Merge

src/cramFile/file.ts

@@ -137,12 +137,8 @@ export default class CramFile {
       return parseHeaderText('')
     }
     const content = firstBlock.content
-    // find the end of the trailing zeros in the header text
     const headerLength = content.readInt32LE(0)
     const textStart = 4
-    // let textEnd = content.length - 1
-    // while (textEnd >= textStart && !content[textEnd]) textEnd -= 1
-    // trim off the trailing zeros
     const text = content.toString('utf8', textStart, textStart + headerLength)
     this.header = text
     return parseHeaderText(text)
@@ -189,7 +185,8 @@ export default class CramFile {
           position = block._endPosition
         }
       } else {
-        // otherwise, just traverse to the next container using the container's length
+        // otherwise, just traverse to the next container using the container's
+        // length
         position += currentHeader._size + currentHeader.length
       }
     }
@@ -230,9 +227,9 @@ export default class CramFile {
       if (!currentHeader) {
         break
       }
-      // if this is the first container, read all the blocks in the
-      // container, because we cannot trust the container
-      // header's given length due to a bug somewhere in htslib
+      // if this is the first container, read all the blocks in the container,
+      // because we cannot trust the container header's given length due to a
+      // bug somewhere in htslib
       if (containerCount === 0) {
         position = currentHeader._endPosition
         for (let j = 0; j < currentHeader.numBlocks; j++) {
@@ -243,7 +240,8 @@ export default class CramFile {
           position = block._endPosition
         }
       } else {
-        // otherwise, just traverse to the next container using the container's length
+        // otherwise, just traverse to the next container using the container's
+        // length
         position += currentHeader._size + currentHeader.length
       }
       containerCount += 1

test/dump3.test.ts

@@ -0,0 +1,25 @@
+// @ts-nocheck
+import { test } from 'vitest'
+import { t3 as testFileList } from './lib/testFileList'
+import { testDataFile } from './lib/util'
+import { dumpWholeFile } from './lib/dumpFile'
+import { CramFile } from '../src/index'
+import { FetchableSmallFasta } from './lib/fasta'
+
+testFileList.forEach(filename => {
+  test(`can dump the whole ${filename} without error`, async () => {
+    let seqFetch
+    if (filename.includes('#')) {
+      const referenceFileName = filename.replace(/#.+$/, '.fa')
+      const fasta = new FetchableSmallFasta(testDataFile(referenceFileName))
+      seqFetch = fasta.fetch.bind(fasta)
+    }
+
+    const filehandle = testDataFile(filename)
+    const file = new CramFile({
+      filehandle,
+      seqFetch,
+    })
+    await dumpWholeFile(file) // just try to decode it, no snapshot test for now as it is large
+  }, 10000)
+})

test/lib/testFileList.ts

@@ -123,4 +123,15 @@ ML_test.cram
   .split(/\s+/)
   .filter(f => !!f)
 
-export { t1, t2 }
+const t3 = `
+hts-specs/0902_comp_bz2.cram
+hts-specs/0903_comp_lzma.cram
+hts-specs/3.1/passed/level-3.cram
+hts-specs/3.1/passed/level-4.cram
+hts-specs/3.1/passed/level-1.cram
+hts-specs/3.1/passed/level-2.cram
+`
+  .split(/\s+/)
+  .filter(f => !!f)
+
+export { t1, t2, t3 }