re-enable typescript-eslint rules and fix violations

Re-enable no-explicit-any (error), no-this-alias, no-non-null-assertion,
and the no-unsafe-* rule cluster by fixing their root causes:
- Add types:["node"] to tsconfig.lint.json so @types/node resolves
- Fix test imports to use explicit .ts extensions and node: prefix
  (required by moduleResolution: nodenext)
- Replace ~30 non-null assertions with ?? '' / conditional guards
- Cast JSON.parse result to Record<string,unknown> at use site

Also simplify parseMetaString (for-of over parts array, .map for trim),
parseBreakend (for-of over tokens array), and parse.ts (direct match
index access instead of match.slice(1,3)).

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

Author: cmdcolin

eslint.config.mjs

@@ -34,6 +34,7 @@ export default defineConfig(
   {
     rules: {
       curly: 'error',
+      eqeqeq: 'error',
       '@typescript-eslint/consistent-type-imports': 'error',
       'no-console': [
         'warn',
@@ -61,14 +62,7 @@ export default defineConfig(
         'error',
         { 'ts-expect-error': 'allow-with-description', 'ts-ignore': true },
       ],
-      '@typescript-eslint/no-this-alias': 'off',
-      '@typescript-eslint/no-unsafe-member-access': 'off',
-      '@typescript-eslint/no-unsafe-argument': 'off',
-      '@typescript-eslint/no-explicit-any': 'warn',
-      '@typescript-eslint/no-unsafe-assignment': 'off',
-      '@typescript-eslint/no-unsafe-call': 'off',
-      '@typescript-eslint/no-unsafe-return': 'off',
-      '@typescript-eslint/no-non-null-assertion': 'off',
+      '@typescript-eslint/no-explicit-any': 'error',
       '@typescript-eslint/restrict-template-expressions': 'off',
       '@typescript-eslint/prefer-for-of': 'off',
 

src/Variant.ts

@@ -46,7 +46,7 @@ export class Variant {
     const fields = line.slice(0, splitPos).split('\t')
     const rest = line.slice(splitPos + 1)
     const [CHROM, POS, ID, REF, ALT, QUAL, FILTER] = fields
-    const filter = FILTER === '.' ? undefined : FILTER!.split(';')
+    const filter = !FILTER || FILTER === '.' ? undefined : FILTER.split(';')
 
     if (strict && !fields[7]) {
       throw new Error(
@@ -55,11 +55,11 @@ export class Variant {
     }
 
     this.CHROM = CHROM
-    this.POS = +POS!
-    this.ID = ID === '.' ? undefined : ID!.split(';')
+    this.POS = +(POS ?? '')
+    this.ID = !ID || ID === '.' ? undefined : ID.split(';')
     this.REF = REF
-    this.ALT = ALT === '.' ? undefined : ALT!.split(',')
-    this.QUAL = QUAL === '.' ? undefined : +QUAL!
+    this.ALT = !ALT || ALT === '.' ? undefined : ALT.split(',')
+    this.QUAL = !QUAL || QUAL === '.' ? undefined : +QUAL
     this.FILTER = filter?.length === 1 && filter[0] === 'PASS' ? 'PASS' : filter
     this.INFO =
       fields[7] === undefined || fields[7] === '.'
@@ -82,7 +82,7 @@ export class Variant {
     const pairsLen = infoPairs.length
 
