@fishka/seqio 0.4.0 → 0.6.0

package/dist/abif/index.mjs.map

@@ -1 +1 @@
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* Tiny binary helpers used across the ABIF reader/writer.\n *\n * Everything here operates on Uint8Array + DataView so the same code runs in\n * Node (where Buffer extends Uint8Array) and the browser.\n */\n\nexport function asciiString(bytes: Uint8Array): string {\n  let s = '';\n  for (let i = 0; i < bytes.length; i++) s += String.fromCharCode(bytes[i]);\n  return s;\n}\n\nexport function asciiBytes(s: string): Uint8Array {\n  const out = new Uint8Array(s.length);\n  for (let i = 0; i < s.length; i++) out[i] = s.charCodeAt(i) & 0xff;\n  return out;\n}\n\n/** Returns a DataView over the given bytes, regardless of input shape. */\nexport function asDataView(bytes: Uint8Array): DataView {\n  return new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);\n}\n\n/** Returns a Uint8Array view over a slice; never copies. */\nexport function subview(bytes: Uint8Array, start: number, length: number): Uint8Array {\n  return bytes.subarray(start, start + length);\n}\n\n/** Tag name encoded as a big-endian uint32 (e.g. \"DATA\" → 0x44415441). */\nexport function tagNameToInt32(tag: string): number {\n  return (\n    ((tag.charCodeAt(0) & 0xff) << 24) |\n    ((tag.charCodeAt(1) & 0xff) << 16) |\n    ((tag.charCodeAt(2) & 0xff) << 8) |\n    (tag.charCodeAt(3) & 0xff)\n  );\n}\n\nexport function tagNameFromInt32(n: number): string {\n  return String.fromCharCode((n >>> 24) & 0xff, (n >>> 16) & 0xff, (n >>> 8) & 0xff, n & 0xff);\n}\n","/**\n * Low-level ABIF reader/writer.\n *\n * Round-trip without loss: every directory entry (including unknown vendor\n * tags) is preserved as a raw payload (Uint8Array). The high-level layer\n * (view.ts, parser.ts) provides typed access on top of this.\n *\n * ABIF file layout:\n *   [0..3]      \"ABIF\" magic\n *   [4..5]      version (int16 BE; 101 = v1.01)\n *   [6..33]     TdirEntry describing the directory itself\n *   [34..127]   reserved (94 bytes, zero-filled)\n *   [...]       directory block (N * 28-byte entries) and payload blocks\n *\n * TdirEntry (28 bytes, big-endian):\n *   off  size  field\n *     0   4    tagName        (ASCII)\n *     4   4    tagNumber      (int32)\n *     8   2    elementType    (int16)\n *    10   2    elementSize    (int16)\n *    12   4    elementCount   (int32)\n *    16   4    dataSize       (int32; total payload bytes — authoritative; for\n *                              well-formed entries equals count*size, but user/\n *                              opaque types may differ, so we read by dataSize)\n *    20   4    dataOffset     (int32) OR inline data if dataSize <= 4\n *    24   4    dataHandle     (int32; usually 0)\n *\n * Inline rule (per ABIF spec): when the declared dataSize <= 4 the payload bytes\n * are stored directly in the dataOffset field (left-aligned, padded to 4 bytes).\n *\n * MacBinary preamble: some ABIF files (older Mac-origin) start with a 128-byte\n * MacBinary header before the actual ABIF magic. We detect and skip it.\n */\n\nimport { asciiBytes, asciiString, asDataView, subview, tagNameFromInt32 } from './bytes';\nimport { AbifByteRange, AbifDirectory, AbifEntry, AbifFile } from './types';\n\nexport const HEADER_SIZE = 128;\nexport const ENTRY_SIZE = 28;\n\n/**\n * Parse an ABIF file from raw bytes into its verbatim directory structure.\n *\n * This is the RAW source of truth: it reads the tdir header and every entry as\n * stored — real dataSize, dataOffset, numElements (see `entry.raw`), the 4 inline\n * bytes, and the tdir/directory metadata — and interprets nothing. For a\n * high-level, opinionated view (typed channels, basecalls, metadata) layer\n * {@link parseAbif} on top.\n *\n * Accepts Uint8Array (works in Node and the browser). Node's Buffer extends\n * Uint8Array, so `readAbif(buffer)` and `readAbif(new Uint8Array(arrayBuffer))`\n * both work.\n *\n * Throws if the magic header is missing. Does NOT require any specific tags\n * (PBAS, DATA, ...) to be present — raw pre-basecalled files are supported.\n */\nexport function readAbif(bytes: Uint8Array): AbifFile {\n  if (bytes.byteLength < HEADER_SIZE) {\n    throw new Error(`ABIF too small: ${bytes.byteLength} bytes`);\n  }\n\n  // MacBinary wrap support: skip 128 bytes if magic is at offset 128.\n  let macBinaryOffset = 0;\n  if (asciiString(subview(bytes, 0, 4)) !== 'ABIF') {\n    if (bytes.byteLength >= 128 + 4 && asciiString(subview(bytes, 128, 4)) === 'ABIF') {\n      macBinaryOffset = 128;\n    } else {\n      throw new Error('Not an ABIF file: missing \"ABIF\" magic.');\n    }\n  }\n  const base = macBinaryOffset;\n  // After skipping any MacBinary wrap, the ABIF part itself must still hold a full 128-byte header;\n  // otherwise reading version/tdir below would run past the DataView (a raw RangeError, not ours).\n  if (bytes.byteLength - base < HEADER_SIZE) {\n    throw new Error(`ABIF too small: ${bytes.byteLength - base} bytes after offset ${base}`);\n  }\n  const view = asDataView(bytes);\n\n  const version = view.getInt16(base + 4, false);\n\n  // Header bytes [base+6 .. base+34) are a TdirEntry describing the directory itself.\n  const dirEntry = decodeEntry(bytes, view, base + 6, base);\n  if (dirEntry.tagName !== 'tdir') {\n    throw new Error(`Expected \"tdir\" header entry, got \"${dirEntry.tagName}\"`);\n  }\n  if (dirEntry.elementSize !== ENTRY_SIZE) {\n    throw new Error(`Expected dir element size ${ENTRY_SIZE}, got ${dirEntry.elementSize}`);\n  }\n\n  // The directory's numElements (raw) is the authoritative entry count — like BioPython, we trust\n  // it rather than clamp against tdir.dataSize, which is a redundant byte-count that some writers\n  // desync. Physical bounds are enforced below; a negative/garbage count just yields 0 entries.\n  const rawDirCount = dirEntry.raw?.elementCount ?? dirEntry.elementCount;\n  const numEntries = Math.max(0, rawDirCount);\n  // tdir.dataSize is always > 4 (28*N), so the dataOffset field is an external offset.\n  const dirOffset = view.getInt32(base + 6 + 20, false);\n  if (dirOffset < 0 || dirOffset + numEntries * ENTRY_SIZE > bytes.byteLength - base) {\n    throw new Error(\n      `Directory out of bounds: offset=${dirOffset}, entries=${numEntries}, file=${bytes.byteLength - base}`,\n    );\n  }\n\n  const entries: AbifEntry[] = [];\n  for (let i = 0; i < numEntries; i++) {\n    entries.push(decodeEntry(bytes, view, base + dirOffset + i * ENTRY_SIZE, base));\n  }\n\n  // Root directory (tdir) header, as read — its dataSize may exceed numEntries*28 (directory padding).\n  const dirDataSize = dirEntry.raw?.dataSize ?? numEntries * ENTRY_SIZE;\n  const entriesEnd = base + dirOffset + numEntries * ENTRY_SIZE;\n  const padLen = Math.min(\n    Math.max(0, dirDataSize - numEntries * ENTRY_SIZE),\n    Math.max(0, bytes.byteLength - entriesEnd),\n  );\n  const tdir: AbifDirectory = {\n    entryCount: numEntries, // effective count actually read (== entries.length)\n    rawEntryCount: rawDirCount, // tdir numElements verbatim, before any reconciliation\n    elementType: dirEntry.elementType, // 1023 (tdir)\n    tagNumber: dirEntry.tagNumber, // usually 1\n    entrySize: dirEntry.elementSize,\n    dataSize: dirDataSize,\n    dataOffset: dirOffset,\n    dataOffsetBytes: dirEntry.raw?.dataOffsetBytes ?? new Uint8Array(4),\n    dataHandle: dirEntry.dataHandle,\n    paddingBytes: new Uint8Array(subview(bytes, entriesEnd, padLen)),\n  };\n\n  // Reserved header bytes [base+34 .. base+128) — verbatim, so a raw reader keeps the whole header.\n  const headerReserved = new Uint8Array(subview(bytes, base + 6 + ENTRY_SIZE, HEADER_SIZE - 6 - ENTRY_SIZE));\n\n  // The MacBinary preamble bytes themselves, when present — verbatim, so the wrapper is reproducible.\n  const macBinaryHeader = macBinaryOffset === 128 ? new Uint8Array(subview(bytes, 0, 128)) : undefined;\n\n  const unreferencedRanges = computeUnreferencedRanges(bytes, base, dirOffset, dirDataSize, entries, macBinaryOffset);\n\n  return { version, tdir, entries, macBinaryOffset, macBinaryHeader, headerReserved, unreferencedRanges };\n}\n\n/**\n * Find the file's physical byte ranges that no header/directory/entry payload covers — orphaned\n * blocks, trailing padding, etc. Computes the complement of every referenced interval so a raw\n * reader can account for all bytes without the writer having to be byte-exact.