@gmod/cram 3.0.4 → 3.0.5

package/src/cramFile/slice/decodeRecord.ts

@@ -1,4 +1,3 @@
-import Long from 'long'
 import { CramMalformedError } from '../../errors'
 import {
   BamFlagsDecoder,
@@ -22,7 +21,7 @@ import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes'
 function readNullTerminatedString(buffer: Uint8Array) {
   let r = ''
   for (let i = 0; i < buffer.length && buffer[i] !== 0; i++) {
-    r += String.fromCharCode(buffer[i])
+    r += String.fromCharCode(buffer[i]!)
   }
   return r
 }
@@ -31,9 +30,9 @@ function readNullTerminatedString(buffer: Uint8Array) {
  * parse a BAM tag's array value from a binary buffer
  * @private
  */
-function parseTagValueArray(buffer: Buffer) {
-  const arrayType = String.fromCharCode(buffer[0])
-  const length = Int32Array.from(buffer.slice(1))[0]
+function parseTagValueArray(buffer: Uint8Array) {
+  const arrayType = String.fromCharCode(buffer[0]!)
+  const length = Int32Array.from(buffer.slice(1))[0]!
 
   const array: number[] = new Array(length)
   buffer = buffer.slice(5)
@@ -41,37 +40,37 @@ function parseTagValueArray(buffer: Buffer) {
   if (arrayType === 'c') {
     const arr = new Int8Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 'C') {
     const arr = new Uint8Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 's') {
     const arr = new Int16Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 'S') {
     const arr = new Uint16Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 'i') {
     const arr = new Int32Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 'I') {
     const arr = new Uint32Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 'f') {
     const arr = new Float32Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else {
     throw new Error(`unknown type: ${arrayType}`)
@@ -80,15 +79,15 @@ function parseTagValueArray(buffer: Buffer) {
   return array
 }
 
-function parseTagData(tagType: string, buffer: any) {
+function parseTagData(tagType: string, buffer: Uint8Array) {
   if (tagType === 'Z') {
     return readNullTerminatedString(buffer)
   }
   if (tagType === 'A') {
-    return String.fromCharCode(buffer[0])
+    return String.fromCharCode(buffer[0]!)
   }
   if (tagType === 'I') {
-    return Long.fromBytesLE(buffer).toNumber()
+    return new Uint32Array(buffer.buffer)[0]
   }
   if (tagType === 'i') {
     return new Int32Array(buffer.buffer)[0]
@@ -103,7 +102,7 @@ function parseTagData(tagType: string, buffer: any) {
     return new Int8Array(buffer.buffer)[0]
   }
   if (tagType === 'C') {
-    return buffer[0] as number
+    return buffer[0]!
   }
   if (tagType === 'f') {
     return new Float32Array(buffer.buffer)[0]
@@ -311,27 +310,18 @@ export default function decodeRecord(
 
   const tags: Record<string, any> = {}
   // TN = tag names
-  const TN = compressionScheme.getTagNames(TLindex)
+  const TN = compressionScheme.getTagNames(TLindex)!
   const ntags = TN.length
-
   for (let i = 0; i < ntags; i += 1) {
-    const tagId = TN[i]
+    const tagId = TN[i]!
     const tagName = tagId.slice(0, 2)
     const tagType = tagId.slice(2, 3)
 
-    const tagCodec = compressionScheme.getCodecForTag(tagId)
-    if (!tagCodec) {
-      throw new CramMalformedError(
-        `no codec defined for auxiliary tag ${tagId}`,
-      )
-    }
-    const tagData = tagCodec.decode(
-      slice,
-      coreDataBlock,
-      blocksByContentId,
-      cursors,
-    )
-    tags[tagName] = parseTagData(tagType, tagData)
+    const tagData = compressionScheme
+      .getCodecForTag(tagId)
+      .decode(slice, coreDataBlock, blocksByContentId, cursors)
+    tags[tagName] =
+      typeof tagData === 'number' ? tagData : parseTagData(tagType, tagData)
   }
 
   let readFeatures: ReadFeature[] | undefined

package/src/cramFile/slice/index.ts

@@ -90,9 +90,10 @@ function calculateIntraSliceMatePairTemplateLength(
 }
 
 /**
- * @private establishes a mate-pair relationship between two records in the same slice.
- * CRAM compresses mate-pair relationships between records in the same slice down into
- * just one record having the index in the slice of its mate
+ * @private establishes a mate-pair relationship between two records in the
+ * same slice. CRAM compresses mate-pair relationships between records in the
+ * same slice down into just one record having the index in the slice of its
+ * mate
  */
 function associateIntraSliceMate(
   allRecords: CramRecord[],
@@ -100,12 +101,6 @@ function associateIntraSliceMate(
   thisRecord: CramRecord,
   mateRecord: CramRecord,
 ) {
-  if (!mateRecord) {
-    throw new CramMalformedError(
-      'could not resolve intra-slice mate pairs, file seems truncated or malformed',
-    )
-  }
-
   const complicatedMultiSegment = !!(
     mateRecord.mate ||
     (mateRecord.mateRecordNumber !== undefined &&
@@ -186,7 +181,7 @@ export default class CramSlice {
   constructor(
     public container: CramContainer,
     public containerPosition: number,
-    _unused: number,
+    public sliceSize: number,
   ) {
     this.file = container.file
   }
@@ -242,7 +237,7 @@ export default class CramSlice {
         throw new Error('block undefined')
       }
       blocks[i] = block
-      blockPosition = blocks[i]._endPosition
+      blockPosition = blocks[i]!._endPosition
     }
 