     for (let i = 0; i < pairsLen; i++) {
-      const pair = infoPairs[i]!
+      const pair = infoPairs[i] ?? ''
       const eqIdx = pair.indexOf('=')
       const key = eqIdx === -1 ? pair : pair.slice(0, eqIdx)
       const val = eqIdx === -1 ? undefined : pair.slice(eqIdx + 1)
@@ -100,7 +100,7 @@ export class Variant {
         if (hasDecode) {
           const items: (string | number | undefined)[] = []
           for (let j = 0; j < itemsLen; j++) {
-            const v = rawItems[j]!
+            const v = rawItems[j] ?? ''
             if (v === '.') {
               items.push(undefined)
             } else {
@@ -112,7 +112,7 @@ export class Variant {
         } else {
           const items: (string | number | undefined)[] = []
           for (let j = 0; j < itemsLen; j++) {
-            const v = rawItems[j]!
+            const v = rawItems[j] ?? ''
             if (v === '.') {
               items.push(undefined)
             } else {
@@ -137,18 +137,18 @@ export class Variant {
       const formatKeys = format.split(':')
       const isNumberType: boolean[] = []
       for (let i = 0; i < formatKeys.length; i++) {
-        const r = this.formatMeta[formatKeys[i]!]?.Type
+        const r = this.formatMeta[formatKeys[i] ?? '']?.Type
         isNumberType.push(r === 'Integer' || r === 'Float')
       }
       const numKeys = formatKeys.length
       const samplesLen = this.sampleNames.length
       for (let i = 0; i < samplesLen; i++) {
-        const sample = this.sampleNames[i]!
+        const sample = this.sampleNames[i] ?? ''
         const sampleData: Record<
           string,
           (string | number | undefined)[] | undefined
         > = {}
-        const sampleStr = rest[i]!
+        const sampleStr = rest[i] ?? ''
         const sampleStrLen = sampleStr.length
         let colStart = 0
         let colIdx = 0
@@ -157,22 +157,22 @@ export class Variant {
           if (j === sampleStrLen || sampleStr[j] === ':') {
             const val = sampleStr.slice(colStart, j)
             if (val === '' || val === '.') {
-              sampleData[formatKeys[colIdx]!] = undefined
+              sampleData[formatKeys[colIdx] ?? ''] = undefined
             } else {
               const items = val.split(',')
               const result: (string | number | undefined)[] = []
               if (isNumberType[colIdx]) {
                 for (let k = 0; k < items.length; k++) {
-                  const ent = items[k]!
+                  const ent = items[k] ?? ''
                   result.push(ent === '.' ? undefined : +ent)
                 }
               } else {
                 for (let k = 0; k < items.length; k++) {
-                  const ent = items[k]!
+                  const ent = items[k] ?? ''
                   result.push(ent === '.' ? undefined : ent)
                 }
               }
-              sampleData[formatKeys[colIdx]!] = result
+              sampleData[formatKeys[colIdx] ?? ''] = result
             }
             colStart = j + 1
             colIdx += 1

src/parse.ts

@@ -39,7 +39,7 @@ export default class VCFParser {
 
     let lastLine: string | undefined
     for (let i = 0; i < headerLines.length; i++) {
-      const line = headerLines[i]!
+      const line = headerLines[i] ?? ''
       if (!line.startsWith('#')) {
         throw new Error(`Bad line in header:\n${line}`)
       } else if (line.startsWith('##')) {
@@ -87,9 +87,8 @@ export default class VCFParser {
     if (!match) {
       throw new Error(`Line is not a valid metadata line: ${line}`)
     }
-    const [metaKey, metaVal] = match.slice(1, 3)
-
-    const r = metaKey!
+    const r = match[1] ?? ''
+    const metaVal = match[2]
     if (metaVal?.startsWith('<')) {
       if (!(r in this.metadata)) {
         this.metadata[r] = {}
@@ -147,7 +146,9 @@ export default class VCFParser {
       if (typeof filteredMetadata !== 'object' || filteredMetadata === null) {
         return undefined
       }
-      filteredMetadata = (filteredMetadata as Record<string, unknown>)[args[i]!]
+      filteredMetadata = (filteredMetadata as Record<string, unknown>)[
+        args[i] ?? ''
+      ]
       if (!filteredMetadata) {
         return filteredMetadata
       }

src/parseBreakend.ts

@@ -24,9 +24,7 @@ export function parseBreakend(breakendString: string): Breakend | undefined {
     let Join
     let Replacement
     let MatePosition
-    const tokensLen = tokens.length
-    for (let i = 0; i < tokensLen; i++) {
-      const tok = tokens[i]!
+    for (const tok of tokens) {
       if (tok) {
         if (tok.includes(':')) {
           MatePosition = tok
@@ -69,7 +67,7 @@ export function parseBreakend(breakendString: string): Breakend | undefined {
           Join: 'left',
           Replacement,
           MateDirection: 'right',
-          MatePosition: `<${res[1]!}>:1`,
+          MatePosition: `<${res[1] ?? ''}>:1`,
         }
       : undefined
   }
@@ -85,7 +83,7 @@ export function parseBreakend(breakendString: string): Breakend | undefined {
           Join: 'right',
           Replacement,
           MateDirection: 'right',
-          MatePosition: `<${res[2]!}>:1`,
+          MatePosition: `<${res[2] ?? ''}>:1`,
         }
       : undefined
   }