\n */\nfunction computeUnreferencedRanges(\n  bytes: Uint8Array,\n  base: number,\n  dirOffset: number,\n  dirDataSize: number,\n  entries: AbifEntry[],\n  macBinaryOffset: number,\n): AbifByteRange[] {\n  const total = bytes.byteLength;\n  const covered: Array<[number, number]> = [];\n  if (macBinaryOffset === 128) covered.push([0, 128]); // preamble\n  covered.push([base, base + HEADER_SIZE]); // 128-byte header (magic/version/tdir/reserved)\n  // Directory spans the bytes actually read (numElements entries) OR the declared dataSize when it is\n  // larger (padding) — whichever is bigger, so a desynced dataSize < numElements*28 doesn't mislabel\n  // already-read entries as orphan bytes. A negative dataSize collapses to the physical entry span.\n  const dirCovered = Math.max(entries.length * ENTRY_SIZE, Math.max(0, dirDataSize));\n  covered.push([base + dirOffset, base + dirOffset + dirCovered]);\n  for (const e of entries) {\n    if (e.raw && !e.raw.inline) {\n      const start = base + e.raw.dataOffset;\n      covered.push([start, start + e.payload.byteLength]); // external payload\n    }\n  }\n\n  const norm = covered\n    .map(([s, en]): [number, number] => [Math.max(0, Math.min(s, total)), Math.max(0, Math.min(en, total))])\n    .filter(([s, en]) => en > s)\n    .sort((a, b) => a[0] - b[0]);\n\n  const merged: Array<[number, number]> = [];\n  for (const [s, en] of norm) {\n    const last = merged[merged.length - 1];\n    if (last && s <= last[1]) last[1] = Math.max(last[1], en);\n    else merged.push([s, en]);\n  }\n\n  const gaps: AbifByteRange[] = [];\n  let cursor = 0;\n  for (const [s, en] of merged) {\n    if (s > cursor) gaps.push({ offset: cursor, bytes: new Uint8Array(subview(bytes, cursor, s - cursor)) });\n    cursor = Math.max(cursor, en);\n  }\n  if (cursor < total) gaps.push({ offset: cursor, bytes: new Uint8Array(subview(bytes, cursor, total - cursor)) });\n  return gaps;\n}\n\n/**\n * Decode a 28-byte TdirEntry at the given absolute byte offset.\n *\n * Two robustness measures applied here that BioPython also uses and that real\n * ABIF files in the wild require:\n *\n *   1. The payload is exactly `dataSize` bytes — the authoritative directory field.\n *      ABIF allows `numElements * elementSize != dataSize` for user/opaque types,\n *      so we never derive the payload length from count*size (that both truncates\n *      a larger declared payload and over-reads a smaller one).\n *\n *   2. Inline vs external follows the spec: inline iff `dataSize <= 4` (the payload\n *      fits in the 4-byte dataOffset field). Data > 4 bytes is always external,\n *      even when count*size <= 4. We fall back to count*size only when the declared\n *      field is negative/garbage.\n *\n *   3. `elementCount` is reconciled down to what the payload can hold, so a desynced\n *      (over-large) count can't drive readers past the real bytes.\n *\n *   4. External payload offsets are relative to the ABIF start, so we add `base`\n *      (the MacBinary preamble length) when reading them.\n */\nfunction decodeEntry(bytes: Uint8Array, view: DataView, off: number, base: number): AbifEntry {\n  const tagName = asciiString(subview(bytes, off, 4));\n  const tagNumber = view.getInt32(off + 4, false);\n  const elementType = view.getInt16(off + 8, false);\n  const elementSize = view.getInt16(off + 10, false);\n  const rawElementCount = view.getInt32(off + 12, false);\n  const declaredDataSize = view.getInt32(off + 16, false);\n  const dataHandle = view.getInt32(off + 24, false);\n\n  const computedDataSize = Math.max(0, rawElementCount * Math.max(0, elementSize));\n  // Payload length is the declared dataSize; a negative/garbage declared field falls back to the\n  // computed count*size (consistent with the inline decision below).\n  const payloadSize = declaredDataSize >= 0 ? declaredDataSize : computedDataSize;\n  // Inline iff dataSize <= 4; fall back to computed size only for an invalid declared field.\n  const inline = declaredDataSize >= 0 ? declaredDataSize <= 4 : computedDataSize <= 4;\n  // Reconcile the element count down to what the payload holds, and never expose a negative count\n  // (a malformed numElements would otherwise crash Array/TypedArray helpers downstream). When\n  // elementSize <= 0 the per-element stride is unknown, so cap by payloadSize (≤ 1 byte/element)\n  // rather than trusting the raw count — otherwise a typed getter reads past a 0-byte payload.\n  const elementCount = Math.max(\n    0,\n    elementSize > 0 ? Math.min(rawElementCount, Math.floor(payloadSize / elementSize)) : Math.min(rawElementCount, payloadSize),\n  );\n\n  let payload: Uint8Array;\n  let dataOffset: number;\n  if (inline) {\n    dataOffset = -1;\n    payload = new Uint8Array(subview(bytes, off + 20, Math.min(4, payloadSize)));\n  } else {\n    dataOffset = view.getInt32(off + 20, false);\n    const at = base + dataOffset;\n    if (dataOffset < 0 || at + payloadSize > bytes.byteLength) {\n      throw new Error(\n        `Entry ${tagName}${tagNumber}: payload out of bounds (offset=${dataOffset}, size=${payloadSize})`,\n      );\n    }\n    payload = new Uint8Array(subview(bytes, at, payloadSize));\n  }\n\n  // The raw 4 bytes of the data/offset slot, verbatim (payload+padding when inline, offset when external).\n  const dataOffsetBytes = new Uint8Array(subview(bytes, off + 20, 4));\n\n  return {\n    tagName,\n    tagNumber,\n    elementType,\n    elementSize,\n    elementCount,\n    payload,\n    dataHandle,\n    raw: { elementCount: rawElementCount, dataSize: declaredDataSize, dataOffset, inline, dataOffsetBytes },\n  };\n}\n\n/**\n * Serialize an AbifFile back to a Uint8Array.\n *\n * Layout produced: header (128 B) + directory (N*28 B) + payload block.\n * External payloads are packed tightly in entry order. Payloads <= 4 bytes are\n * stored inline inside their directory entry.\n *\n * Meaning-lossless, not byte-exact: the payload bytes, tag fields and dataSize\n * (= payload length) round-trip, but physical layout does not — payloads are\n * repacked, directory/header padding and any MacBinary preamble are dropped. A\n * byte-exact layout-preserving mode is a possible future opt-in.\n */\nexport function writeAbif(file: AbifFile): Uint8Array {\n  const numEntries = file.entries.length;\n  const dirOffset = HEADER_SIZE;\n  const dirSize = numEntries * ENTRY_SIZE;\n\n  // Compute external payload offsets. The payload bytes are authoritative: dataSize\n  // written = payload.byteLength (may differ from count*size for user/opaque types).\n  let payloadCursor = dirOffset + dirSize;\n  const externalOffsets: number[] = new Array(numEntries);\n  for (let i = 0; i < numEntries; i++) {\n    const dataSize = file.entries[i].payload.byteLength;\n    if (dataSize > 4) {\n      externalOffsets[i] = payloadCursor;\n      payloadCursor += dataSize;\n    } else {\n      externalOffsets[i] = -1; // inline\n    }\n  }\n\n  const totalSize = payloadCursor;\n  const out = new Uint8Array(totalSize);\n  const outView = asDataView(out);\n\n  // Header: \"ABIF\" + version (int16 BE) + tdir entry + zeros.\n  out.set(asciiBytes('ABIF'), 0);\n  outView.setInt16(4, file.version, false);\n  // The tdir entry's dataOffset is the directory offset (explicit, not from\n  // the AbifEntry payload — the tdir is structural).\n  writeEntry(\n    {\n      tagName: 'tdir',\n      tagNumber: 1,\n      elementType: 1023,\n      elementSize: ENTRY_SIZE,\n      elementCount: numEntries,\n      payload: new Uint8Array(0),\n      dataHandle: 0,\n    },\n    out,\n    outView,\n    6,\n    /* externalOffset */ -1,\n    /* externalDataSize */ dirSize,\n    /* explicitDirOffset */ dirOffset,\n  );\n\n  // Directory entries.\n  for (let i = 0; i < numEntries; i++) {\n    const e = file.entries[i];\n    writeEntry(e, out, outView, dirOffset + i * ENTRY_SIZE, externalOffsets[i]);\n  }\n\n  // Payload block.\n  for (let i = 0; i < numEntries; i++) {\n    const off = externalOffsets[i];\n    if (off >= 0) {\n      out.set(file.entries[i].payload, off);\n    }\n  }\n\n  return out;\n}\n\nfunction writeEntry(\n  e: AbifEntry,\n  out: Uint8Array,\n  outView: DataView,\n  off: number,\n  externalOffset: number,\n  externalDataSize?: number,\n  explicitDirOffset?: number,\n): void {\n  if (e.tagName.length !== 4) {\n    throw new Error(`tagName must be 4 chars: \"${e.tagName}\"`);\n  }\n  out.set(asciiBytes(e.tagName), off);\n  outView.setInt32(off + 4, e.tagNumber, false);\n  outView.setInt16(off + 8, e.elementType, false);\n  outView.setInt16(off + 10, e.elementSize, false);\n  outView.setInt32(off + 12, e.elementCount, false);\n  const dataSize = externalDataSize ?? e.payload.byteLength;\n  outView.setInt32(off + 16, dataSize, false);\n\n  if (explicitDirOffset !== undefined) {\n    outView.setInt32(off + 20, explicitDirOffset, false);\n  } else if (dataSize <= 4) {\n    // Inline: clear 4 bytes then place payload at off+20.