     return blocks
@@ -251,8 +246,7 @@ export default class CramSlice {
   // no memoize
   async getCoreDataBlock() {
     const blocks = await this.getBlocks()
-    // the core data block is always the first block in the slice
-    return blocks[0]
+    return blocks[0]!
   }
 
   // memoize
@@ -357,10 +351,6 @@ export default class CramSlice {
     }
 
     const sliceHeader = await this.getHeader()
-    if (sliceHeader === undefined) {
-      throw new Error('slice header undefined')
-    }
-
     const blocksByContentId = await this._getBlocksContentIdIndex()
 
     // check MD5 of reference if available
@@ -429,7 +419,9 @@ export default class CramSlice {
       )
       return decoded
     }
-    let records: CramRecord[] = new Array(sliceHeader.parsedContent.numRecords)
+    const records: CramRecord[] = new Array(
+      sliceHeader.parsedContent.numRecords,
+    )
     for (let i = 0; i < records.length; i += 1) {
       try {
         const init = decodeRecord(
@@ -456,7 +448,6 @@ export default class CramSlice {
           console.warn(
             'read attempted beyond end of buffer, file seems truncated.',
           )
-          records = records.filter(r => !!r)
           break
         } else {
           throw e
@@ -467,13 +458,13 @@ export default class CramSlice {
     // interpret `recordsToNextFragment` attributes to make standard `mate`
     // objects Resolve mate pair cross-references between records in this slice
     for (let i = 0; i < records.length; i += 1) {
-      const { mateRecordNumber } = records[i]
+      const { mateRecordNumber } = records[i]!
       if (mateRecordNumber !== undefined && mateRecordNumber >= 0) {
         associateIntraSliceMate(
           records,
           i,
-          records[i],
-          records[mateRecordNumber],
+          records[i]!,
+          records[mateRecordNumber]!,
         )
       }
     }
@@ -580,6 +571,6 @@ export default class CramSlice {
 }
 
 // memoize several methods in the class for performance
-'getHeader getBlocks _getBlocksContentIdIndex'
-  .split(' ')
-  .forEach(method => tinyMemoize(CramSlice, method))
+'getHeader getBlocks _getBlocksContentIdIndex'.split(' ').forEach(method => {
+  tinyMemoize(CramSlice, method)
+})

package/src/cramFile/util.ts

@@ -20,34 +20,34 @@ export function itf8Size(v: number) {
 
 export function parseItf8(buffer: Uint8Array, initialOffset: number) {
   let offset = initialOffset
-  const countFlags = buffer[offset]
+  const countFlags = buffer[offset]!
   let result: number
   if (countFlags < 0x80) {
     result = countFlags
     offset = offset + 1
   } else if (countFlags < 0xc0) {
-    result = ((countFlags << 8) | buffer[offset + 1]) & 0x3fff
+    result = ((countFlags << 8) | buffer[offset + 1]!) & 0x3fff
     offset = offset + 2
   } else if (countFlags < 0xe0) {
     result =
-      ((countFlags << 16) | (buffer[offset + 1] << 8) | buffer[offset + 2]) &
+      ((countFlags << 16) | (buffer[offset + 1]! << 8) | buffer[offset + 2]!) &
       0x1fffff
     offset = offset + 3
   } else if (countFlags < 0xf0) {
     result =
       ((countFlags << 24) |
-        (buffer[offset + 1] << 16) |
-        (buffer[offset + 2] << 8) |
-        buffer[offset + 3]) &
+        (buffer[offset + 1]! << 16) |
+        (buffer[offset + 2]! << 8) |
+        buffer[offset + 3]!) &
       0x0fffffff
     offset = offset + 4
   } else {
     result =
       ((countFlags & 0x0f) << 28) |
-      (buffer[offset + 1] << 20) |
-      (buffer[offset + 2] << 12) |
-      (buffer[offset + 3] << 4) |
-      (buffer[offset + 4] & 0x0f)
+      (buffer[offset + 1]! << 20) |
+      (buffer[offset + 2]! << 12) |
+      (buffer[offset + 3]! << 4) |
+      (buffer[offset + 4]! & 0x0f)
     // x=((0xff & 0x0f)<<28) | (0xff<<20) | (0xff<<12) | (0xff<<4) | (0x0f & 0x0f);
     // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
     offset = offset + 5
@@ -62,56 +62,56 @@ export function parseItf8(buffer: Uint8Array, initialOffset: number) {
 