src/parseGenotypesOnly.ts

@@ -21,7 +21,7 @@ export function parseGenotypesOnly(
       while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
         pos++
       }
-      genotypes[samples[idx]!] = prerest.slice(start, pos)
+      genotypes[samples[idx] ?? ''] = prerest.slice(start, pos)
       pos++
     }
     return genotypes
@@ -44,7 +44,7 @@ export function parseGenotypesOnly(
       ) {
         pos++
       }
-      genotypes[samples[idx]!] = prerest.slice(start, pos)
+      genotypes[samples[idx] ?? ''] = prerest.slice(start, pos)
       while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
         pos++
       }
@@ -72,7 +72,7 @@ export function parseGenotypesOnly(
     for (let j = sampleStart; j <= tabIdx; j++) {
       if (j === tabIdx || prerest.charCodeAt(j) === COLON) {
         if (colons === colonCount) {
-          genotypes[samples[idx]!] = prerest.slice(fieldStart, j)
+          genotypes[samples[idx] ?? ''] = prerest.slice(fieldStart, j)
           break
         }
         colons++

src/parseMetaString.ts

@@ -1,11 +1,3 @@
-// constructed with the assistance of claude AI
-//
-// I first prompted it with a regex that splits a comma separated string with
-// awareness of quotation from this stackoverflow question
-// https://stackoverflow.com/a/18893443/2129219, and asked it to add support
-// for square brackets
-//
-// it undid the regex into serial logic and the result was this function
 function customSplit(str: string) {
   const result = []
   const chars = []
@@ -14,7 +6,7 @@ function customSplit(str: string) {
   const strLen = str.length
 
   for (let i = 0; i < strLen; i++) {
-    const char = str[i]!
+    const char = str[i] ?? ''
     if (char === '"') {
       inQuotes = !inQuotes
       chars.push(char)
@@ -48,15 +40,16 @@ export function parseMetaString(metaString: string) {
   const inside = metaString.slice(1, -1)
   const parts = customSplit(inside)
   const entries: [string, string | string[]][] = []
-  for (let i = 0; i < parts.length; i++) {
-    const f = parts[i]!
+  for (const f of parts) {
     const [key, val] = splitFirst(f, '=')
     if (val && val.startsWith('[') && val.endsWith(']')) {
-      const items = val.slice(1, -1).split(',')
-      for (let j = 0; j < items.length; j++) {
-        items[j] = items[j]!.trim()
-      }
-      entries.push([key, items])
+      entries.push([
+        key,
+        val
+          .slice(1, -1)
+          .split(',')
+          .map(s => s.trim()),
+      ])
     } else if (val && val.startsWith('"') && val.endsWith('"')) {
       entries.push([key, val.slice(1, -1)])
     } else {

test/index.test.ts

@@ -1,8 +1,8 @@
 import { describe, expect, it } from 'vitest'
 
-import { parseBreakend } from '../src'
+import { parseBreakend } from '../src/index.ts'
 
-import type { Breakend } from '../src'
+import type { Breakend } from '../src/index.ts'
 
 describe('testBreakend', () => {
   it('can parse breakends', () => {

test/parse.test.ts

@@ -1,11 +1,11 @@
-import fs from 'fs'
+import { readFileSync } from 'node:fs'
 
 import { expect, test } from 'vitest'
 
-import VCF, { Variant, parseBreakend } from '../src'
+import VCF, { Variant, parseBreakend } from '../src/index.ts'
 