\n    out.fill(0, off + 20, off + 24);\n    out.set(e.payload.subarray(0, dataSize), off + 20);\n  } else {\n    if (externalOffset < 0) {\n      throw new Error(`External payload requires offset for ${e.tagName}${e.tagNumber}`);\n    }\n    outView.setInt32(off + 20, externalOffset, false);\n  }\n  outView.setInt32(off + 24, e.dataHandle, false);\n}\n\n// =====================================================================\n// Lookup / mutation helpers\n// =====================================================================\n\n/** Find an entry by name+number, or undefined. */\nexport function findEntry(file: AbifFile, name: string, number: number): AbifEntry | undefined {\n  return file.entries.find(e => e.tagName === name && e.tagNumber === number);\n}\n\n/** Find all entries with the given tag name. */\nexport function findEntries(file: AbifFile, name: string): AbifEntry[] {\n  return file.entries.filter(e => e.tagName === name);\n}\n\n/**\n * Replace the payload of an existing entry, or append a new one.\n * elementType/elementSize/elementCount must be supplied for new entries.\n */\nexport function upsertEntry(\n  file: AbifFile,\n  name: string,\n  number: number,\n  payload: Uint8Array,\n  defaults: { elementType: number; elementSize: number; elementCount: number },\n): void {\n  if (payload.byteLength !== defaults.elementCount * defaults.elementSize) {\n    throw new Error(\n      `upsertEntry ${name}${number}: payload length ${payload.byteLength} != count*size`,\n    );\n  }\n  const existing = findEntry(file, name, number);\n  if (existing) {\n    existing.elementType = defaults.elementType;\n    existing.elementSize = defaults.elementSize;\n    existing.elementCount = defaults.elementCount;\n    existing.payload = payload;\n  } else {\n    file.entries.push({\n      tagName: name,\n      tagNumber: number,\n      elementType: defaults.elementType,\n      elementSize: defaults.elementSize,\n      elementCount: defaults.elementCount,\n      payload,\n      dataHandle: 0,\n    });\n  }\n}\n\n/** Re-export for users who want to interpret raw tag bytes themselves. */\nexport { tagNameFromInt32 };\n","/**\n * High-level typed view over an AbifFile.\n *\n * Reading helpers that interpret the raw payloads of well-known tags. For\n * mutation helpers (setSequence, setConfidences, ...) see ./setters.\n */\n\nimport { asciiString, asDataView } from './bytes';\nimport { findEntry } from './raw';\nimport { AbifDataChannelRole, AbifEntry, AbifFile } from './types';\n\n/** Get DATA<n> as a signed-int16 array, or undefined. */\nexport function getDataChannel(file: AbifFile, n: number): Int16Array | undefined {\n  const e = findEntry(file, 'DATA', n);\n  if (!e) return undefined;\n  if (e.elementSize !== 2) {\n    throw new Error(`DATA${n}: expected elementSize=2, got ${e.elementSize}`);\n  }\n  const arr = new Int16Array(e.elementCount);\n  const view = asDataView(e.payload);\n  for (let i = 0; i < e.elementCount; i++) {\n    arr[i] = view.getInt16(i * 2, false);\n  }\n  return arr;\n}\n\n/**\n * Dye order, 4 ASCII chars (e.g. \"GATC\"). Defaults to \"GATC\" if FWO_ absent.\n *\n * GATC is the dye order produced by modern ABI 3730/3500 instruments and the\n * dominant default in the wild. Older \"ACGT\" defaults caused channel\n * mis-mapping on files where FWO_ is missing or malformed.\n */\nexport function getFwo(file: AbifFile): string {\n  const e = findEntry(file, 'FWO_', 1);\n  if (!e) return 'GATC';\n  // Read only the declared elements — payload may carry trailing padding beyond elementCount.\n  return asciiString(e.payload.subarray(0, e.elementCount));\n}\n\n/**\n * Whether an FWO_ string is a genuine dye order: a permutation of A/C/G/T with all\n * four bases distinct. `\"GATC\"` passes; `\"AAAA\"` (regex-valid but degenerate) does\n * not — mapping four channels through it would collapse them onto one base.\n */\nexport function isFwoPermutation(fwo: string): boolean {\n  return /^[ACGT]{4}$/.test(fwo) && new Set(fwo).size === 4;\n}\n\n/**\n * Fact: the file carries a second dye-trace block, DATA9..12 (all four tags), in\n * addition to DATA1..4. Reports presence only — it does NOT say which block is\n * raw and which is analyzed/processed; that convention isn't stored in the file.\n */\nexport function hasData9To12Block(file: AbifFile): boolean {\n  return !!(\n    findEntry(file, 'DATA', 9) &&\n    findEntry(file, 'DATA', 10) &&\n    findEntry(file, 'DATA', 11) &&\n    findEntry(file, 'DATA', 12)\n  );\n}\n\n/**\n * Spec-defined role of a DATA<n> tag, limited to the numbers the ABIF spec names:\n *\n *   - `'trace'`     — dye-signal channels: DATA1..4 (raw dyes 1-4), DATA9..12\n *                     (analyzed dyes 1-4), and the two optional 5th-dye blocks\n *                     DATA105 (raw dye 5) and DATA205 (analyzed dye 5).\n *   - `'telemetry'` — DATA5..8: instrument run telemetry (voltage, current,\n *                     power, temperature), one value per scan — NOT dye signal.\n *   - `'other'`     — any other DATA number. The spec does not enumerate higher\n *                     extra-dye tags (106/206/…), so we don't claim a role for them.\n *\n * A fact from the ABIF specification, not an inference about content.\n */\nexport function dataChannelRole(n: number): AbifDataChannelRole {\n  if (n >= 5 && n <= 8) return 'telemetry';\n  if ((n >= 1 && n <= 4) || (n >= 9 && n <= 12) || n === 105 || n === 205) return 'trace';\n  return 'other';\n}\n\n/**\n * Whether the file declares its sequence already reverse-complemented, from the\n * RevC1 flag (int16, non-zero = true). undefined when RevC1 is absent. Reported\n * as-is; the consumer decides how to act on it.\n */\nexport function getReverseComplemented(file: AbifFile): boolean | undefined {\n  const e = findEntry(file, 'RevC', 1);\n  if (!e) return undefined;\n  const view = asDataView(e.payload);\n  return e.payload.byteLength >= 2 ? view.getInt16(0, false) !== 0 : e.payload.some(b => b !== 0);\n}\n\n/**\n * Map from base letter (\"A\"|\"C\"|\"G\"|\"T\") to the DATA1..4 tag number that holds\n * its channel, using the dye order declared by FWO_. If FWO_=\"GATC\" then\n * G→1, A→2, T→3, C→4.\n *\n * This follows the file's own FWO_ declaration for the DATA1..4 block; it makes\n * no claim about whether that block is raw or processed.\n */\nexport function getChannelMap(file: AbifFile): Record<'A' | 'C' | 'G' | 'T', number> {\n  const fwo = getFwo(file);\n  if (!isFwoPermutation(fwo)) {\n    throw new Error(`FWO_ is not a permutation of A/C/G/T: \"${fwo}\"`);\n  }\n  return {\n    [fwo[0]]: 1,\n    [fwo[1]]: 2,\n    [fwo[2]]: 3,\n    [fwo[3]]: 4,\n  } as Record<'A' | 'C' | 'G' | 'T', number>;\n}\n\n/** Get PBAS sequence (prefer PBAS2 over PBAS1). undefined if neither present. */\nexport function getSequence(file: AbifFile): string | undefined {\n  // Bound by elementCount (payload may be padded) and drop trailing NULs, matching parseAbif.\n  const read = (e: AbifEntry): string => asciiString(e.payload.subarray(0, e.elementCount)).replace(/\\0+$/g, '');\n  const e2 = findEntry(file, 'PBAS', 2);\n  if (e2) return read(e2);\n  const e1 = findEntry(file, 'PBAS', 1);\n  if (e1) return read(e1);\n  return undefined;\n}\n\n/**\n * Get per-base Phred-like quality scores (0..255 byte values, typically 0..60\n * for Sanger). Prefers PCON2 over PCON1.\n *\n * PCON is declared in the ABIF spec as elementType=2 (char) but the byte\n * values ARE the Q-scores — we read raw bytes regardless of declared type.\n */\nexport function getConfidences(file: AbifFile): number[] | undefined {\n  const e = findEntry(file, 'PCON', 2) ?? findEntry(file, 'PCON', 1);\n  if (!e) return undefined;\n  const out: number[] = new Array(e.elementCount);\n  for (let i = 0; i < e.elementCount; i++) out[i] = e.payload[i];\n  return out;\n}\n\n/**\n * Get peak scan positions (one per base). Prefers PLOC2 over PLOC1.\n *\n * Read as UNSIGNED int16: PLOC indexes into the sample trace and is always\n * non-negative, but values > 32767 (long traces) would wrap to negative\n * if interpreted as signed.\n */\nexport function getPositions(file: AbifFile): number[] | undefined {\n  const e = findEntry(file, 'PLOC', 2) ?? findEntry(file, 'PLOC', 1);\n  if (!e) return undefined;\n  if (e.elementSize !== 2) {\n    throw new Error(`PLOC: expected elementSize=2, got ${e.elementSize}`);\n  }\n  const view = asDataView(e.payload);\n  const out: number[] = new Array(e.elementCount);\n  for (let i = 0; i < e.elementCount; i++) out[i] = view.getUint16(i * 2, false);\n  return out;\n}\n\n/**\n * Get average peak spacing (samples per base), from SPAC/1.