More opt

Author: cmdcolin

src/csi.ts

@@ -69,6 +69,7 @@ export default class CSI extends IndexFile {
     }
     const metaValue = dataView.getInt32(offset + 16, true)
     const metaChar = metaValue ? String.fromCharCode(metaValue) : undefined
+    const metaCharCode = metaValue || 0
     const skipLines = dataView.getInt32(offset + 20, true)
     const nameSectionLength = dataView.getInt32(offset + 24, true)
 
@@ -81,6 +82,7 @@ export default class CSI extends IndexFile {
       refNameToId,
       skipLines,
       metaChar,
+      metaCharCode,
       columnNumbers,
       format,
       coordinateType,
@@ -113,6 +115,7 @@ export default class CSI extends IndexFile {
             refIdToName: [],
             refNameToId: {},
             metaChar: undefined,
+            metaCharCode: 0,
             columnNumbers: { ref: 0, start: 1, end: 2 },
             coordinateType: 'zero-based-half-open',
             format: 'generic',

src/indexFile.ts

@@ -11,6 +11,7 @@ export interface IndexData {
   refNameToId: Record<string, number>
   refIdToName: string[]
   metaChar: string | undefined
+  metaCharCode: number
   columnNumbers: { ref: number; start: number; end: number }
   coordinateType: string
   format: string

src/tabixIndexedFile.ts

@@ -12,6 +12,7 @@ import { checkAbortSignal } from './util.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
 const NO_OVERLAP = { overlaps: false, startCoordinate: undefined } as const
+const OVERLAP_RESULT = { overlaps: true, startCoordinate: 0 }
 const END_REGEX = /(?:^|;)END=([^;]+)/
 const ZERO = '0'.charCodeAt(0)
 
@@ -441,8 +442,8 @@ export default class TabixIndexedFile {
     regionEnd: number,
     line: string,
   ) {
-    const { columnNumbers, metaChar, coordinateType, format } = metadata
-    if (metaChar && line.charCodeAt(0) === metaChar.charCodeAt(0)) {
+    const { columnNumbers, metaCharCode, coordinateType, format } = metadata
+    if (metaCharCode && line.charCodeAt(0) === metaCharCode) {
       return NO_OVERLAP
     }
 
@@ -518,7 +519,8 @@ export default class TabixIndexedFile {
       currentColumnNumber += 1
     }
 
-    return { startCoordinate, overlaps: true }
+    OVERLAP_RESULT.startCoordinate = startCoordinate
+    return OVERLAP_RESULT
   }
 
   _getVcfEnd(startCoordinate: number, refSeqLength: number, info: string) {

src/tbi.ts

@@ -141,6 +141,7 @@ export default class TabixIndex extends IndexFile {
     return {
       indices,
       metaChar,
+      metaCharCode: metaValue || 0,
       maxBinNumber,
       maxRefLength,
       skipLines,

test/csi.test.ts

@@ -32,6 +32,7 @@ test('loads test.gff3.gz.csi', async () => {
     format: 'generic',
     firstDataLine: new VirtualOffset(0, 130),
     metaChar: '#',
+    metaCharCode: 35,
     refIdToName: ['1', 'ctgB'],
     refNameToId: { 1: 0, ctgB: 1 },
     skipLines: 0,
@@ -69,6 +70,7 @@ test('loads test.vcf.gz.csi', async () => {
     coordinateType: '1-based-closed',
     format: 'VCF',
     metaChar: '#',
+    metaCharCode: 35,
     firstDataLine: new VirtualOffset(0, 2560),
     refIdToName: ['1'],
     refNameToId: { 1: 0 },

test/tabixindexedfile.test.ts

@@ -72,6 +72,7 @@ test('can read ctgA:1000..4000', async () => {
     maxBlockSize: 1 << 16,
     format: 'VCF',
     metaChar: '#',
+    metaCharCode: 35,
     firstDataLine: new VirtualOffset(0, 10431),
     refIdToName: ['ctgA'],
     refNameToId: { ctgA: 0 },

test/tbi.test.ts

@@ -25,6 +25,7 @@ test('loads', async () => {
     coordinateType: '1-based-closed',
     format: 'VCF',
     metaChar: '#',
+    metaCharCode: 35,
     maxBinNumber: 37449,
     firstDataLine: new VirtualOffset(0, 10431),
     refIdToName: ['contigA'],