Misc

CHANGELOG.md

@@ -1,27 +1,15 @@
 ## [5.0.5](https://github.com/GMOD/bam-js/compare/v5.0.4...v5.0.5) (2024-12-18)
 
-
-
 ## [5.0.4](https://github.com/GMOD/bam-js/compare/v5.0.2...v5.0.4) (2024-12-18)
 
-
-
 ## [5.0.3](https://github.com/GMOD/bam-js/compare/v5.0.2...v5.0.3) (2024-12-18)
 
-
-
 ## [5.0.2](https://github.com/GMOD/bam-js/compare/v5.0.1...v5.0.2) (2024-12-17)
 
-
-
 ## [5.0.1](https://github.com/GMOD/bam-js/compare/v5.0.0...v5.0.1) (2024-12-12)
 
-
-
 # [5.0.0](https://github.com/GMOD/bam-js/compare/v4.0.1...v5.0.0) (2024-12-12)
 
-
-
 ## [4.0.1](https://github.com/GMOD/bam-js/compare/v4.0.0...v4.0.1) (2024-11-12)
 
 # [4.0.0](https://github.com/GMOD/bam-js/compare/v3.0.3...v4.0.0) (2024-11-12)

eslint.config.mjs

@@ -83,6 +83,7 @@ export default tseslint.config(
       'unicorn/prefer-number-properties': 'off',
       'unicorn/no-process-exit': 'off',
       'unicorn/prefer-at': 'off',
+      '@typescript-eslint/no-non-null-assertion': 'off',
       '@typescript-eslint/no-unsafe-member-access': 'off',
       '@typescript-eslint/no-unsafe-argument': 'off',
       '@typescript-eslint/no-unsafe-assignment': 'off',

src/bai.ts

@@ -128,7 +128,7 @@ export default class BAI extends IndexFile {
     const range = start !== undefined
     const indexData = await this.parse(opts)
     const seqIdx = indexData.indices[seqId]
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+
     if (!seqIdx) {
       return []
     }
@@ -141,18 +141,18 @@ export default class BAI extends IndexFile {
     const depths = range
       ? new Array((e - s) / v)
       : new Array(linearIndex.length - 1)
-    const totalSize = linearIndex[linearIndex.length - 1].blockPosition
+    const totalSize = linearIndex[linearIndex.length - 1]!.blockPosition
     if (e > (linearIndex.length - 1) * v) {
       throw new Error('query outside of range of linear index')
     }
-    let currentPos = linearIndex[s / v].blockPosition
+    let currentPos = linearIndex[s / v]!.blockPosition
     for (let i = s / v, j = 0; i < e / v; i++, j++) {
       depths[j] = {
-        score: linearIndex[i + 1].blockPosition - currentPos,
+        score: linearIndex[i + 1]!.blockPosition - currentPos,
         start: i * v,
         end: i * v + v,
       }
-      currentPos = linearIndex[i + 1].blockPosition
+      currentPos = linearIndex[i + 1]!.blockPosition
     }
     return depths.map(d => ({
       ...d,
@@ -176,7 +176,7 @@ export default class BAI extends IndexFile {
       return []
     }
     const ba = indexData.indices[refId]
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+
     if (!ba) {
       return []
     }
@@ -188,9 +188,8 @@ export default class BAI extends IndexFile {
     // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (ba.binIndex[bin]) {
-          const binChunks = ba.binIndex[bin]
+          const binChunks = ba.binIndex[bin]!
           for (const binChunk of binChunks) {
             chunks.push(new Chunk(binChunk.minv, binChunk.maxv, bin))
           }
@@ -207,7 +206,6 @@ export default class BAI extends IndexFile {
     for (let i = minLin; i <= maxLin; ++i) {
       const vp = ba.linearIndex[i]
 
-      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
         lowest = vp
       }

src/bamFile.ts

@@ -375,22 +375,18 @@ export default class BamFile {
     return mateFeatPromises.flat()
   }
 