\n *\n * ABIF spec defines SPAC as float32 (elementType=7); some legacy files\n * mislabel it as long (type=5). Both are 4 bytes and on disk the payload\n * is always a 32-bit float, so we read as float regardless of declared type.\n *\n * Returns undefined if SPAC is absent or non-positive.\n */\nexport function getSamplingRate(file: AbifFile): number | undefined {\n  const e = findEntry(file, 'SPAC', 1);\n  if (!e || e.elementSize !== 4 || e.payload.byteLength < 4) return undefined;\n  const v = asDataView(e.payload).getFloat32(0, false);\n  return Number.isFinite(v) && v > 0 ? v : undefined;\n}\n","/**\n * Mutation helpers for AbifFile: write PBAS/PCON/PLOC/SPAC and ensure DATA9..12\n * are present. Used by basecallers to author ABIF output.\n */\n\nimport { asciiBytes, asDataView } from './bytes';\nimport { findEntry, upsertEntry } from './raw';\nimport { hasData9To12Block } from './view';\nimport { AbifFile } from './types';\n\n/** Set PBAS2 (replaces if present). */\nexport function setSequence(file: AbifFile, sequence: string): void {\n  upsertEntry(file, 'PBAS', 2, asciiBytes(sequence), {\n    elementType: 2, // char\n    elementSize: 1,\n    elementCount: sequence.length,\n  });\n}\n\n/** Set PCON2 (replaces if present). Values clamped to [0, 255]. */\nexport function setConfidences(file: AbifFile, q: ArrayLike<number>): void {\n  const buf = new Uint8Array(q.length);\n  for (let i = 0; i < q.length; i++) {\n    buf[i] = Math.max(0, Math.min(255, Math.round(q[i])));\n  }\n  upsertEntry(file, 'PCON', 2, buf, {\n    elementType: 2,\n    elementSize: 1,\n    elementCount: q.length,\n  });\n}\n\n/**\n * Set PLOC2 (replaces if present).\n *\n * Written as UNSIGNED int16 so positions up to 65535 are preserved on disk\n * (signed int16 would wrap on traces with > 32k scans).\n */\nexport function setPositions(file: AbifFile, positions: ArrayLike<number>): void {\n  const buf = new Uint8Array(positions.length * 2);\n  const view = asDataView(buf);\n  for (let i = 0; i < positions.length; i++) {\n    view.setUint16(i * 2, Math.max(0, Math.min(0xffff, positions[i])), false);\n  }\n  upsertEntry(file, 'PLOC', 2, buf, {\n    elementType: 4,\n    elementSize: 2,\n    elementCount: positions.length,\n  });\n}\n\n/**\n * Set SPAC/1, SPAC/2, SPAC/3 — the standard ABIF \"average peak spacing\" trio\n * that KB-basecaller writes and downstream tools (BioPython, Sequencher,\n * KB-aware viewers) expect:\n *\n *   - SPAC/1 (float32) — average peak spacing used in last analysis.\n *   - SPAC/2 (pString) — basecaller name / identifier.\n *   - SPAC/3 (float32) — average peak spacing computed by the basecaller.\n *\n * Both float fields are written with the same value.\n */\nexport function setAveragePeakSpacing(file: AbifFile, spacing: number, basecallerName: string): void {\n  const f1 = new Uint8Array(4);\n  asDataView(f1).setFloat32(0, spacing, false);\n  upsertEntry(file, 'SPAC', 1, f1, { elementType: 7, elementSize: 4, elementCount: 1 });\n\n  const nameBytes = asciiBytes(basecallerName);\n  const len = Math.min(255, nameBytes.length);\n  const p = new Uint8Array(1 + len);\n  p[0] = len;\n  p.set(nameBytes.subarray(0, len), 1);\n  upsertEntry(file, 'SPAC', 2, p, { elementType: 18, elementSize: 1, elementCount: 1 + len });\n\n  const f3 = new Uint8Array(4);\n  asDataView(f3).setFloat32(0, spacing, false);\n  upsertEntry(file, 'SPAC', 3, f3, { elementType: 7, elementSize: 4, elementCount: 1 });\n}\n\n/**\n * Mean consecutive peak-to-peak distance in scans, from a positions array.\n * Returns 0 when fewer than 2 positions are present.\n */\nexport function averagePeakSpacing(positions: ArrayLike<number>): number {\n  if (positions.length < 2) return 0;\n  return (positions[positions.length - 1] - positions[0]) / (positions.length - 1);\n}\n\n/**\n * Ensure DATA9..12 are present in the file. Many downstream consumers\n * (BioPython-style readers, viewers) read the chromatogram signal from\n * DATA9..12 by convention — these tags are the raw fluorescence on newer\n * instruments. Older files that only carry DATA1..8 break those consumers\n * with a \"no signal\" error after re-basecalling.\n *\n * We populate DATA9..12 by copying DATA1..4 (which on DATA1..8-only files IS\n * the raw signal). The DATA1..4 tags are left untouched so any tool that\n * reads them keeps working.\n *\n * No-op when DATA9..12 already exist.\n */\nexport function ensureRawDataChannels(file: AbifFile): void {\n  if (hasData9To12Block(file)) return;\n  for (let i = 1; i <= 4; i++) {\n    const src = findEntry(file, 'DATA', i);\n    if (!src) continue;\n    const target = 8 + i;\n    if (findEntry(file, 'DATA', target)) continue;\n    file.entries.push({\n      tagName: 'DATA',\n      tagNumber: target,\n      elementType: src.elementType,\n      elementSize: src.elementSize,\n      elementCount: src.elementCount,\n      payload: new Uint8Array(src.payload),\n      dataHandle: 0,\n    });\n  }\n}\n","/**\n * High-level \"parse everything\" wrapper around the raw + view layers.\n *\n * Returns a single ParsedAbif object with metadata, the FWO_-aware\n * DATA1..4 / DATA9..12 channel split, basecalls, and decoded directory entries\n * for diagnostics. Mirrors what typical viewers (chromatogram UIs, sample\n * inspectors) need from a single file.\n *\n * For round-trip authoring (basecallers), prefer {@link readAbif} +\n * setters from ./setters which operate directly on the raw AbifFile.\n */\n\nimport { asciiString, asDataView, subview } from './bytes';\nimport { readAbif } from './raw';\nimport { getFwo, isFwoPermutation } from './view';\nimport {\n  AbifBaseCallVariant,\n  AbifBaseCalls,\n  AbifChromatogramBundle,\n  AbifDecodedValue,\n  AbifDirEntry,\n  AbifEntry,\n  AbifMetadata,\n  ChannelSignals,\n  ParsedAbif,\n} from './types';\n\nconst TYPE_NAMES: Record<number, string> = {\n  1: 'byte',\n  2: 'char',\n  3: 'word',\n  4: 'short',\n  5: 'long',\n  7: 'float',\n  8: 'double',\n  10: 'date',\n  11: 'time',\n  12: 'thumb',\n  13: 'bool',\n  18: 'pString',\n  19: 'cString',\n  1023: 'tdir',\n};\n\nfunction typeName(t: number): string {\n  return TYPE_NAMES[t] ?? (t >= 1024 ? `user${t}` : `type${t}`);\n}\n\nfunction previewNumbers(arr: number[], max = 10): string {\n  if (arr.length <= max) return `[${arr.join(', ')}]`;\n  return `[${arr.slice(0, max).join(', ')}, … +${arr.length - max}] (n=${arr.length})`;\n}\n\nfunction truncate(s: string, n = 80): string {\n  return s.length > n ? s.slice(0, n) + '…' : s;\n}\n\nfunction previewBytes(bytes: Uint8Array): string {\n  const slice = bytes.subarray(0, 16);\n  const hex = Array.from(slice, b => b.toString(16).padStart(2, '0')).join(' ');\n  return `${bytes.byteLength}B [${hex}${bytes.byteLength > 16 ? ' …' : ''}]`;\n}\n\n/** Coerce a decoded value to a number array, treating a single scalar as a one-element array. */\nfunction asNumbers(d: AbifDecodedValue): number[] | undefined {\n  if (d.kind === 'numbers') return d.value;\n  if (d.kind === 'number') return [d.value];\n  return undefined;\n}\n\n/**\n * Decode a run of fixed-width numbers, bounded by BOTH the element count and the\n * actual payload length — so a malformed entry whose declared elementSize/dataSize\n * disagrees with the type's real width can never drive a read past the buffer.\n */\nfunction decodeNumeric(\n  byteLength: number,\n  elementCount: number,\n  size: number,\n  read: (offset: number) => number,\n): AbifDecodedValue {\n  const n = Math.max(0, Math.min(elementCount, Math.floor(byteLength / size)));\n  const arr: number[] = [];\n  for (let i = 0; i < n; i++) arr.push(read(i * size));\n  return arr.length === 1 ? { kind: 'number', value: arr[0] } : { kind: 'numbers', value: arr };\n}\n\n/**\n * Decode a payload best-effort by ABIF element type.\n *\n * Strings have trailing NULs stripped (cString/pString convention).\n * pString (type 18) is decoded as `length-prefix + chars`.\n */\nfunction decodePayload(elementType: number, elementCount: number, payload: Uint8Array): AbifDecodedValue {\n  const view = asDataView(payload);\n  switch (elementType) {\n    case 1: {\n      const arr = Array.from(payload.subarray(0, elementCount));\n      return { kind: 'numbers', value: arr };\n    }\n    case 2:\n    case 19: {\n      const s = asciiString(payload.subarray(0, elementCount)).replace(/\\0+$/g, '');\n      return { kind: 'string', value: s };\n    }\n    case 3:\n      return decodeNumeric(payload.byteLength, elementCount, 2, o => view.getUint16(o, false));\n    case 4:\n      return decodeNumeric(payload.byteLength, elementCount, 2, o => view.getInt16(o, false));\n    case 5:\n      return decodeNumeric(payload.byteLength, elementCount, 4, o => view.getInt32(o, false));\n    case 7:\n      return decodeNumeric(payload.byteLength, elementCount, 4, o => view.getFloat32(o, false));\n    case 8:\n      return decodeNumeric(payload.byteLength, elementCount, 8, o => view.getFloat64(o, false));\n    case 10: {\n      // A date needs 4 bytes; a short/truncated payload falls back to raw bytes rather than throwing.