@gmod/bam 7.3.2 → 7.3.4

package/esm/util.js

@@ -47,7 +47,7 @@ export function optimizeChunks(chunks, lowest) {
             const cmp = chunkMaxBlock - lastMaxBlock ||
                 chunk.maxv.dataPosition - lastChunk.maxv.dataPosition;
             if (cmp > 0) {
-                mergedChunks[mergedChunks.length - 1] = new Chunk(lastChunk.minv, chunk.maxv, lastChunk.bin);
+                mergedChunks[mergedChunks.length - 1] = new Chunk(lastChunk.minv, chunk.maxv, lastChunk.bin, chunk.endPosition);
                 lastMaxBlock = chunkMaxBlock;
             }
         }
@@ -64,6 +64,38 @@ export function parsePseudoBin(bytes, offset) {
         lineCount: longFromBytesToUnsigned(bytes, offset),
     };
 }
+// Tighten each chunk's endPosition (default: a full max-size BGZF block past
+// maxv) down to the next known block boundary. Every chunk min/maxv blockPosition
+// and every extraBoundary (e.g. linear-index entries) is a real BGZF block start;
+// since blocks don't overlap, the first boundary strictly greater than a chunk's
+// maxv.blockPosition is an upper bound on where that final block ends — always at
+// least the true block end, so the clamped fetch still contains the whole block.
+// Shrinks both the byte estimate and the actual fetch with no extra I/O.
+export function clampChunkEnds(chunks, extraBoundaries = []) {
+    const boundaries = [...extraBoundaries];
+    for (const c of chunks) {
+        boundaries.push(c.minv.blockPosition, c.maxv.blockPosition);
+    }
+    boundaries.sort((a, b) => a - b);
+    for (const c of chunks) {
+        const max = c.maxv.blockPosition;
+        // first boundary strictly greater than max
+        let lo = 0;
+        let hi = boundaries.length;
+        while (lo < hi) {
+            const mid = (lo + hi) >>> 1;
+            if (boundaries[mid] > max) {
+                hi = mid;
+            }
+            else {
+                lo = mid + 1;
+            }
+        }
+        if (lo < boundaries.length) {
+            c.endPosition = Math.min(c.endPosition, boundaries[lo]);
+        }
+    }
+}
 // Parse the BAM reference-sequence table (SAMv1.pdf §4.2). Returns undefined
 // if `uncba` doesn't yet contain the full table — caller fetches more bytes
 // and retries.

package/esm/util.js.map

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package/esm/virtualOffset.d.ts

@@ -11,4 +11,4 @@ export declare class VirtualOffset {
     toString(): string;
     compareTo(b: VirtualOffset): number;
 }
-export declare function fromBytes(bytes: Uint8Array, offset?: number, bigendian?: boolean): VirtualOffset;
+export declare function fromBytes(bytes: Uint8Array, offset?: number): VirtualOffset;

package/esm/virtualOffset.js

@@ -12,10 +12,7 @@ export class VirtualOffset {
         return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
     }
 }
-export function fromBytes(bytes, offset = 0, bigendian = false) {
-    if (bigendian) {
-        throw new Error('big-endian virtual file offsets not implemented');
-    }
+export function fromBytes(bytes, offset = 0) {
     return new VirtualOffset(bytes[offset + 7] * 0x10000000000 +
         bytes[offset + 6] * 0x100000000 +
         bytes[offset + 5] * 0x1000000 +

package/esm/virtualOffset.js.map

@@ -1 +1 @@
-{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAOA,MAAM,OAAO,aAAa;IACjB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACxE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAOA,MAAM,OAAO,aAAa;IACjB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC;IACrD,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.3.2",
+  "version": "7.3.4",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": {

package/src/bai.ts

@@ -1,6 +1,6 @@
 import Chunk from './chunk.ts'
 import IndexFile, { memoizeByRefId } from './indexFile.ts'
-import { findFirstData, parsePseudoBin } from './util.ts'
+import { clampChunkEnds, findFirstData, parsePseudoBin } from './util.ts'
 import { fromBytes } from './virtualOffset.ts'
 
 import type { ParsedIndexBase, RefIndex } from './indexFile.ts'
@@ -146,6 +146,10 @@ export default class BAI extends IndexFile<BaiParsed> {
         curr += 8
       }
 
+      clampChunkEnds(
+        Object.values(binIndex).flat(),
+        linearIndex.map(v => v.blockPosition),
+      )
       return {
         binIndex,
         linearIndex,

package/src/chunk.ts

@@ -2,12 +2,26 @@ import type { Offset } from './virtualOffset.ts'
 