 const readVcf = (file: string) => {
-  const f = fs.readFileSync(file, 'utf8')
+  const f = readFileSync(file, 'utf8')
   const lines = f.split('\n')
   const header = [] as string[]
   const rest = [] as string[]
@@ -123,7 +123,7 @@ test('sniffles vcf', () => {
   const VCFParser = new VCF({
     header,
   })
-  const variant = VCFParser.parseLine(lines[0])
+  const variant = VCFParser.parseLine(lines[0] ?? '')
   expect(variant).toMatchSnapshot()
   expect(variant.SAMPLES()).toMatchSnapshot()
 })
@@ -133,8 +133,8 @@ test('can parse a line from the VCF spec Y chrom (haploid))', () => {
   const VCFParser = new VCF({
     header,
   })
-  const variant = VCFParser.parseLine(lines[0])
-  const variant2 = VCFParser.parseLine(lines[1])
+  const variant = VCFParser.parseLine(lines[0] ?? '')
+  const variant2 = VCFParser.parseLine(lines[1] ?? '')
   expect(variant).toMatchSnapshot()
   expect(variant.SAMPLES()).toMatchSnapshot()
   expect(variant2).toMatchSnapshot()
@@ -176,7 +176,7 @@ test('test no info strict', () => {
     header,
     strict: true,
   })
-  expect(() => VCFParser.parseLine(lines[0])).toThrow(/INFO/)
+  expect(() => VCFParser.parseLine(lines[0] ?? '')).toThrow(/INFO/)
 })
 
 test('test no info non-strict', () => {
@@ -185,8 +185,8 @@ test('test no info non-strict', () => {
     header,
     strict: false,
   })
-  expect(VCFParser.parseLine(lines[0])).toBeTruthy()
-  expect(VCFParser.parseLine(lines[0]).GENOTYPES()).toEqual({})
+  expect(VCFParser.parseLine(lines[0] ?? '')).toBeTruthy()
+  expect(VCFParser.parseLine(lines[0] ?? '').GENOTYPES()).toEqual({})
 })
 
 test('empty header lines', () => {
@@ -205,7 +205,7 @@ test('shortcut parsing with vcf 4.3 bnd example', () => {
 
   const VCFParser = new VCF({ header })
   const variants = lines.map(line => VCFParser.parseLine(line))
-  expect(variants.map(m => m.ALT?.[0].toString())).toEqual(
+  expect(variants.map(m => m.ALT?.[0]?.toString())).toEqual(
     lines.map(line => line.split('\t')[4]),
   )
 
@@ -250,8 +250,9 @@ test('sample to genotype information', () => {
   const VCFParser = new VCF({
     header,
   })
-  expect(VCFParser.getMetadata().META).toMatchSnapshot()
-  expect(VCFParser.getMetadata().SAMPLES).toMatchSnapshot()
+  const metadata = VCFParser.getMetadata() as Record<string, unknown>
+  expect(metadata.META).toMatchSnapshot()
+  expect(metadata.SAMPLES).toMatchSnapshot()
 })
 
 test('pedigree', () => {
@@ -311,7 +312,10 @@ test('Variant serializes without methods', () => {
   const variant = VCFParser.parseLine(
     '20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;DP=14;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:.,.',
   )
-  const serialized = JSON.parse(JSON.stringify(variant))
+  const serialized = JSON.parse(JSON.stringify(variant)) as Record<
+    string,
+    unknown
+  >
 
   expect(serialized.SAMPLES).toBeUndefined()
   expect(serialized.GENOTYPES).toBeUndefined()

test/parseGenotypesOnly-edge-cases.test.ts

@@ -1,6 +1,6 @@
 import { expect, test } from 'vitest'
 
-import { parseGenotypesOnly } from '../src/parseGenotypesOnly'
+import { parseGenotypesOnly } from '../src/parseGenotypesOnly.ts'
 
 test('last sample with 3-char GT and no trailing tab', () => {
   // Single sample, no trailing tab
@@ -120,7 +120,7 @@ test('haploid genotypes - many samples', () => {
 
   const expected = {} as Record<string, string>
   samples.forEach((s, i) => {
-    expected[s] = gts[i]!
+    expected[s] = gts[i] ?? ''
   })
 
   expect(result).toEqual(expected)
@@ -368,7 +368,7 @@ test('large scale mixed ploidy', () => {
 
   const expected = {} as Record<string, string>
   samples.forEach((s, i) => {
-    expected[s] = gts[i]!
+    expected[s] = gts[i] ?? ''
   })
 
   expect(result).toEqual(expected)

test/parseGenotypesOnly-ultrafast-edge.test.ts

@@ -1,6 +1,6 @@
 import { expect, test } from 'vitest'
 
-import { parseGenotypesOnly } from '../src/parseGenotypesOnly'
+import { parseGenotypesOnly } from '../src/parseGenotypesOnly.ts'
 
 test('ultra-fast path should not be tricked by mixed ploidy with matching length', () => {
   // 4 samples with total length = 15 = 4*4-1