\n      if (payload.byteLength < 4) return { kind: 'unknown', value: payload };\n      const year = view.getInt16(0, false);\n      const month = view.getUint8(2);\n      const day = view.getUint8(3);\n      return { kind: 'date', value: { year, month, day } };\n    }\n    case 11: {\n      // A time needs 4 bytes; short payload → raw bytes, not a RangeError.\n      if (payload.byteLength < 4) return { kind: 'unknown', value: payload };\n      return {\n        kind: 'time',\n        value: {\n          hour: view.getUint8(0),\n          minute: view.getUint8(1),\n          second: view.getUint8(2),\n          hsec: view.getUint8(3),\n        },\n      };\n    }\n    case 13: {\n      const arr: boolean[] = [];\n      for (let i = 0; i < Math.min(elementCount, payload.byteLength); i++) arr.push(view.getUint8(i) !== 0);\n      return { kind: 'bools', value: arr };\n    }\n    case 18: {\n      // pString = length prefix + chars; an empty payload is just the empty string.\n      if (payload.byteLength < 1) return { kind: 'string', value: '' };\n      const len = view.getUint8(0);\n      const s = asciiString(subview(payload, 1, Math.min(len, Math.max(0, elementCount - 1))));\n      return { kind: 'string', value: s };\n    }\n    default:\n      return { kind: 'unknown', value: payload };\n  }\n}\n\nfunction previewDecoded(d: AbifDecodedValue, elementType: number): string {\n  switch (d.kind) {\n    case 'number':\n      return String(d.value);\n    case 'numbers':\n      return previewNumbers(d.value);\n    case 'string':\n      return truncate(JSON.stringify(d.value));\n    case 'bools':\n      return d.value.length === 1 ? String(d.value[0]) : `[${d.value.join(', ')}]`;\n    case 'date': {\n      const { year, month, day } = d.value;\n      return `${year}-${String(month).padStart(2, '0')}-${String(day).padStart(2, '0')}`;\n    }\n    case 'time': {\n      const { hour, minute, second } = d.value;\n      return `${String(hour).padStart(2, '0')}:${String(minute).padStart(2, '0')}:${String(second).padStart(2, '0')}`;\n    }\n    case 'bytes':\n      return `${typeName(elementType)} ${previewBytes(d.value)}`;\n    case 'unknown':\n      return `${typeName(elementType)} ${previewBytes(d.value)}`;\n  }\n}\n\n/**\n * Parse an ABIF file into a high-level view: metadata, channels, basecalls,\n * and decoded directory entries.\n *\n * This is the INTERPRETING layer — it makes convenience choices (FWO_ → \"GATC\"\n * fallback, derived samplingRate, preferred/upper-cased PBAS2 baseCalls). It is\n * not the raw structural truth: for that use {@link readAbif}, which reads the\n * directory verbatim (raw dataSize/offset/counts, tdir, inline bytes) and makes\n * no interpretation. `parseAbif` builds on top of it.\n *\n * Accepts ArrayBuffer or Uint8Array (Buffer in Node works too — it extends\n * Uint8Array). The `fileName` argument is informational only; it's preserved\n * in the result.\n */\nexport function parseAbif(input: ArrayBuffer | Uint8Array, fileName = ''): ParsedAbif {\n  const bytes = input instanceof Uint8Array ? input : new Uint8Array(input);\n  const file = readAbif(bytes);\n\n  const entries: AbifDirEntry[] = file.entries.map(e => {\n    // PCON is declared char (type 2) but its bytes ARE Q-scores; decode it as numbers so the\n    // diagnostic view keeps zeros the char decoder would strip (matches baseCalls.confidences).\n    const decoded =\n      e.tagName === 'PCON' && e.elementSize === 1\n        ? decodePayload(1, e.elementCount, e.payload) // type 1 = byte → { kind: 'numbers' }\n        : decodePayload(e.elementType, e.elementCount, e.payload);\n    // Prefer the real on-disk directory fields (present when read from a file) over\n    // reconciled/computed values, so the diagnostic view reflects the actual record.\n    return {\n      tag: e.tagName,\n      tagNumber: e.tagNumber,\n      elementType: e.elementType,\n      elementTypeName: typeName(e.elementType),\n      elementSize: e.elementSize,\n      elementCount: e.elementCount,\n      rawElementCount: e.raw?.elementCount ?? e.elementCount,\n      dataSize: e.raw?.dataSize ?? e.elementCount * e.elementSize,\n      dataOffset: e.raw?.dataOffset ?? -1,\n      inline: e.raw?.inline ?? e.elementCount * e.elementSize <= 4,\n      decoded,\n      preview: previewDecoded(decoded, e.elementType),\n    };\n  });\n\n  // FWO_ → base order. Fall back to GATC unless FWO_ is a real permutation of A/C/G/T\n  // (a degenerate value like \"AAAA\" is regex-valid but would collapse channels).\n  let baseOrder = getFwo(file);\n  if (!isFwoPermutation(baseOrder)) baseOrder = 'GATC';\n\n  const dataChannels: Record<number, number[]> = {};\n  const data1To4: ChannelSignals = { A: [], C: [], G: [], T: [] };\n  const data9To12: ChannelSignals = { A: [], C: [], G: [], T: [] };\n  const metadata: AbifMetadata = { comments: [] };\n  const pbas: Record<number, string> = {};\n  const pcon: Record<number, number[]> = {};\n  const ploc: Record<number, number[]> = {};\n\n  const channelKey = (i: number): keyof ChannelSignals => baseOrder[i] as keyof ChannelSignals;\n\n  for (let idx = 0; idx < file.entries.length; idx++) {\n    const e = file.entries[idx];\n    const decoded = entries[idx].decoded;\n\n    if (e.tagName === 'DATA') {\n      // Accept single-element channels too (decodePayload collapses length-1 to a scalar).\n      const nums = asNumbers(decoded);\n      if (nums) {\n        dataChannels[e.tagNumber] = nums;\n        if (e.tagNumber >= 1 && e.tagNumber <= 4) data1To4[channelKey(e.tagNumber - 1)] = nums;\n        else if (e.tagNumber >= 9 && e.tagNumber <= 12) data9To12[channelKey(e.tagNumber - 9)] = nums;\n      }\n    } else if (e.tagName === 'PBAS' && decoded.kind === 'string') {\n      pbas[e.tagNumber] = decoded.value;\n    } else if (e.tagName === 'PCON') {\n      // PCON Q-scores are 1 byte each (elementType=2/char). Read them straight from the payload —\n      // a trailing zero is a valid score, but the char decoder strips trailing NULs and would drop it.\n      const nums = e.elementSize === 1 ? Array.from(e.payload.subarray(0, e.elementCount)) : asNumbers(decoded);\n      if (nums) pcon[e.tagNumber] = nums;\n    } else if (e.tagName === 'PLOC') {\n      // PLOC sample indices are always non-negative — reinterpret int16 as uint16.\n      const nums = asNumbers(decoded);\n      if (nums) ploc[e.tagNumber] = nums.map(v => (v < 0 ? v + 0x10000 : v));\n    } else if (e.tagName === 'SPAC') {\n      // ABIF spec defines SPAC as float (elementType=7). Some legacy files mislabel\n      // it as long (type=5); both are 4 bytes and the payload is always a float.\n      if (e.elementSize === 4 && e.payload.byteLength >= 4) {\n        const v = asDataView(e.payload).getFloat32(0, false);\n        if (Number.isFinite(v) && v > 0) metadata.samplingRate = v;\n      } else if (decoded.kind === 'number') {\n        metadata.samplingRate = decoded.value;\n      }\n    } else if (e.tagName === 'SMPL' && decoded.kind === 'string') {\n      metadata.sampleName = decoded.value;\n    } else if (e.tagName === 'LANE' && decoded.kind === 'number') {\n      metadata.laneNumber = decoded.value;\n    } else if (e.tagName === 'TUBE' && decoded.kind === 'string') {\n      metadata.tube = decoded.value;\n    } else if (e.tagName === 'MCHN' && decoded.kind === 'string') {\n      metadata.machineName = decoded.value;\n    } else if (e.tagName === 'MODL' && decoded.kind === 'string') {\n      metadata.machineModel = decoded.value;\n    } else if (e.tagName === 'RUND' && decoded.kind === 'date') {\n      const d = decoded.value;\n      metadata.runDate = `${d.year}-${String(d.month).padStart(2, '0')}-${String(d.day).padStart(2, '0')}`;\n    } else if (e.tagName === 'RUNT' && decoded.kind === 'time') {\n      const t = decoded.value;\n      metadata.runTime = `${String(t.hour).padStart(2, '0')}:${String(t.minute).padStart(2, '0')}:${String(t.second).padStart(2, '0')}`;\n    } else if (e.tagName === 'CMNT' && decoded.kind === 'string') {\n      metadata.comments.push(decoded.value);\n    } else if (e.tagName === 'RevC' && e.tagNumber === 1) {\n      // RevC1 (int16): file's own flag for whether the sequence is already\n      // reverse-complemented. Only tagNumber 1 is defined by the spec. Reported\n      // as-is; we draw no conclusion from it.\n      if (decoded.kind === 'number') metadata.reverseComplemented = decoded.value !