({
-    filehandle: new LocalFile(require.resolve('./data/test.gff3.gz.csi')),
+    filehandle: new LocalFile(
+      new URL('data/test.gff3.gz.csi', import.meta.url).pathname,
+    ),
   })
   const indexData = await ti.parse()
   expect(indexData.columnNumbers.start).toEqual(4)
@@ -42,7 +44,9 @@ test('loads test.gff3.gz.csi', async () => {
 })
 test('loads test.vcf.gz.csi', async () => {
   const ti = new CSI({
-    filehandle: new LocalFile(require.resolve('./data/test.vcf.gz.csi')),
+    filehandle: new LocalFile(
+      new URL('data/test.vcf.gz.csi', import.meta.url).pathname,
+    ),
   })
   const indexData = await ti.parse()
   expect(indexData.columnNumbers.start).toEqual(2)

test/tabixindexedfile.test.ts

@@ -36,8 +36,8 @@ class RecordCollector {
 }
 test('can read contigA:1000..4000', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/volvox.test.vcf.gz'),
-    tbiPath: require.resolve('./data/volvox.test.vcf.gz.tbi'),
+    path: new URL('data/volvox.test.vcf.gz', import.meta.url).pathname,
+    tbiPath: new URL('data/volvox.test.vcf.gz.tbi', import.meta.url).pathname,
   })
   const items = new RecordCollector()
   await f.getLines('contigA', 1000, 4000, items.callback)
@@ -81,8 +81,8 @@ test('can read contigA:1000..4000', async () => {
 })
 test('can read contigA:10000', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/volvox.test.vcf.gz'),
-    tbiPath: require.resolve('./data/volvox.test.vcf.gz.tbi'),
+    path: new URL('data/volvox.test.vcf.gz', import.meta.url).pathname,
+    tbiPath: new URL('data/volvox.test.vcf.gz.tbi', import.meta.url).pathname,
   })
   const items = new RecordCollector()
   await f.getLines('contigA', 10_000, undefined, items.callback)
@@ -97,8 +97,8 @@ test('can read contigA:10000', async () => {
 })
 test('can read contigA', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/volvox.test.vcf.gz'),
-    tbiPath: require.resolve('./data/volvox.test.vcf.gz.tbi'),
+    path: new URL('data/volvox.test.vcf.gz', import.meta.url).pathname,
+    tbiPath: new URL('data/volvox.test.vcf.gz.tbi', import.meta.url).pathname,
   })
   const items = new RecordCollector()
   await f.getLines('contigA', undefined, undefined, items.callback)
@@ -112,32 +112,32 @@ test('can read contigA', async () => {
 })
 test('can count lines with TBI', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/volvox.test.vcf.gz'),
-    tbiPath: require.resolve('./data/volvox.test.vcf.gz.tbi'),
+    path: new URL('data/volvox.test.vcf.gz', import.meta.url).pathname,
+    tbiPath: new URL('data/volvox.test.vcf.gz.tbi', import.meta.url).pathname,
   })
   expect(await f.lineCount('contigA')).toEqual(109)
   expect(await f.lineCount('nonexistent')).toEqual(-1)
 })
 test('can count lines with CSI', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/volvox.test.vcf.gz'),
-    csiPath: require.resolve('./data/volvox.test.vcf.gz.csi'),
+    path: new URL('data/volvox.test.vcf.gz', import.meta.url).pathname,
+    csiPath: new URL('data/volvox.test.vcf.gz.csi', import.meta.url).pathname,
   })
   expect(await f.lineCount('contigA')).toEqual(109)
   expect(await f.lineCount('nonexistent')).toEqual(-1)
 })
 test("can't count lines without pseudo-bin", async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/volvox.test.vcf.gz'),
-    tbiPath: require.resolve('./data/volvox.test.vcf.gz.tbi.no_pseudo'),
+    path: new URL('data/volvox.test.vcf.gz', import.meta.url).pathname,
+    tbiPath: new URL('data/volvox.test.vcf.gz.tbi.no_pseudo', import.meta.url).pathname,
   })
   expect(await f.lineCount('contigA')).toEqual(-1)
 })
 
 test('can query volvox.sort.gff3.gz.1', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/volvox.sort.gff3.gz.1'),
-    tbiPath: require.resolve('./data/volvox.sort.gff3.gz.tbi'),
+    path: new URL('data/volvox.sort.gff3.gz.1', import.meta.url).pathname,
+    tbiPath: new URL('data/volvox.sort.gff3.gz.tbi', import.meta.url).pathname,
   })
 
   const headerString = await f.getHeader()
@@ -169,7 +169,7 @@ test('can query volvox.sort.gff3.gz.1', async () => {
 })
 test('can query gvcf.vcf.gz', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/gvcf.vcf.gz'),
+    path: new URL('data/gvcf.vcf.gz', import.meta.url).pathname,
   })
 
   const headerString = await f.getHeader()
@@ -202,7 +202,7 @@ test('can query gvcf.vcf.gz', async () => {
 
 test('can query out.gff.gz with a TBI index', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/out.gff.gz'),
+    path: new URL('data/out.gff.gz', import.meta.url).pathname,
   })
 
   const headerString = await f.getHeader()
@@ -233,8 +233,8 @@ test('can query out.gff.gz with a TBI index', async () => {
 
 test('can query test.vcf.gz with a CSI index', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/test.vcf.gz'),
-    csiPath: require.resolve('./data/test.vcf.gz.csi'),
+    path: new URL('data/test.vcf.gz', import.meta.url).pathname,
+    csiPath: new URL('data/test.vcf.gz.csi', import.meta.url).pathname,
   })
 