 // little class representing a chunk in the index
 export default class Chunk {
+  public minv: Offset
+  public maxv: Offset
+  public bin: number
+  // Absolute byte offset where the fetch for this chunk ends. The compressed
+  // size of the final BGZF block (the one at maxv.blockPosition) is unknown
+  // from the index, so this defaults to a full max-size block past maxv. It can
+  // be tightened to the next known block boundary via clampChunkEnds.
+  public endPosition: number
+
   constructor(
-    public minv: Offset,
-    public maxv: Offset,
-    public bin: number,
-    public _fetchedSize?: number,
-  ) {}
+    minv: Offset,
+    maxv: Offset,
+    bin: number,
+    endPosition = maxv.blockPosition + (1 << 16),
+  ) {
+    this.minv = minv
+    this.maxv = maxv
+    this.bin = bin
+    this.endPosition = endPosition
+  }
 
   toString() {
     return `${this.minv.toString()}..${this.maxv.toString()} (bin ${
@@ -24,9 +38,6 @@ export default class Chunk {
   }
 
   fetchedSize() {
-    if (this._fetchedSize !== undefined) {
-      return this._fetchedSize
-    }
-    return this.maxv.blockPosition + (1 << 16) - this.minv.blockPosition
+    return this.endPosition - this.minv.blockPosition
   }
 }

package/src/csi.ts

@@ -2,7 +2,12 @@ import { unzip } from '@gmod/bgzf-filehandle'
 
 import Chunk from './chunk.ts'
 import IndexFile, { memoizeByRefId } from './indexFile.ts'
-import { findFirstData, parseNameBytes, parsePseudoBin } from './util.ts'
+import {
+  clampChunkEnds,
+  findFirstData,
+  parseNameBytes,
+  parsePseudoBin,
+} from './util.ts'
 import { VirtualOffset, fromBytes } from './virtualOffset.ts'
 
 import type { BaseOpts } from './util.ts'
@@ -150,6 +155,7 @@ export default class CSI extends IndexFile {
         }
       }
 
+      clampChunkEnds(Object.values(binIndex).flat())
       return {
         binIndex,
         stats: pseudoBinStats,

package/src/long.ts

@@ -1,5 +1,4 @@
-export const TWO_PWR_16_DBL = 1 << 16
-export const TWO_PWR_32_DBL = TWO_PWR_16_DBL * TWO_PWR_16_DBL
+const TWO_PWR_32_DBL = 2 ** 32
 
 // avoids dependency on long.js
 export function longFromBytesToUnsigned(source: Uint8Array, i = 0) {

package/src/record.ts

@@ -127,6 +127,97 @@ function bArrayByteLength(Btype: number, limit: number) {
   }
 }
 