== 0;\n      else if (decoded.kind === 'numbers') metadata.reverseComplemented = decoded.value.some(v => v !== 0);\n    }\n  }\n\n  // Every basecall version the file carries, exactly as stored — the source of\n  // truth. Per-version PCON/PLOC are kept strictly (no cross-version borrowing):\n  // a variant reports only what its own tag number holds.\n  const baseCallVariants: AbifBaseCallVariant[] = Object.keys(pbas)\n    .map(Number)\n    .sort((a, b) => a - b)\n    .map((v): AbifBaseCallVariant => ({\n      version: v,\n      role: v === 1 ? 'edited' : v === 2 ? 'called' : 'unknown',\n      // As stored: case is preserved (lower-case can encode masking/edits). The\n      // uppercased convenience view lives on `baseCalls`, not here.\n      sequence: pbas[v],\n      confidences: pcon[v] ?? [],\n      positions: ploc[v] ?? [],\n    }));\n\n  // Basecalls: prefer PBAS2 (called) over PBAS1 (edited) — a spec-role choice. Test key\n  // presence, not string truthiness, so an existing-but-empty PBAS2 is still honored.\n  let baseCalls: AbifBaseCalls | undefined;\n  const pbasVersion = 2 in pbas ? 2 : 1 in pbas ? 1 : Object.keys(pbas).map(Number)[0];\n  if (pbasVersion !== undefined && pbas[pbasVersion] !== undefined) {\n    // Don't .trim(): keep length aligned with PCON/PLOC (trailing nulls already stripped).\n    const seq = pbas[pbasVersion].toUpperCase();\n    // Fall back to whichever PCON has a length matching the chosen PBAS — some\n    // files ship PCON only under one tagNumber even when PBAS exists under both.\n    // Fall back to whichever version's PCON/PLOC matches the chosen PBAS length — triggered when the\n    // preferred version's array is missing OR present-but-length-mismatched. Expose none rather than a\n    // broken array when nothing matches, so baseCalls stays self-consistent (baseCallVariants stays strict).\n    let confidences = pcon[pbasVersion] ?? [];\n    if (confidences.length !== seq.length) {\n      confidences = Object.keys(pcon).map(Number).map(v => pcon[v]).find(c => c.length === seq.length) ?? [];\n    }\n    let positions = ploc[pbasVersion] ?? [];\n    if (positions.length !== seq.length) {\n      positions = Object.keys(ploc).map(Number).map(v => ploc[v]).find(pp => pp.length === seq.length) ?? [];\n    }\n    baseCalls = { sequence: seq, confidences, positions, pbasVersion };\n  }\n\n  // SPAC fallback: derive from PLOC positions or DATA9 length when missing.\n  if (!Number.isFinite(metadata.samplingRate) || (metadata.samplingRate ?? 0) <= 0) {\n    const pos = baseCalls?.positions;\n    const data9Len = Math.max(\n      data9To12.A.length,\n      data9To12.C.length,\n      data9To12.G.length,\n      data9To12.T.length,\n    );\n    if (pos && pos.length > 1) {\n      metadata.samplingRate = (pos[pos.length - 1] - pos[0]) / (pos.length - 1);\n    } else if (baseCalls && baseCalls.sequence.length > 0 && data9Len > 0) {\n      metadata.samplingRate = data9Len / baseCalls.sequence.length;\n    }\n  }\n\n  const chromatogram: AbifChromatogramBundle = { baseOrder, dataChannels, data1To4, data9To12 };\n\n  return {\n    fileName,\n    fileSize: bytes.byteLength,\n    abifVersion: file.version,\n    macBinaryOffset: file.macBinaryOffset,\n    dirEntryCount: file.entries.length,\n    metadata,\n    chromatogram,\n    baseCalls,\n    baseCallVariants,\n    entries,\n  };\n}\n\n/** True when any channel has at least one signal value. */\nexport function hasSignals(s: ChannelSignals): boolean {\n  return s.A.length > 0 || s.C.length > 0 || s.G.length > 0 || s.T.length > 0;\n}\n\n/** Length of the longest channel in a ChannelSignals bundle. */\nexport function channelMaxLength(s: ChannelSignals): number {\n  return Math.max(s.A.length, s.C.length, s.G.length, s.T.length);\n}\n\n// Quiet unused-import for the AbifEntry type if it isn't reachable elsewhere.\nexport type { AbifEntry };\n"]}
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* Tiny binary helpers used across the ABIF reader/writer.\n *\n * Everything here operates on Uint8Array + DataView so the same code runs in\n * Node (where Buffer extends Uint8Array) and the browser.\n */\n\nexport function asciiString(bytes: Uint8Array): string {\n  let s = '';\n  for (let i = 0; i < bytes.length; i++) s += String.fromCharCode(bytes[i]);\n  return s;\n}\n\nexport function asciiBytes(s: string): Uint8Array {\n  const out = new Uint8Array(s.length);\n  for (let i = 0; i < s.length; i++) out[i] = s.charCodeAt(i) & 0xff;\n  return out;\n}\n\n/** Returns a DataView over the given bytes, regardless of input shape. */\nexport function asDataView(bytes: Uint8Array): DataView {\n  return new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);\n}\n\n/** Returns a Uint8Array view over a slice; never copies. */\nexport function subview(bytes: Uint8Array, start: number, length: number): Uint8Array {\n  return bytes.subarray(start, start + length);\n}\n\n/** Tag name encoded as a big-endian uint32 (e.g. \"DATA\" → 0x44415441). */\nexport function tagNameToInt32(tag: string): number {\n  return (\n    ((tag.charCodeAt(0) & 0xff) << 24) |\n    ((tag.charCodeAt(1) & 0xff) << 16) |\n    ((tag.charCodeAt(2) & 0xff) << 8) |\n    (tag.charCodeAt(3) & 0xff)\n  );\n}\n\nexport function tagNameFromInt32(n: number): string {\n  return String.fromCharCode((n >>> 24) & 0xff, (n >>> 16) & 0xff, (n >>> 8) & 0xff, n & 0xff);\n}\n","/**\n * Raw layer: the ABIF byte<->struct codec. Every directory entry (including unknown\n * vendor tags) is preserved as a raw payload (Uint8Array), and writeAbif() reproduces\n * the original bytes exactly for an unmodified round-trip (see its own doc comment).\n * The domain layer (view.ts, setters.ts, parser.ts, abif-op-*.ts) provides typed,\n * format-aware access on top of this — this file knows nothing about what any tag\n * means.\n *\n * ABIF file layout:\n *   [0..3]      \"ABIF\" magic\n *   [4..5]      version (int16 BE; 101 = v1.01)\n *   [6..33]     TdirEntry describing the directory itself\n *   [34..127]   reserved (94 bytes, zero-filled)\n *   [...]       directory block (N * 28-byte entries) and payload blocks\n *\n * TdirEntry (28 bytes, big-endian):\n *   off  size  field\n *     0   4    tagName        (ASCII)\n *     4   4    tagNumber      (int32)\n *     8   2    elementType    (int16)\n *    10   2    elementSize    (int16)\n *    12   4    elementCount   (int32)\n *    16   4    dataSize       (int32; total payload bytes — authoritative; for\n *                              well-formed entries equals count*size, but user/\n *                              opaque types may differ, so we read by dataSize)\n *    20   4    dataOffset     (int32) OR inline data if dataSize <= 4\n *    24   4    dataHandle     (int32; usually 0)\n *\n * Inline rule (per ABIF spec): when the declared dataSize <= 4 the payload bytes\n * are stored directly in the dataOffset field (left-aligned, padded to 4 bytes).\n *\n * MacBinary preamble: some ABIF files (older Mac-origin) start with a 128-byte\n * MacBinary header before the actual ABIF magic. We detect and skip it.\n */\n\nimport { asciiBytes, asciiString, asDataView, subview, tagNameFromInt32 } from './bytes';\nimport { AbifByteRange, AbifDirectory, AbifEntry, AbifEntryRaw, AbifFile } from './types';\n\nexport const HEADER_SIZE = 128;\nexport const ENTRY_SIZE = 28;\n\n/**\n * Parse an ABIF file from raw bytes into its verbatim directory structure.\n *\n * This is the RAW source of truth: it reads the tdir header and every entry as\n * stored — real dataSize, dataOffset, numElements (see `entry.raw`), the 4 inline\n * bytes, and the tdir/directory metadata — and interprets nothing. For a\n * high-level, opinionated view (typed channels, basecalls, metadata) layer\n * {@link parseAbif} on top.\n *\n * Accepts Uint8Array (works in Node and the browser). Node's Buffer extends\n * Uint8Array, so `readAbif(buffer)` and `readAbif(new Uint8Array(arrayBuffer))`\n * both work.\n *\n * Throws if the magic header is missing. Does NOT require any specific tags\n * (PBAS, DATA, ...) to be present — raw pre-basecalled files are supported.\n */\nexport function readAbif(bytes: Uint8Array): AbifFile {\n  if (bytes.byteLength < HEADER_SIZE) {\n    throw new Error(`ABIF too small: ${bytes.byteLength} bytes`);\n  }\n\n  // MacBinary wrap support: skip 128 bytes if magic is at offset 128.\n  let macBinaryOffset = 0;\n  if (asciiString(subview(bytes, 0, 4)) !== 'ABIF') {\n    if (bytes.byteLength >= 128 + 4 && asciiString(subview(bytes, 128, 4)) === 'ABIF') {\n      macBinaryOffset = 128;\n    } else {\n      throw new Error('Not an ABIF file: missing \"ABIF\" magic.');\n    }\n  }\n  const base = macBinaryOffset;\n  // After skipping any MacBinary wrap, the ABIF part itself must still hold a full 128-byte header;\n  // otherwise reading version/tdir below would run past the DataView (a raw RangeError, not ours).