Fix tests

Author: cmdcolin

src/bamFile.ts

@@ -105,8 +105,9 @@ export default class BamFile {
     this.chunkSizeLimit = chunkSizeLimit || 300000000 // 300MB
   }
 
-  async getHeader(opts: AbortSignal | BaseOpts = {}) {
-    const indexData = await this.index.parse(makeOpts(opts))
+  async getHeader(origOpts: AbortSignal | BaseOpts = {}) {
+    const opts = makeOpts(origOpts)
+    const indexData = await this.index.parse(opts)
     const ret = indexData.firstDataLine ? indexData.firstDataLine.blockPosition + 65535 : undefined
     let buffer
     if (ret) {
@@ -433,6 +434,9 @@ export default class BamFile {
             start: blockStart,
             end: blockEnd,
           },
+          // the below results in an automatically calculated file-offset based ID
+          // if the info for that is available, otherwise crc32 of the features
+          //
           // cpositions[pos] refers to actual file offset of a bgzip block boundaries
           //
           // we multiply by (1 <<8) in order to make sure each block has a "unique"

src/htsget.ts

@@ -1,5 +1,5 @@
-import { BaseOpts } from './indexFile'
-import BamFile, { BamOpts, BAM_MAGIC } from './bamFile'
+import { BaseOpts, BamOpts } from './util'
+import BamFile, { BAM_MAGIC } from './bamFile'
 import 'cross-fetch/polyfill'
 import Chunk from './chunk'
 import { unzip } from '@gmod/bgzf-filehandle'

src/indexFile.ts

@@ -3,6 +3,7 @@ import QuickLRU from 'quick-lru'
 import { GenericFilehandle } from 'generic-filehandle'
 import VirtualOffset from './virtualOffset'
 import Chunk from './chunk'
+import { BaseOpts } from './util'
 
 export default abstract class IndexFile {
   public filehandle: GenericFilehandle