@gmod/cram 3.0.0 → 3.0.1

package/src/cramFile/file.ts

@@ -1,11 +1,12 @@
-import { unzip } from '../unzip'
+import { Buffer } from 'buffer'
 import crc32 from 'buffer-crc32'
 import QuickLRU from 'quick-lru'
 import htscodecs from '@jkbonfield/htscodecs'
-// @ts-expect-error
 import bzip2 from 'bzip2'
 import { XzReadableStream } from 'xz-decompress'
 import { CramMalformedError, CramUnimplementedError } from '../errors'
+// locals
+import { unzip } from '../unzip'
 import ransuncompress from '../rans'
 import {
   BlockHeader,
@@ -13,13 +14,11 @@ import {
   cramFileDefinition,
   getSectionParsers,
 } from './sectionParsers'
-
 import CramContainer from './container'
-
+import CramRecord from './record'
 import { open } from '../io'
 import { parseItem, tinyMemoize } from './util'
 import { parseHeaderText } from '../sam'
-import CramRecord from './record'
 import { Filehandle } from './filehandle'
 
 function bufferToStream(buf: Buffer) {
@@ -31,7 +30,7 @@ function bufferToStream(buf: Buffer) {
   })
 }
 
-// source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
+// source: https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
 function getEndianness() {
   const uInt32 = new Uint32Array([0x11223344])
   const uInt8 = new Uint8Array(uInt32.buffer)
@@ -163,7 +162,7 @@ export default class CramFile {
     const { cramContainerHeader1 } = sectionParsers
 
     // skip with a series of reads to the proper container
-    let currentContainer
+    let currentContainer: CramContainer | undefined
     for (let i = 0; i <= containerNumber; i++) {
       // if we are about to go off the end of the file
       // and have not found that container, it does not exist
@@ -282,7 +281,7 @@ export default class CramFile {
     size = section.maxLength,
     preReadBuffer = undefined,
   ) {
-    let buffer
+    let buffer: Buffer
     if (preReadBuffer) {
       buffer = preReadBuffer
     } else {
@@ -314,15 +313,15 @@ export default class CramFile {
       const bits = bzip2.array(inputBuffer)
       let size = bzip2.header(bits)
       let j = 0
-      let chunk
+      let chunk: Uint8Array | -1
       do {
         chunk = bzip2.decompress(bits, size)
-        if (chunk != -1) {
+        if (chunk !== -1) {
           Buffer.from(chunk).copy(outputBuffer, j)
           j += chunk.length
           size -= chunk.length
         }
-      } while (chunk != -1)
+      } while (chunk !== -1)
     } else if (compressionMethod === 'lzma') {
       const decompressedResponse = new Response(
         new XzReadableStream(bufferToStream(inputBuffer)),

package/src/cramFile/record.ts

@@ -18,10 +18,7 @@ export interface ReadFeature {
   sub?: string
 }
 
-function decodeReadSequence(
-  cramRecord: CramRecord,
-  refRegion: RefRegion,
-): string | null {
+function decodeReadSequence(cramRecord: CramRecord, refRegion: RefRegion) {
   // if it has no length, it has no sequence
   if (!cramRecord.lengthOnRef && !cramRecord.readLength) {
     return null
@@ -215,8 +212,8 @@ function makeFlagsHelper<T>(
 ): FlagsDecoder<T> & FlagsEncoder<T> {
   const r: any = {}
   for (const [code, name] of x) {
-    r['is' + name] = (flags: number) => !!(flags & code)
-    r['set' + name] = (flags: number) => flags | code
+    r[`is${name}`] = (flags: number) => !!(flags & code)
+    r[`set${name}`] = (flags: number) => flags | code
   }
 
   return r

package/src/cramFile/sectionParsers.ts

@@ -314,7 +314,7 @@ function cramUnmappedSliceHeader(majorVersion: number) {
     }
 
     // the md5 sum is missing in cram v1
-    let md5
+    let md5: TupleOf<number, 16> | undefined
     if (majorVersion >= 2) {
       md5 = [...buffer.subarray(offset, offset + 16)] as TupleOf<number, 16>
       offset += 16
@@ -391,7 +391,7 @@ function cramMappedSliceHeader(majorVersion: number) {
       // EL2
 