+// Cursor position just past a tag's value — i.e. the start of the next tag —
+// given the value starts at `p`. For null-terminated Z/H this steps over the
+// terminator. Returns 0 for an unknown type, whose value width is unknowable so
+// the caller must stop. Shared by _findTag and _computeTags so the two loops
+// can't drift in how they walk the tag layout. (0 is an impossible real end:
+// `p` is always past the fixed record prefix.)
+function tagValueEnd(
+  ba: Uint8Array,
+  dataView: DataView,
+  type: number,
+  p: number,
+  blockEnd: number,
+) {
+  switch (type) {
+    case 0x41: // 'A'
+    case 0x63: // 'c'
+    case 0x43: // 'C'
+      return p + 1
+    case 0x73: // 's'
+    case 0x53: // 'S'
+      return p + 2
+    case 0x69: // 'i'
+    case 0x49: // 'I'
+    case 0x66: {
+      // 'f'
+      return p + 4
+    }
+    case 0x5a: // 'Z'
+    case 0x48: {
+      // 'H'
+      let q = p
+      while (q < blockEnd && ba[q] !== 0) {
+        q++
+      }
+      return q + 1 // step past the null terminator
+    }
+    case 0x42: {
+      // 'B'
+      const Btype = ba[p]!
+      const limit = dataView.getInt32(p + 1, true)
+      return p + 5 + bArrayByteLength(Btype, limit)
+    }
+    default:
+      console.error('Unknown BAM tag type', type)
+      return 0
+  }
+}
+
+// Decode the value of a tag of `type` whose bytes start at `p`; `end` is the
+// next-tag cursor from tagValueEnd (used only to bound Z/H strings, whose bytes
+// run up to the null terminator at end-1). When `raw`, Z/H return the undecoded
+// byte subarray. Assumes `type` is a known scalar/string/B type.
+function decodeTagValue(
+  ba: Uint8Array,
+  dataView: DataView,
+  type: number,
+  p: number,
+  end: number,
+  raw: boolean,
+): unknown {
+  switch (type) {
+    case 0x41: // 'A'
+      return String.fromCharCode(ba[p]!)
+    case 0x69: // 'i'
+      return dataView.getInt32(p, true)
+    case 0x49: // 'I'
+      return dataView.getUint32(p, true)
+    case 0x63: // 'c'
+      return dataView.getInt8(p)
+    case 0x43: // 'C'
+      return dataView.getUint8(p)
+    case 0x73: // 's'
+      return dataView.getInt16(p, true)
+    case 0x53: // 'S'
+      return dataView.getUint16(p, true)
+    case 0x66: // 'f'
+      return dataView.getFloat32(p, true)
+    case 0x5a: // 'Z'
+    case 0x48: // 'H'
+      return raw
+        ? ba.subarray(p, end - 1)
+        : textDecoder.decode(ba.subarray(p, end - 1))
+    default: {
+      // 'B'
+      const Btype = ba[p]!
+      const limit = dataView.getInt32(p + 1, true)
+      return decodeBArrayTag(ba, dataView, p + 5, Btype, limit)
+    }
+  }
+}
+
 export default class BamRecord {
   public fileOffset: number
   private _byteArray: Uint8Array
@@ -261,172 +352,47 @@ export default class BamRecord {
   private _findTag(tagName: string, raw: boolean) {
     const tag1 = tagName.charCodeAt(0)
     const tag2 = tagName.charCodeAt(1)
-
-    let p = this.tagsStart
-
     const blockEnd = this._end
     const ba = this._byteArray
+    let p = this.tagsStart
     while (p < blockEnd) {
-      const currentTag1 = ba[p]
-      const currentTag2 = ba[p + 1]
-      const type = ba[p + 2]
-      p += 3
-
-      const isMatch = currentTag1 === tag1 && currentTag2 === tag2
-
-      switch (type) {
-        case 0x41: // 'A'
-          if (isMatch) {
-            return String.fromCharCode(ba[p]!)
-          }
-          p += 1
-          break
-        case 0x69: // 'i'
-          if (isMatch) {
-            return this._dataView.getInt32(p, true)
-          }
-          p += 4
-          break
-        case 0x49: // 'I'
-          if (isMatch) {
-            return this._dataView.getUint32(p, true)
-          }
-          p += 4
-          break
-        case 0x63: // 'c'
-          if (isMatch) {
-            return this._dataView.getInt8(p)
-          }
-          p += 1
-          break
-        case 0x43: // 'C'
-          if (isMatch) {
-            return this._dataView.getUint8(p)
-          }
-          p += 1
-          break
-        case 0x73: // 's'
-          if (isMatch) {
-            return this._dataView.getInt16(p, true)
-          }
-          p += 2
-          break
-        case 0x53: // 'S'
-          if (isMatch) {
-            return this._dataView.getUint16(p, true)
-          }
-          p += 2
-          break
-        case 0x66: // 'f'
-          if (isMatch) {
-            return this._dataView.getFloat32(p, true)
-          }
-          p += 4
-          break
-        case 0x5a: // 'Z'
-        case 0x48: {
-          // 'H'
-          const start = p
-          while (p < blockEnd && ba[p] !== 0) {
-            p++
-          }
-          if (isMatch) {
-            return raw
-              ? ba.subarray(start, p)
-              : textDecoder.decode(ba.subarray(start, p))
-          }
-          p++ // advance past null terminator
-          break
-        }
-        case 0x42: {
-          // 'B'
-          const Btype = ba[p++]!
-          const limit = this._dataView.getInt32(p, true)
-          p += 4
-          if (isMatch) {
-            return decodeBArrayTag(ba, this._dataView, p, Btype, limit)
-          }
-          p += bArrayByteLength(Btype, limit)
-          break
-        }
-        default:
-          if (type !== undefined) {
-            console.error('Unknown BAM tag type', type)
-          }
-          break
+      const isMatch = ba[p] === tag1 && ba[p + 1] === tag2
+      const type = ba[p + 2]!
+      const valueStart = p + 3
+      const end = tagValueEnd(ba, this._dataView, type, valueStart, blockEnd)
+      if (end === 0) {
+        break // unknown type: can't compute how far to advance
+      }
+      if (isMatch) {
+        return decodeTagValue(ba, this._dataView, type, valueStart, end, raw)
       }
+      p = end
     }
     return undefined
   }
 