\n  if (bytes.byteLength - base < HEADER_SIZE) {\n    throw new Error(`ABIF too small: ${bytes.byteLength - base} bytes after offset ${base}`);\n  }\n  const view = asDataView(bytes);\n\n  const version = view.getInt16(base + 4, false);\n\n  // Header bytes [base+6 .. base+34) are a TdirEntry describing the directory itself.\n  const dirEntry = decodeEntry(bytes, view, base + 6, base);\n  if (dirEntry.tagName !== 'tdir') {\n    throw new Error(`Expected \"tdir\" header entry, got \"${dirEntry.tagName}\"`);\n  }\n  if (dirEntry.elementSize !== ENTRY_SIZE) {\n    throw new Error(`Expected dir element size ${ENTRY_SIZE}, got ${dirEntry.elementSize}`);\n  }\n\n  // The directory's numElements (raw) is the authoritative entry count — like BioPython, we trust\n  // it rather than clamp against tdir.dataSize, which is a redundant byte-count that some writers\n  // desync. Physical bounds are enforced below; a negative/garbage count just yields 0 entries.\n  const rawDirCount = dirEntry.raw?.elementCount ?? dirEntry.elementCount;\n  const numEntries = Math.max(0, rawDirCount);\n  // tdir.dataSize is always > 4 (28*N), so the dataOffset field is an external offset.\n  const dirOffset = view.getInt32(base + 6 + 20, false);\n  if (dirOffset < 0 || dirOffset + numEntries * ENTRY_SIZE > bytes.byteLength - base) {\n    throw new Error(\n      `Directory out of bounds: offset=${dirOffset}, entries=${numEntries}, file=${bytes.byteLength - base}`,\n    );\n  }\n\n  const entries: AbifEntry[] = [];\n  for (let i = 0; i < numEntries; i++) {\n    entries.push(decodeEntry(bytes, view, base + dirOffset + i * ENTRY_SIZE, base));\n  }\n\n  // Root directory (tdir) header, as read — its dataSize may exceed numEntries*28 (directory padding).\n  const dirDataSize = dirEntry.raw?.dataSize ?? numEntries * ENTRY_SIZE;\n  const entriesEnd = base + dirOffset + numEntries * ENTRY_SIZE;\n  const padLen = Math.min(\n    Math.max(0, dirDataSize - numEntries * ENTRY_SIZE),\n    Math.max(0, bytes.byteLength - entriesEnd),\n  );\n  const tdir: AbifDirectory = {\n    entryCount: numEntries, // effective count actually read (== entries.length)\n    rawEntryCount: rawDirCount, // tdir numElements verbatim, before any reconciliation\n    elementType: dirEntry.elementType, // 1023 (tdir)\n    tagNumber: dirEntry.tagNumber, // usually 1\n    entrySize: dirEntry.elementSize,\n    dataSize: dirDataSize,\n    dataOffset: dirOffset,\n    dataOffsetBytes: dirEntry.raw?.dataOffsetBytes ?? new Uint8Array(4),\n    dataHandle: dirEntry.dataHandle,\n    paddingBytes: new Uint8Array(subview(bytes, entriesEnd, padLen)),\n  };\n\n  // Reserved header bytes [base+34 .. base+128) — verbatim, so a raw reader keeps the whole header.\n  const headerReserved = new Uint8Array(subview(bytes, base + 6 + ENTRY_SIZE, HEADER_SIZE - 6 - ENTRY_SIZE));\n\n  // The MacBinary preamble bytes themselves, when present — verbatim, so the wrapper is reproducible.\n  const macBinaryHeader = macBinaryOffset === 128 ? new Uint8Array(subview(bytes, 0, 128)) : undefined;\n\n  const unreferencedRanges = computeUnreferencedRanges(bytes, base, dirOffset, dirDataSize, entries, macBinaryOffset);\n\n  return { version, tdir, entries, macBinaryOffset, macBinaryHeader, headerReserved, unreferencedRanges };\n}\n\n/**\n * Find the file's physical byte ranges that no header/directory/entry payload covers — orphaned\n * blocks, trailing padding, etc. Computes the complement of every referenced interval so a raw\n * reader can account for all bytes without the writer having to be byte-exact.\n */\nfunction computeUnreferencedRanges(\n  bytes: Uint8Array,\n  base: number,\n  dirOffset: number,\n  dirDataSize: number,\n  entries: AbifEntry[],\n  macBinaryOffset: number,\n): AbifByteRange[] {\n  const total = bytes.byteLength;\n  const covered: Array<[number, number]> = [];\n  if (macBinaryOffset === 128) covered.push([0, 128]); // preamble\n  covered.push([base, base + HEADER_SIZE]); // 128-byte header (magic/version/tdir/reserved)\n  // Directory spans the bytes actually read (numElements entries) OR the declared dataSize when it is\n  // larger (padding) — whichever is bigger, so a desynced dataSize < numElements*28 doesn't mislabel\n  // already-read entries as orphan bytes. A negative dataSize collapses to the physical entry span.\n  const dirCovered = Math.max(entries.length * ENTRY_SIZE, Math.max(0, dirDataSize));\n  covered.push([base + dirOffset, base + dirOffset + dirCovered]);\n  for (const e of entries) {\n    if (e.raw && !e.raw.inline) {\n      const start = base + e.raw.dataOffset;\n      covered.push([start, start + e.payload.byteLength]); // external payload\n    }\n  }\n\n  const norm = covered\n    .map(([s, en]): [number, number] => [Math.max(0, Math.min(s, total)), Math.max(0, Math.min(en, total))])\n    .filter(([s, en]) => en > s)\n    .sort((a, b) => a[0] - b[0]);\n\n  const merged: Array<[number, number]> = [];\n  for (const [s, en] of norm) {\n    const last = merged[merged.length - 1];\n    if (last && s <= last[1]) last[1] = Math.max(last[1], en);\n    else merged.push([s, en]);\n  }\n\n  const gaps: AbifByteRange[] = [];\n  let cursor = 0;\n  for (const [s, en] of merged) {\n    if (s > cursor) gaps.push({ offset: cursor, bytes: new Uint8Array(subview(bytes, cursor, s - cursor)) });\n    cursor = Math.max(cursor, en);\n  }\n  if (cursor < total) gaps.push({ offset: cursor, bytes: new Uint8Array(subview(bytes, cursor, total - cursor)) });\n  return gaps;\n}\n\n/**\n * Decode a 28-byte TdirEntry at the given absolute byte offset.\n *\n * Two robustness measures applied here that BioPython also uses and that real\n * ABIF files in the wild require:\n *\n *   1. The payload is exactly `dataSize` bytes — the authoritative directory field.\n *      ABIF allows `numElements * elementSize != dataSize` for user/opaque types,\n *      so we never derive the payload length from count*size (that both truncates\n *      a larger declared payload and over-reads a smaller one).\n *\n *   2. Inline vs external follows the spec: inline iff `dataSize <= 4` (the payload\n *      fits in the 4-byte dataOffset field). Data > 4 bytes is always external,\n *      even when count*size <= 4. We fall back to count*size only when the declared\n *      field is negative/garbage.\n *\n *   3. `elementCount` is reconciled down to what the payload can hold, so a desynced\n *      (over-large) count can't drive readers past the real bytes.\n *\n *   4. External payload offsets are relative to the ABIF start, so we add `base`\n *      (the MacBinary preamble length) when reading them.\n */\nfunction decodeEntry(bytes: Uint8Array, view: DataView, off: number, base: number): AbifEntry {\n  const tagName = asciiString(subview(bytes, off, 4));\n  const tagNumber = view.getInt32(off + 4, false);\n  const elementType = view.getInt16(off + 8, false);\n  const elementSize = view.getInt16(off + 10, false);\n  const rawElementCount = view.getInt32(off + 12, false);\n  const declaredDataSize = view.getInt32(off + 16, false);\n  const dataHandle = view.getInt32(off + 24, false);\n\n  const computedDataSize = Math.max(0, rawElementCount * Math.max(0, elementSize));\n  // Payload length is the declared dataSize; a negative/garbage declared field falls back to the\n  // computed count*size (consistent with the inline decision below).\n  const payloadSize = declaredDataSize >= 0 ? declaredDataSize : computedDataSize;\n  // Inline iff dataSize <= 4; fall back to computed size only for an invalid declared field.\n  const inline = declaredDataSize >= 0 ? declaredDataSize <= 4 : computedDataSize <= 4;\n  // Reconcile the element count down to what the payload holds, and never expose a negative count\n  // (a malformed numElements would otherwise crash Array/TypedArray helpers downstream). When\n  // elementSize <= 0 the per-element stride is unknown, so cap by payloadSize (≤ 1 byte/element)\n  // rather than trusting the raw count — otherwise a typed getter reads past a 0-byte payload.\n  const elementCount = Math.max(\n    0,\n    elementSize > 0\n      ? Math.min(rawElementCount, Math.floor(payloadSize / elementSize))\n      : Math.min(rawElementCount, payloadSize),\n  );\n\n  let payload: Uint8Array;\n  let dataOffset: number;\n  if (inline) {\n    dataOffset = -1;\n    payload = new Uint8Array(subview(bytes, off + 20, Math.min(4, payloadSize)));\n  } else {\n    dataOffset = view.getInt32(off + 20, false);\n    const at = base + dataOffset;\n    if (dataOffset < 0 || at + payloadSize > bytes.byteLength) {\n      throw new Error(\n        `Entry ${tagName}${tagNumber}: payload out of bounds (offset=${dataOffset}, size=${payloadSize})`,\n      );\n    }\n    payload = new Uint8Array(subview(bytes, at, payloadSize));\n  }\n\n  // The raw 4 bytes of the data/offset slot, verbatim (payload+padding when inline, offset when external).