-  async _readRegion(position: number, size: number, opts: BaseOpts = {}) {
-    return this.bam.read(size, position, opts)
-  }
-
   async _readChunk({ chunk, opts }: { chunk: Chunk; opts: BaseOpts }) {
-    const buffer = await this._readRegion(
-      chunk.minv.blockPosition,
+    const buf = await this.bam.read(
       chunk.fetchedSize(),
+      chunk.minv.blockPosition,
       opts,
     )
 
     const {
       buffer: data,
       cpositions,
       dpositions,
-    } = await unzipChunkSlice(buffer, chunk)
+    } = await unzipChunkSlice(buf, chunk)
     return { data, cpositions, dpositions, chunk }
   }
 
@@ -413,7 +409,7 @@ export default class BamFile {
       // increment position to the current decompressed status
       // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       if (dpositions) {
-        while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]) {}
+        while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]!) {}
         pos--
       }
 
@@ -447,8 +443,8 @@ export default class BamFile {
           // realistically happen
           fileOffset:
             cpositions.length > 0
-              ? cpositions[pos] * (1 << 8) +
-                (blockStart - dpositions[pos]) +
+              ? cpositions[pos]! * (1 << 8) +
+                (blockStart - dpositions[pos]!) +
                 chunk.minv.dataPosition +
                 1
               : // this shift >>> 0 is equivalent to crc32(b).unsigned but uses the

src/csi.ts

@@ -163,7 +163,7 @@ export default class CSI extends IndexFile {
 
     const indexData = await this.parse(opts)
     const ba = indexData.indices[refId]
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+
     if (!ba) {
       return []
     }
@@ -177,9 +177,8 @@ export default class CSI extends IndexFile {
     // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (ba.binIndex[bin]) {
-          const binChunks = ba.binIndex[bin]
+          const binChunks = ba.binIndex[bin]!
           for (const c of binChunks) {
             chunks.push(c)
           }

src/long.ts

@@ -3,14 +3,14 @@ export const TWO_PWR_32_DBL = TWO_PWR_16_DBL * TWO_PWR_16_DBL
 
 export function longFromBytesToUnsigned(source: Uint8Array, i = 0) {
   const low =
-    source[i] |
-    (source[i + 1] << 8) |
-    (source[i + 2] << 16) |
-    (source[i + 3] << 24)
+    source[i]! |
+    (source[i + 1]! << 8) |
+    (source[i + 2]! << 16) |
+    (source[i + 3]! << 24)
   const high =
-    source[i + 4] |
-    (source[i + 5] << 8) |
-    (source[i + 6] << 16) |
-    (source[i + 7] << 24)
+    source[i + 4]! |
+    (source[i + 5]! << 8) |
+    (source[i + 6]! << 16) |
+    (source[i + 7]! << 24)
   return (high >>> 0) * TWO_PWR_32_DBL + (low >>> 0)
 }

src/record.ts

@@ -77,7 +77,7 @@ export default class BamRecord {
   get name() {
     let str = ''
     for (let i = 0; i < this.read_name_length - 1; i++) {
-      str += String.fromCharCode(this.byteArray[this.b0 + i])
+      str += String.fromCharCode(this.byteArray[this.b0 + i]!)
     }
     return str
   }
@@ -93,12 +93,15 @@ export default class BamRecord {
     const blockEnd = this.bytes.end
     const tags = {} as Record<string, unknown>
     while (p < blockEnd) {
-      const tag = String.fromCharCode(this.byteArray[p], this.byteArray[p + 1])
-      const type = String.fromCharCode(this.byteArray[p + 2])
+      const tag = String.fromCharCode(
+        this.byteArray[p]!,
+        this.byteArray[p + 1]!,
+      )
+      const type = String.fromCharCode(this.byteArray[p + 2]!)
       p += 3
 