 export function parseLtf8(buffer: Buffer, initialOffset: number) {
   let offset = initialOffset
-  const countFlags = buffer[offset]
+  const countFlags = buffer[offset]!
   let n: number | Long
   if (countFlags < 0x80) {
     n = countFlags
     offset += 1
   } else if (countFlags < 0xc0) {
-    n = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff
+    n = ((buffer[offset]! << 8) | buffer[offset + 1]!) & 0x3fff
     offset += 2
   } else if (countFlags < 0xe0) {
     n =
-      ((buffer[offset] << 16) |
-        (buffer[offset + 1] << 8) |
-        buffer[offset + 2]) &
+      ((buffer[offset]! << 16) |
+        (buffer[offset + 1]! << 8) |
+        buffer[offset + 2]!) &
       0x1fffff
     n = ((countFlags & 63) << 16) | buffer.readUInt16LE(offset + 1)
     offset += 3
   } else if (countFlags < 0xf0) {
     n =
-      ((buffer[offset] << 24) |
-        (buffer[offset + 1] << 16) |
-        (buffer[offset + 2] << 8) |
-        buffer[offset + 3]) &
+      ((buffer[offset]! << 24) |
+        (buffer[offset + 1]! << 16) |
+        (buffer[offset + 2]! << 8) |
+        buffer[offset + 3]!) &
       0x0fffffff
     offset += 4
   } else if (countFlags < 0xf8) {
     n =
-      ((buffer[offset] & 15) * 2 ** 32 + (buffer[offset + 1] << 24)) |
-      ((buffer[offset + 2] << 16) |
-        (buffer[offset + 3] << 8) |
-        buffer[offset + 4])
+      ((buffer[offset]! & 15) * 2 ** 32 + (buffer[offset + 1]! << 24)) |
+      ((buffer[offset + 2]! << 16) |
+        (buffer[offset + 3]! << 8) |
+        buffer[offset + 4]!)
     // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
     offset += 5
   } else if (countFlags < 0xfc) {
     n =
-      ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * 2 ** 32 +
-        (buffer[offset + 2] << 24)) |
-      ((buffer[offset + 3] << 16) |
-        (buffer[offset + 4] << 8) |
-        buffer[offset + 5])
+      ((((buffer[offset]! & 7) << 8) | buffer[offset + 1]!) * 2 ** 32 +
+        (buffer[offset + 2]! << 24)) |
+      ((buffer[offset + 3]! << 16) |
+        (buffer[offset + 4]! << 8) |
+        buffer[offset + 5]!)
     offset += 6
   } else if (countFlags < 0xfe) {
     n =
-      ((((buffer[offset] & 3) << 16) |
-        (buffer[offset + 1] << 8) |
-        buffer[offset + 2]) *
+      ((((buffer[offset]! & 3) << 16) |
+        (buffer[offset + 1]! << 8) |
+        buffer[offset + 2]!) *
         2 ** 32 +
-        (buffer[offset + 3] << 24)) |
-      ((buffer[offset + 4] << 16) |
-        (buffer[offset + 5] << 8) |
-        buffer[offset + 6])
+        (buffer[offset + 3]! << 24)) |
+      ((buffer[offset + 4]! << 16) |
+        (buffer[offset + 5]! << 8) |
+        buffer[offset + 6]!)
     offset += 7
   } else if (countFlags < 0xff) {
     n = Long.fromBytesBE(
@@ -167,6 +167,7 @@ export function tinyMemoize(_class: any, methodName: any) {
       const res = method.call(this)
       this[memoAttrName] = res
       Promise.resolve(res).catch(() => {
+         
         delete this[memoAttrName]
       })
     }

package/src/indexedCramFile.ts

@@ -63,9 +63,6 @@ export default class IndexedCramFile {
     }
 
     this.index = args.index
-    if (!this.index.getEntriesForRange) {
-      throw new Error('invalid arguments: not an index')
-    }
   }
 
   /**
@@ -163,7 +160,7 @@ export default class IndexedCramFile {
         .sort((a, b) => a.toString().localeCompare(b.toString()))
         .filter(
           (item, pos, ary) =>
-            !pos || item.toString() !== ary[pos - 1].toString(),
+            !pos || item.toString() !== ary[pos - 1]!.toString(),
         )
 
       const mateRecordPromises = []

package/src/rans/d04.ts

@@ -1,4 +1,4 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import { TF_SHIFT } from './constants'

package/src/rans/d14.ts

@@ -1,4 +1,4 @@
-//@ts-nocheck
+// @ts-nocheck
 import { TF_SHIFT } from './constants'
 import Decoding from './decoding'
 

package/src/rans/decoding.ts

@@ -1,4 +1,4 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import { RANS_BYTE_L } from './constants'

package/src/rans/frequencies.ts

@@ -1,4 +1,4 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors'
 
 import { TOTFREQ } from './constants'

package/src/rans/index.ts

@@ -1,4 +1,4 @@
-//@ts-nocheck
+// @ts-nocheck
 import { Buffer } from 'buffer'
 import { CramMalformedError } from '../errors'