       // the md5 sum is missing in cram v1
-      let md5
+      let md5: TupleOf<number, 16> | undefined
       if (majorVersion >= 2) {
         md5 = [...buffer.subarray(offset, offset + 16)] as TupleOf<number, 16>
         offset += 16
@@ -674,7 +674,7 @@ function cramContainerHeader1(majorVersion: number) {
         console.warn('setting recordCounter=0')
       }
 
-      let numBases
+      let numBases: number | undefined
       if (majorVersion > 1) {
         const [n, newOffset5] = parseLtf8(buffer, offset)
         numBases = n
@@ -716,7 +716,7 @@ function cramContainerHeader2(majorVersion: number) {
         landmarks.push(landmark)
       }
 
-      let crc32
+      let crc32: number | undefined
       if (majorVersion >= 3) {
         crc32 = dataView.getUint32(offset, true)
         offset += 4

package/src/cramFile/slice/decodeRecord.ts

@@ -74,7 +74,7 @@ function parseTagValueArray(buffer: Buffer) {
       array[i] = arr[i]
     }
   } else {
-    throw new Error('unknown type: ' + arrayType)
+    throw new Error(`unknown type: ${arrayType}`)
   }
 
   return array
@@ -249,20 +249,27 @@ export default function decodeRecord(
   cursors.lastAlignmentStart = alignmentStart
   const readGroupId = decodeDataSeries('RG')
 
-  let readName
+  let readName: string | undefined
   if (compressionScheme.readNamesIncluded) {
     readName = readNullTerminatedString(decodeDataSeries('RN'))
   }
 
-  let mateToUse
-  let templateSize
-  let mateRecordNumber
+  let mateToUse:
+    | {
+        mateFlags: number
+        mateSequenceId: number
+        mateAlignmentStart: number
+        mateReadName: string | undefined
+      }
+    | undefined
+  let templateSize: number | undefined
+  let mateRecordNumber: number | undefined
   // mate record
   if (CramFlagsDecoder.isDetached(cramFlags)) {
-    // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
-    // const mate: any = {}
+    // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't
+    // matter for javascript
     const mateFlags = decodeDataSeries('MF')
-    let mateReadName
+    let mateReadName: string | undefined
     if (!compressionScheme.readNamesIncluded) {
       mateReadName = readNullTerminatedString(decodeDataSeries('RN'))
       readName = mateReadName
@@ -327,9 +334,9 @@ export default function decodeRecord(
     tags[tagName] = parseTagData(tagType, tagData)
   }
 
-  let readFeatures
-  let lengthOnRef
-  let mappingQuality
+  let readFeatures: ReadFeature[] | undefined
+  let lengthOnRef: number | undefined
+  let mappingQuality: number | undefined
   let qualityScores: number[] | undefined | null
   let readBases = undefined
   if (!BamFlagsDecoder.isSegmentUnmapped(flags)) {
@@ -345,7 +352,8 @@ export default function decodeRecord(
       )
     }
 
-    // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
+    // compute the read's true span on the reference sequence, and the end
+    // coordinate of the alignment on the reference
     lengthOnRef = readLength
     if (readFeatures) {
       for (const { code, data } of readFeatures) {

package/src/cramFile/slice/index.ts

@@ -177,7 +177,7 @@ function associateIntraSliceMate(
 
   // delete this last because it's used by the
   // complicated template length estimation
-  delete thisRecord.mateRecordNumber
+  thisRecord.mateRecordNumber = undefined
 }
 
 export default class CramSlice {
@@ -524,7 +524,7 @@ export default class CramSlice {
             refRegion = {
               id: seqId,
               start: record.alignmentStart,
-              end: -Infinity,
+              end: Number.NEGATIVE_INFINITY,
               seq: null,
             }
             refRegions[seqId] = refRegion