   const headerString = await f.getHeader()
@@ -280,7 +280,7 @@ test('can query test.vcf.gz with a CSI index', async () => {
 
 test('can fetch the entire header for a very large vcf header', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/large_vcf_header.vcf.gz'),
+    path: new URL('data/large_vcf_header.vcf.gz', import.meta.url).pathname,
   })
 
   const h = await f.getHeader()
@@ -292,7 +292,7 @@ test('can fetch the entire header for a very large vcf header', async () => {
 
 test('can fetch a CNV with length defined by END in INFO field', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/CNVtest.vcf.gz'),
+    path: new URL('data/CNVtest.vcf.gz', import.meta.url).pathname,
   })
 
   const lines = new RecordCollector()
@@ -302,7 +302,7 @@ test('can fetch a CNV with length defined by END in INFO field', async () => {
 
 test('can fetch a CNV with length defined by END in INFO field using the opts.lineCallback', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/CNVtest.vcf.gz'),
+    path: new URL('data/CNVtest.vcf.gz', import.meta.url).pathname,
   })
 
   const lines = new RecordCollector()
@@ -314,7 +314,7 @@ test('can fetch a CNV with length defined by END in INFO field using the opts.li
 
 test('returns and empty string for `getHeader()` if there is no header', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/test.bed.gz'),
+    path: new URL('data/test.bed.gz', import.meta.url).pathname,
   })
 
   const headerString = await f.getHeader()
@@ -323,7 +323,7 @@ test('returns and empty string for `getHeader()` if there is no header', async (
 
 test('can fetch NC_000001.11:184099343..184125655 correctly', async () => {
   const f = new TabixIndexedFile({
-    path: require.resolve('./data/ncbi_human.sorted.gff.gz'),
+    path: new URL('data/ncbi_human.sorted.gff.gz', import.meta.url).pathname,
   })
 
   // const headerString = await f.getHeader()
@@ -363,7 +363,7 @@ NC_000001.11	Gnomon	exon	184121787	184122540	.	+	.	Parent=lnc_RNA1661;Dbxref=Gen
 
 test('usage of the chr22 ultralong nanopore as a bed file', async () => {
   const ti = new TabixIndexedFile({
-    path: require.resolve('./data/chr22_nanopore_subset.bed.gz'),
+    path: new URL('data/chr22_nanopore_subset.bed.gz', import.meta.url).pathname,
   })
   await ti.getHeader()
   const ret1 = new RecordCollector()
@@ -381,7 +381,7 @@ test('usage of the chr22 ultralong nanopore as a bed file', async () => {
 
 test('too few', async () => {
   const ti = new TabixIndexedFile({
-    path: require.resolve('./data/too_few_reads_if_chunk_merging_on.bed.gz'),
+    path: new URL('data/too_few_reads_if_chunk_merging_on.bed.gz', import.meta.url).pathname,
   })
   await ti.getHeader()
 
@@ -392,7 +392,7 @@ test('too few', async () => {
 
 test('long read consistent IDs', async () => {
   const ti = new TabixIndexedFile({
-    path: require.resolve('./data/CHM1_pacbio_clip2.bed.gz'),
+    path: new URL('data/CHM1_pacbio_clip2.bed.gz', import.meta.url).pathname,
   })
   await ti.getHeader()
   const ret1 = new RecordCollector()
@@ -412,8 +412,8 @@ test('long read consistent IDs', async () => {
 
 test('fake large chromosome', async () => {
   const ti = new TabixIndexedFile({
-    path: require.resolve('./data/fake_large_chromosome/test.gff3.gz'),
-    csiPath: require.resolve('./data/fake_large_chromosome/test.gff3.gz.csi'),
+    path: new URL('data/fake_large_chromosome/test.gff3.gz', import.meta.url).pathname,
+    csiPath: new URL('data/fake_large_chromosome/test.gff3.gz.csi', import.meta.url).pathname,
   })
   await ti.getHeader()
 
@@ -425,8 +425,8 @@ test('fake large chromosome', async () => {
 })
 test('start equal to end in tabix columns', async () => {
   const ti = new TabixIndexedFile({
-    path: require.resolve('./data/out.bed.gz'),
-    tbiPath: require.resolve('./data/out.bed.gz.tbi'),
+    path: new URL('data/out.bed.gz', import.meta.url).pathname,
+    tbiPath: new URL('data/out.bed.gz.tbi', import.meta.url).pathname,
   })
   await ti.getHeader()
 

test/tbi.test.ts

@@ -6,7 +6,9 @@ import VirtualOffset from '../src/virtualOffset.ts'
 
 test('loads', async () => {
   const ti = new TBI({
-    filehandle: new LocalFile(require.resolve('./data/volvox.test.vcf.gz.tbi')),
+    filehandle: new LocalFile(
+      new URL('data/volvox.test.vcf.gz.tbi', import.meta.url).pathname,
+    ),
   })
   const indexData = await ti.parse()
   expect(indexData.columnNumbers.start).toEqual(2)
@@ -44,7 +46,7 @@ test('loads', async () => {
 test('failing tabix', async () => {
   const ti = new TBI({
     filehandle: new LocalFile(
-      require.resolve('./data/failing_tabix.vcf.gz.tbi'),
+      new URL('data/failing_tabix.vcf.gz.tbi', import.meta.url).pathname,
     ),
   })
 

tsconfig.json

@@ -3,6 +3,7 @@
   "compilerOptions": {
     "outDir": "dist",
     "lib": ["dom", "esnext"],
+    "types": ["node"],
     "declaration": true,
     "moduleResolution": "bundler",
     "module": "esnext",