Couple more

GMOD · Dec 15, 2024 · d3b1da6 · d3b1da6
1 parent 57971d6
commit d3b1da6
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Showing 5 changed files with 14 additions and 56 deletions.
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -12,6 +12,7 @@ export default tseslint.config(
       '*.mjs',
       'example/*',
       'src/htscodecs',
+      'coverage',
     ],
   },
   {

diff --git a/src/cramFile/codecs/external.ts b/src/cramFile/codecs/external.ts
@@ -1,5 +1,5 @@
 import CramCodec, { Cursor, Cursors } from './_base'
-import { CramMalformedError, CramUnimplementedError } from '../../errors'
+import { CramUnimplementedError } from '../../errors'
 import { CramFileBlock } from '../file'
 import CramSlice from '../slice'
 import { parseItf8 } from '../util'

diff --git a/src/cramFile/container/index.ts b/src/cramFile/container/index.ts
@@ -28,9 +28,6 @@ export default class CramContainer {
     const sectionParsers = getSectionParsers(majorVersion)
 
     const block = await this.getFirstBlock()
-    if (block === undefined) {
-      return undefined
-    }
     if (block.contentType !== 'COMPRESSION_HEADER') {
       throw new CramMalformedError(
         `invalid content type ${block.contentType} in compression header block`,

diff --git a/src/cramFile/file.ts b/src/cramFile/file.ts
@@ -102,7 +102,6 @@ export default class CramFile {
     }
   }
 
-  // can just stat this object like a filehandle
   read(length: number, position: number) {
     return this.file.read(length, position)
   }
@@ -128,20 +127,17 @@ export default class CramFile {
     }
 
     const firstBlock = await firstContainer.getFirstBlock()
-    if (firstBlock === undefined) {
-      return parseHeaderText('')
-    } else {
-      const content = firstBlock.content
-      const dataView = new DataView(content.buffer)
-      const headerLength = dataView.getInt32(0, true)
-      const textStart = 4
-      const decoder = new TextDecoder('utf8')
-      const text = decoder.decode(
-        content.subarray(textStart, textStart + headerLength),
-      )
-      this.header = text
-      return parseHeaderText(text)
-    }
+
+    const content = firstBlock.content
+    const dataView = new DataView(content.buffer)
+    const headerLength = dataView.getInt32(0, true)
+    const textStart = 4
+    const decoder = new TextDecoder('utf8')
+    const text = decoder.decode(
+      content.subarray(textStart, textStart + headerLength),
+    )
+    this.header = text
+    return parseHeaderText(text)
   }
 
   async getHeaderText() {
@@ -153,7 +149,6 @@ export default class CramFile {
     const { majorVersion } = await this.getDefinition()
     const sectionParsers = getSectionParsers(majorVersion)
     let position = sectionParsers.cramFileDefinition.maxLength
-    const { cramContainerHeader1 } = sectionParsers
 
     // skip with a series of reads to the proper container
     let currentContainer: CramContainer | undefined
@@ -174,9 +169,6 @@ export default class CramFile {
         position = currentHeader._endPosition
         for (let j = 0; j < currentHeader.numBlocks; j++) {
           const block = await this.readBlock(position)
-          if (block === undefined) {
-            return undefined
-          }
           position = block._endPosition
         }
       } else {
@@ -232,9 +224,6 @@ export default class CramFile {
           position = currentHeader._endPosition
           for (let j = 0; j < currentHeader.numBlocks; j++) {
             const block = await this.readBlock(position)
-            if (block === undefined) {
-              break
-            }
             position = block._endPosition
           }
         } else {
@@ -260,11 +249,6 @@ export default class CramFile {
     const { majorVersion } = await this.getDefinition()
     const sectionParsers = getSectionParsers(majorVersion)
     const { cramBlockHeader } = sectionParsers
-    const { size: fileSize } = await this.file.stat()
-
-    if (position + cramBlockHeader.maxLength >= fileSize) {
-      return undefined
-    }
 
     const buffer = await this.file.read(cramBlockHeader.maxLength, position)
     return parseItem(buffer, cramBlockHeader.parser, 0, position)
@@ -282,16 +266,7 @@ export default class CramFile {
     size = section.maxLength,
     preReadBuffer?: Uint8Array,
   ) {
-    let buffer: Uint8Array
-    if (preReadBuffer) {
-      buffer = preReadBuffer
-    } else {
-      const { size: fileSize } = await this.file.stat()
-      if (position + size >= fileSize) {
-        return undefined
-      }
-      buffer = await this.file.read(size, position)
-    }
+    const buffer = preReadBuffer ?? (await this.file.read(size, position))
     const data = parseItem(buffer, section.parser, 0, position)
     if (data._size !== size) {
       throw new CramMalformedError(
@@ -351,9 +326,6 @@ export default class CramFile {
     const { majorVersion } = await this.getDefinition()
     const sectionParsers = getSectionParsers(majorVersion)
     const blockHeader = await this.readBlockHeader(position)
-    if (blockHeader === undefined) {
-      return undefined
-    }
     const blockContentPosition = blockHeader._endPosition
 
     const d = await this.file.read(
@@ -381,9 +353,6 @@ export default class CramFile {
         sectionParsers.cramBlockCrc32,
         blockContentPosition + blockHeader.compressedSize,
       )
-      if (crc === undefined) {
-        return undefined
-      }
       block.crc32 = crc.crc32
 
       // check the block data crc32

diff --git a/src/cramFile/slice/index.ts b/src/cramFile/slice/index.ts
@@ -198,16 +198,10 @@ export default class CramSlice {
     const { majorVersion } = await this.file.getDefinition()
     const sectionParsers = getSectionParsers(majorVersion)
     const containerHeader = await this.container.getHeader()
-    if (!containerHeader) {
-      throw new Error('no container header detected')
-    }
 
     const header = await this.file.readBlock(
       containerHeader._endPosition + this.containerPosition,
     )
-    if (header === undefined) {
-      throw new Error('block header undefined')
-    }
     if (header.contentType === 'MAPPED_SLICE_HEADER') {
       const content = parseItem(
         header.content,
@@ -239,9 +233,6 @@ export default class CramSlice {
     const blocks: CramFileBlock[] = new Array(header.parsedContent.numBlocks)
     for (let i = 0; i < blocks.length; i++) {
       const block = await this.file.readBlock(blockPosition)
-      if (block === undefined) {
-        continue
-      }
       blocks[i] = block
       blockPosition = blocks[i]!._endPosition
     }