       if (type === 'A') {
-        tags[tag] = String.fromCharCode(this.byteArray[p])
+        tags[tag] = String.fromCharCode(this.byteArray[p]!)
         p += 1
       } else if (type === 'i') {
         tags[tag] = this.#dataView.getInt32(p, true)
@@ -124,7 +127,7 @@ export default class BamRecord {
       } else if (type === 'Z' || type === 'H') {
         const value = []
         while (p <= blockEnd) {
-          const cc = this.byteArray[p++]
+          const cc = this.byteArray[p++]!
           if (cc !== 0) {
             value.push(String.fromCharCode(cc))
           } else {
@@ -133,7 +136,7 @@ export default class BamRecord {
         }
         tags[tag] = value.join('')
       } else if (type === 'B') {
-        const cc = this.byteArray[p++]
+        const cc = this.byteArray[p++]!
         const Btype = String.fromCharCode(cc)
         const limit = this.#dataView.getInt32(p, true)
         p += 4
@@ -143,7 +146,7 @@ export default class BamRecord {
             for (let k = 0; k < limit; k++) {
               const cigop = this.#dataView.getInt32(p, true)
               const lop = cigop >> 4
-              const op = CIGAR_DECODER[cigop & 0xf]
+              const op = CIGAR_DECODER[cigop & 0xf]!
               value.push(lop + op)
               p += 4
             }
@@ -162,7 +165,7 @@ export default class BamRecord {
             for (let k = 0; k < limit; k++) {
               const cigop = this.#dataView.getUint32(p, true)
               const lop = cigop >> 4
-              const op = CIGAR_DECODER[cigop & 0xf]
+              const op = CIGAR_DECODER[cigop & 0xf]!
               value.push(lop + op)
               p += 4
             }
@@ -318,7 +321,7 @@ export default class BamRecord {
       for (let c = 0; c < numCigarOps; ++c) {
         cigop = this.#dataView.getInt32(p, true)
         lop = cigop >> 4
-        op = CIGAR_DECODER[cigop & 0xf]
+        op = CIGAR_DECODER[cigop & 0xf]!
         CIGAR.push(lop + op)
         // soft clip, hard clip, and insertion don't count toward the length on
         // the reference
@@ -357,14 +360,13 @@ export default class BamRecord {
   }
 
   get seq() {
-    const { byteArray } = this.bytes
     const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4
     const seqBytes = this.num_seq_bytes
     const len = this.seq_length
     const buf = []
     let i = 0
     for (let j = 0; j < seqBytes; ++j) {
-      const sb = byteArray[p + j]
+      const sb = this.byteArray[p + j]!
       buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4])
       i++
       if (i < len) {

src/util.ts

@@ -133,7 +133,7 @@ export function parseNameBytes(
       if (currNameStart < i) {
         let refName = ''
         for (let j = currNameStart; j < i; j++) {
-          refName += String.fromCharCode(namesBytes[j])
+          refName += String.fromCharCode(namesBytes[j]!)
         }
         refName = renameRefSeq(refName)
         refIdToName[currRefId] = refName

src/virtualOffset.ts

@@ -15,33 +15,19 @@ export default class VirtualOffset {
       this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition
     )
   }
-
-  static min(...args: VirtualOffset[]) {
-    let min
-    let i = 0
-    for (; !min; i += 1) {
-      min = args[i]
-    }
-    for (; i < args.length; i += 1) {
-      if (min.compareTo(args[i]) > 0) {
-        min = args[i]
-      }
-    }
-    return min
-  }
 }
 export function fromBytes(bytes: Uint8Array, offset = 0, bigendian = false) {
   if (bigendian) {
     throw new Error('big-endian virtual file offsets not implemented')
   }
 
   return new VirtualOffset(
-    bytes[offset + 7] * 0x10000000000 +
-      bytes[offset + 6] * 0x100000000 +
-      bytes[offset + 5] * 0x1000000 +
-      bytes[offset + 4] * 0x10000 +
-      bytes[offset + 3] * 0x100 +
-      bytes[offset + 2],
-    (bytes[offset + 1] << 8) | bytes[offset],
+    bytes[offset + 7]! * 0x10000000000 +
+      bytes[offset + 6]! * 0x100000000 +
+      bytes[offset + 5]! * 0x1000000 +
+      bytes[offset + 4]! * 0x10000 +
+      bytes[offset + 3]! * 0x100 +
+      bytes[offset + 2]!,
+    (bytes[offset + 1]! << 8) | bytes[offset]!,
   )
 }

tsconfig.json

@@ -11,6 +11,7 @@
     "strict": true,
     "noImplicitReturns": true,
     "noFallthroughCasesInSwitch": true,
+    "noUncheckedIndexedAccess": true,
     "esModuleInterop": true
   }
 }