   private _computeTags() {
-    let p = this.tagsStart
-
     const blockEnd = this._end
     const ba = this._byteArray
     const tags: Record<string, unknown> = {}
+    let p = this.tagsStart
     while (p < blockEnd) {
       const tag = String.fromCharCode(ba[p]!, ba[p + 1]!)
       const type = ba[p + 2]!
-      p += 3
-
-      switch (type) {
-        case 0x41: // 'A'
-          tags[tag] = String.fromCharCode(ba[p]!)
-          p += 1
-          break
-        case 0x69: // 'i'
-          tags[tag] = this._dataView.getInt32(p, true)
-          p += 4
-          break
-        case 0x49: // 'I'
-          tags[tag] = this._dataView.getUint32(p, true)
-          p += 4
-          break
-        case 0x63: // 'c'
-          tags[tag] = this._dataView.getInt8(p)
-          p += 1
-          break
-        case 0x43: // 'C'
-          tags[tag] = this._dataView.getUint8(p)
-          p += 1
-          break
-        case 0x73: // 's'
-          tags[tag] = this._dataView.getInt16(p, true)
-          p += 2
-          break
-        case 0x53: // 'S'
-          tags[tag] = this._dataView.getUint16(p, true)
-          p += 2
-          break
-        case 0x66: // 'f'
-          tags[tag] = this._dataView.getFloat32(p, true)
-          p += 4
-          break
-        case 0x5a: // 'Z'
-        case 0x48: {
-          // 'H'
-          const start = p
-          while (p < blockEnd && ba[p] !== 0) {
-            p++
-          }
-          tags[tag] = textDecoder.decode(ba.subarray(start, p))
-          p++ // advance past null terminator
-          break
-        }
-        case 0x42: {
-          // 'B'
-          const Btype = ba[p++]!
-          const limit = this._dataView.getInt32(p, true)
-          p += 4
-          tags[tag] = decodeBArrayTag(ba, this._dataView, p, Btype, limit)
-          p += bArrayByteLength(Btype, limit)
-          break
-        }
-        default:
-          console.error('Unknown BAM tag type', type)
-          break
+      const valueStart = p + 3
+      const end = tagValueEnd(ba, this._dataView, type, valueStart, blockEnd)
+      if (end === 0) {
+        break // unknown type: can't compute how far to advance
       }
+      tags[tag] = decodeTagValue(
+        ba,
+        this._dataView,
+        type,
+        valueStart,
+        end,
+        false,
+      )
+      p = end
     }
     return tags
   }

package/src/util.ts

@@ -99,6 +99,7 @@ export function optimizeChunks(chunks: Chunk[], lowest?: Offset) {
           lastChunk.minv,
           chunk.maxv,
           lastChunk.bin,
+          chunk.endPosition,
         )
         lastMaxBlock = chunkMaxBlock
       }
@@ -118,6 +119,39 @@ export function parsePseudoBin(bytes: Uint8Array, offset: number) {
   }
 }
 
+// Tighten each chunk's endPosition (default: a full max-size BGZF block past
+// maxv) down to the next known block boundary. Every chunk min/maxv blockPosition
+// and every extraBoundary (e.g. linear-index entries) is a real BGZF block start;
+// since blocks don't overlap, the first boundary strictly greater than a chunk's
+// maxv.blockPosition is an upper bound on where that final block ends — always at
+// least the true block end, so the clamped fetch still contains the whole block.
+// Shrinks both the byte estimate and the actual fetch with no extra I/O.
+export function clampChunkEnds(chunks: Chunk[], extraBoundaries: number[] = []) {
+  const boundaries = [...extraBoundaries]
+  for (const c of chunks) {
+    boundaries.push(c.minv.blockPosition, c.maxv.blockPosition)
+  }
+  boundaries.sort((a, b) => a - b)
+
+  for (const c of chunks) {
+    const max = c.maxv.blockPosition
+    // first boundary strictly greater than max
+    let lo = 0
+    let hi = boundaries.length
+    while (lo < hi) {
+      const mid = (lo + hi) >>> 1
+      if (boundaries[mid]! > max) {
+        hi = mid
+      } else {
+        lo = mid + 1
+      }
+    }
+    if (lo < boundaries.length) {
+      c.endPosition = Math.min(c.endPosition, boundaries[lo]!)
+    }
+  }
+}
+
 // Parse the BAM reference-sequence table (SAMv1.pdf §4.2). Returns undefined
 // if `uncba` doesn't yet contain the full table — caller fetches more bytes
 // and retries.

package/src/virtualOffset.ts

@@ -23,11 +23,7 @@ export class VirtualOffset {
     )
   }
 }
-export function fromBytes(bytes: Uint8Array, offset = 0, bigendian = false) {
-  if (bigendian) {
-    throw new Error('big-endian virtual file offsets not implemented')
-  }
-
+export function fromBytes(bytes: Uint8Array, offset = 0) {
   return new VirtualOffset(
     bytes[offset + 7]! * 0x10000000000 +
       bytes[offset + 6]! * 0x100000000 +