Fix lint errors: add mjs/cjs ignores, replace any types with proper types in IndexData and CSI constructor

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

Author: cmdcolin

eslint.config.mjs

@@ -15,6 +15,8 @@ export default defineConfig(
       'profile*',
       'example/*',
       'eslint.config.mjs',
+      '*.mjs',
+      '*.cjs',
     ],
   },
   {
@@ -61,9 +63,8 @@ export default defineConfig(
           ignoreRestSiblings: true,
         },
       ],
-      '@typescript-eslint/no-explicit-any': 'off',
-      '@typescript-eslint/explicit-module-boundary-types': 'off',
-      '@typescript-eslint/ban-ts-comment': 'off',
+      '@typescript-eslint/no-explicit-any': 'warn',
+      '@typescript-eslint/ban-ts-comment': ['error', { 'ts-expect-error': 'allow-with-description', 'ts-ignore': true }],
       '@typescript-eslint/no-non-null-assertion': 'off',
       '@typescript-eslint/restrict-template-expressions': 'off',
       '@typescript-eslint/no-unsafe-member-access': 'off',
@@ -72,7 +73,7 @@ export default defineConfig(
       '@typescript-eslint/no-unsafe-call': 'off',
       '@typescript-eslint/no-unsafe-return': 'off',
       '@typescript-eslint/prefer-nullish-coalescing': 'off',
-      '@typescript-eslint/no-deprecated': 'off',
+      '@typescript-eslint/no-deprecated': 'warn',
       '@typescript-eslint/restrict-plus-operands': 'off',
       'no-empty': 'off',
 

src/csi.ts

@@ -7,6 +7,7 @@ import { optimizeChunks } from './util.ts'
 import VirtualOffset, { fromBytes } from './virtualOffset.ts'
 
 import type { Options } from './indexFile.ts'
+import type { GenericFilehandle } from 'generic-filehandle2'
 
 const CSI1_MAGIC = 21582659 // CSI\1
 const CSI2_MAGIC = 38359875 // CSI\2
@@ -28,7 +29,7 @@ export default class CSI extends IndexFile {
   private maxBinNumber: number
   private depth: number
   private minShift: number
-  constructor(args: any) {
+  constructor(args: { filehandle: GenericFilehandle }) {
     super(args)
     this.maxBinNumber = 0
     this.depth = 0
@@ -44,7 +45,7 @@ export default class CSI extends IndexFile {
     if (!idx) {
       return -1
     }
-    const { stats } = indexData.indices[refId]
+    const { stats } = idx
     if (stats) {
       return stats.lineCount
     }
@@ -202,8 +203,9 @@ export default class CSI extends IndexFile {
     // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
-        if (ba.binIndex[bin]) {
-          for (const c of ba.binIndex[bin]) {
+        const binChunks = ba.binIndex[bin]
+        if (binChunks) {
+          for (const c of binChunks) {
             chunks.push(new Chunk(c.minv, c.maxv, bin))
           }
         }

src/indexFile.ts

@@ -14,7 +14,16 @@ export interface IndexData {
   columnNumbers: { ref: number; start: number; end: number }
   coordinateType: string
   format: string
-  [key: string]: any
+  indices: { binIndex: Record<number | string, Chunk[]>; stats?: { lineCount: number }; linearIndex?: VirtualOffset[] }[]
+  maxRefLength: number
+  skipLines?: number
+  maxBinNumber?: number
+  maxBlockSize: number
+  firstDataLine?: VirtualOffset
+  refCount?: number
+  csi?: boolean
+  csiVersion?: number
+  depth?: number
 }
 
 export default abstract class IndexFile {

src/tbi.ts

@@ -39,7 +39,7 @@ export default class TabixIndex extends IndexFile {
     if (!idx) {
       return -1
     }
-    return indexData.indices[refId].stats?.lineCount ?? -1
+    return idx.stats?.lineCount ?? -1
   }
 
   // fetch and parse the index
@@ -181,11 +181,12 @@ export default class TabixIndex extends IndexFile {
       return []
     }
 
+    const linearIndex = ba.linearIndex ?? []
     const minOffset =
-      ba.linearIndex.length > 0
-        ? ba.linearIndex[
-            min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
-              ? ba.linearIndex.length - 1
+      linearIndex.length > 0
+        ? linearIndex[
+            min >> TAD_LIDX_SHIFT >= linearIndex.length
+              ? linearIndex.length - 1
               : min >> TAD_LIDX_SHIFT
           ]
         : new VirtualOffset(0, 0)
@@ -201,8 +202,9 @@ export default class TabixIndex extends IndexFile {
     // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
-        if (ba.binIndex[bin]) {
-          for (const c of ba.binIndex[bin]) {
+        const binChunks = ba.binIndex[bin]
+        if (binChunks) {
+          for (const c of binChunks) {
             chunks.push(new Chunk(c.minv, c.maxv, bin))
           }
         }
@@ -211,12 +213,12 @@ export default class TabixIndex extends IndexFile {
 
     // Use the linear index to find minimum file position of chunks that could
     // contain alignments in the region
-    const nintv = ba.linearIndex.length
+    const nintv = linearIndex.length
     let lowest: VirtualOffset | undefined
     const minLin = Math.min(min >> 14, nintv - 1)
     const maxLin = Math.min(max >> 14, nintv - 1)
     for (let i = minLin; i <= maxLin; ++i) {
-      const vp = ba.linearIndex[i]
+      const vp = linearIndex[i]
       if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
         lowest = vp
       }