package/src/cramFile/util.ts

@@ -21,7 +21,7 @@ export function itf8Size(v: number) {
 export function parseItf8(buffer: Uint8Array, initialOffset: number) {
   let offset = initialOffset
   const countFlags = buffer[offset]
-  let result
+  let result: number
   if (countFlags < 0x80) {
     result = countFlags
     offset = offset + 1
@@ -63,7 +63,7 @@ export function parseItf8(buffer: Uint8Array, initialOffset: number) {
 export function parseLtf8(buffer: Buffer, initialOffset: number) {
   let offset = initialOffset
   const countFlags = buffer[offset]
-  let n
+  let n: number | Long
   if (countFlags < 0x80) {
     n = countFlags
     offset += 1
@@ -88,7 +88,7 @@ export function parseLtf8(buffer: Buffer, initialOffset: number) {
     offset += 4
   } else if (countFlags < 0xf8) {
     n =
-      ((buffer[offset] & 15) * Math.pow(2, 32) + (buffer[offset + 1] << 24)) |
+      ((buffer[offset] & 15) * 2 ** 32 + (buffer[offset + 1] << 24)) |
       ((buffer[offset + 2] << 16) |
         (buffer[offset + 3] << 8) |
         buffer[offset + 4])
@@ -96,7 +96,7 @@ export function parseLtf8(buffer: Buffer, initialOffset: number) {
     offset += 5
   } else if (countFlags < 0xfc) {
     n =
-      ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2, 32) +
+      ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * 2 ** 32 +
         (buffer[offset + 2] << 24)) |
       ((buffer[offset + 3] << 16) |
         (buffer[offset + 4] << 8) |
@@ -107,7 +107,7 @@ export function parseLtf8(buffer: Buffer, initialOffset: number) {
       ((((buffer[offset] & 3) << 16) |
         (buffer[offset + 1] << 8) |
         buffer[offset + 2]) *
-        Math.pow(2, 32) +
+        2 ** 32 +
         (buffer[offset + 3] << 24)) |
       ((buffer[offset + 4] << 16) |
         (buffer[offset + 5] << 8) |

package/src/rans/d04.ts

@@ -40,7 +40,7 @@ export default function uncompress(
   }
 
   out.setPosition(outputEnd)
-  let /* byte */ c
+  let /* byte */ c: number
   switch (outputSize & 3) {
     case 0:
       break

package/src/rans/decoding.ts

@@ -24,7 +24,7 @@ class AriDecoder {
   }
 }
 
-class Symbol {
+class DecodingSymbol {
   // int start; // Start of range.
   // int freq; // Symbol frequency.
   constructor() {
@@ -36,10 +36,10 @@ class Symbol {
 // Initialize a decoder symbol to start "start" and frequency "freq"
 function symbolInit(sym, start, freq) {
   if (!(start <= 1 << 16)) {
-    throw new CramMalformedError(`assertion failed: start <= 1<<16`)
+    throw new CramMalformedError('assertion failed: start <= 1<<16')
   }
   if (!(freq <= (1 << 16) - start)) {
-    throw new CramMalformedError(`assertion failed: freq <= 1<<16`)
+    throw new CramMalformedError('assertion failed: freq <= 1<<16')
   }
   sym.start = start
   sym.freq = freq
@@ -127,10 +127,10 @@ function symbolInit(sym, start, freq) {
   return r
 }
 
-const Decode = {
+export default {
   FC,
   AriDecoder,
-  Symbol,
+  DecodingSymbol,
   symbolInit,
   advanceStep,
   advanceSymbolStep,
@@ -138,5 +138,3 @@ const Decode = {
   advanceSymbol,
   renormalize,
 }
-
-export default Decode

package/src/rans/index.ts

@@ -1,4 +1,5 @@
 //@ts-nocheck
+import { Buffer } from 'buffer'
 import { CramMalformedError } from '../errors'
 
 import Decoding from './decoding'
@@ -118,7 +119,7 @@ function /* static ByteBuffer */ uncompressOrder0Way4(
   const D = new Decoding.AriDecoder()
   const syms = new Array(256)
   for (let i = 0; i < syms.length; i += 1) {
-    syms[i] = new Decoding.Symbol()
+    syms[i] = new Decoding.DecodingSymbol()
   }
 
   readStatsO0(input, D, syms)
@@ -140,7 +141,7 @@ function /* static ByteBuffer */ uncompressOrder1Way4(
   for (let i = 0; i < syms.length; i += 1) {
     syms[i] = new Array(256)
     for (let j = 0; j < syms[i].length; j += 1) {
-      syms[i][j] = new Decoding.Symbol()
+      syms[i][j] = new Decoding.DecodingSymbol()
     }
   }
   readStatsO1(input, D, syms)