\n  const dataOffsetBytes = new Uint8Array(subview(bytes, off + 20, 4));\n\n  return {\n    tagName,\n    tagNumber,\n    elementType,\n    elementSize,\n    elementCount,\n    payload,\n    dataHandle,\n    raw: { elementCount: rawElementCount, dataSize: declaredDataSize, dataOffset, inline, dataOffsetBytes },\n  };\n}\n\n/**\n * Serialize an AbifFile back to a Uint8Array.\n *\n * Byte-exact on an unmodified round-trip for well-formed records and the tolerated\n * count/dataSize desyncs readAbif() accepts: readAbif() followed right back by\n * writeAbif(), with nothing touched in between, reproduces the original bytes\n * exactly (a MacBinary-wrapped input round-trips its ABIF payload byte-exact, but\n * the preamble itself is never re-added — see the AGENTS.md note on why). The one\n * exception is a genuinely invalid negative `dataSize`/`numElements` field (readAbif\n * tolerates these defensively, falling back to a computed size, but never treats them\n * as verbatim-eligible on write — see the byteLength check below) — such an entry\n * round-trips meaning-lossless (correct payload/content) but its declared dataSize\n * field gets normalized to the real payload length rather than reproducing the\n * original garbage value.\n *\n * This works by keeping every entry whose payload size hasn't changed since it was\n * read (`entry.raw` present — upsertEntry() clears it on any mutation — and\n * `payload.byteLength === raw.dataSize`) at its exact original directory slot and\n * file offset, writing the *original* on-disk numElements/dataSize/offset-or-inline-\n * padding instead of the reconciled/current ones. A new or resized entry is appended\n * past the highest byte offset still known to hold preserved content (every verbatim\n * entry's span, the directory, and any unreferenced range); only its own directory\n * record changes, so every other entry's bytes stay untouched. A resized/removed\n * entry's *old* span is not itself reserved — nothing points at it anymore, so it is\n * free to be reused by whatever gets appended next; the output is not padded out to\n * the original file's true end.\n *\n * The directory is kept at its original file offset as long as the entry count\n * didn't grow (removing entries just shortens it in place; the original directory\n * padding is only reused when the count is exactly unchanged, since a shorter\n * directory can't reuse padding sized for more entries). Only a growing entry count\n * relocates the whole directory to freshly appended space.\n */\nexport function writeAbif(file: AbifFile): Uint8Array {\n  const base = file.macBinaryOffset;\n  const numEntries = file.entries.length;\n  const originalCount = file.tdir.entryCount;\n\n  // An entry is verbatim-eligible when its payload is exactly the size it was read\n  // at — the only case where its original directory record/offset can be reused.\n  const verbatimRaw: Array<AbifEntryRaw | undefined> = file.entries.map(e =>\n    e.raw && e.payload.byteLength === e.raw.dataSize ? e.raw : undefined,\n  );\n\n  // Anchor: the highest byte offset known to belong to the original (unwrapped)\n  // file — header, directory span, every verbatim entry's external payload, and any\n  // orphan byte range. Fresh content is appended after this, so an unmodified\n  // round-trip never appends anything and the output ends exactly here.\n  let anchor = HEADER_SIZE;\n  // A malformed original can declare tdir.dataSize smaller than the entries actually occupy\n  // (readAbif trusts numElements over dataSize — see the \"desynced tdir.dataSize\" test); the\n  // *physical* directory span must still be protected even though the reused dataSize field\n  // below intentionally reproduces the original (desynced) declared value byte-for-byte.\n  anchor = Math.max(anchor, file.tdir.dataOffset + Math.max(file.tdir.dataSize, originalCount * ENTRY_SIZE));\n  for (const raw of verbatimRaw) {\n    if (raw && !raw.inline) anchor = Math.max(anchor, raw.dataOffset + raw.dataSize);\n  }\n  for (const r of file.unreferencedRanges) {\n    anchor = Math.max(anchor, r.offset - base + r.bytes.length);\n  }\n\n  // Directory placement: reuse the original slot unless the entry count grew past it.\n  const dirGrew = numEntries > originalCount;\n  let cursor = anchor;\n  const dirOffset = dirGrew ? cursor : file.tdir.dataOffset;\n  const dirDataSize = numEntries === originalCount ? file.tdir.dataSize : numEntries * ENTRY_SIZE;\n  if (dirGrew) cursor += dirDataSize;\n\n  // Fresh (non-verbatim) external payloads are appended past the anchor, in entry order.\n  const freshOffsets: number[] = new Array(numEntries);\n  for (let i = 0; i < numEntries; i++) {\n    const size = file.entries[i].payload.byteLength;\n    if (verbatimRaw[i] || size <= 4) {\n      freshOffsets[i] = -1; // reused verbatim placement, or inline — no fresh external slot\n      continue;\n    }\n    freshOffsets[i] = cursor;\n    cursor += size;\n  }\n\n  const out = new Uint8Array(cursor);\n  const outView = asDataView(out);\n\n  // Header: \"ABIF\" + version (int16 BE) + tdir entry (below) + reserved bytes verbatim.\n  out.set(asciiBytes('ABIF'), 0);\n  outView.setInt16(4, file.version, false);\n  out.set(file.headerReserved, 6 + ENTRY_SIZE);\n  writeDirRecord(out, outView, 6, {\n    tagName: 'tdir',\n    tagNumber: file.tdir.tagNumber,\n    elementType: file.tdir.elementType,\n    elementSize: file.tdir.entrySize,\n    elementCount: numEntries,\n    dataSize: dirDataSize,\n    dataHandle: file.tdir.dataHandle,\n    offsetSlot: { kind: 'external', value: dirOffset },\n  });\n\n  // Directory padding only carries over when the entry count is exactly unchanged.\n  if (numEntries === originalCount && file.tdir.paddingBytes.length > 0) {\n    out.set(file.tdir.paddingBytes, dirOffset + numEntries * ENTRY_SIZE);\n  }\n\n  for (let i = 0; i < numEntries; i++) {\n    const e = file.entries[i];\n    const raw = verbatimRaw[i];\n    const off = dirOffset + i * ENTRY_SIZE;\n    const dataSize = e.payload.byteLength;\n    writeDirRecord(out, outView, off, {\n      tagName: e.tagName,\n      tagNumber: e.tagNumber,\n      elementType: e.elementType,\n      elementSize: e.elementSize,\n      elementCount: raw ? raw.elementCount : e.elementCount,\n      dataSize: raw ? raw.dataSize : dataSize,\n      dataHandle: e.dataHandle,\n      offsetSlot:\n        dataSize <= 4\n          ? { kind: 'inline', payload: e.payload, dataSize, staleTail: raw?.dataOffsetBytes }\n          : { kind: 'external', value: raw ? raw.dataOffset : freshOffsets[i] },\n    });\n    if (dataSize > 4) {\n      out.set(e.payload, raw ? raw.dataOffset : freshOffsets[i]);\n    }\n  }\n\n  for (const r of file.unreferencedRanges) {\n    out.set(r.bytes, r.offset - base);\n  }\n\n  return out;\n}\n\ntype OffsetSlot =\n  | { kind: 'external'; value: number }\n  | { kind: 'inline'; payload: Uint8Array; dataSize: number; staleTail?: Uint8Array };\n\nfunction writeDirRecord(\n  out: Uint8Array,\n  outView: DataView,\n  off: number,\n  rec: {\n    tagName: string;\n    tagNumber: number;\n    elementType: number;\n    elementSize: number;\n    elementCount: number;\n    dataSize: number;\n    dataHandle: number;\n    offsetSlot: OffsetSlot;\n  },\n): void {\n  if (rec.tagName.length !== 4) {\n    throw new Error(`tagName must be 4 chars: \"${rec.tagName}\"`);\n  }\n  out.set(asciiBytes(rec.tagName), off);\n  outView.setInt32(off + 4, rec.tagNumber, false);\n  outView.setInt16(off + 8, rec.elementType, false);\n  outView.setInt16(off + 10, rec.elementSize, false);\n  outView.setInt32(off + 12, rec.elementCount, false);\n  outView.setInt32(off + 16, rec.dataSize, false);\n  if (rec.offsetSlot.kind === 'external') {\n    outView.setInt32(off + 20, rec.offsetSlot.value, false);\n  } else {\n    // Inline: clear 4 bytes, place the payload, then restore any stale tail byte(s)\n    // beyond dataSize from the original slot — a byte-exact round-trip needs them,\n    // since they're not derivable from any semantic field.\n    const { payload, dataSize, staleTail } = rec.offsetSlot;\n    out.fill(0, off + 20, off + 24);\n    out.set(payload.subarray(0, dataSize), off + 20);\n    if (staleTail && dataSize < 4) {\n      out.set(staleTail.subarray(dataSize, 4), off + 20 + dataSize);\n    }\n  }\n  outView.setInt32(off + 24, rec.dataHandle, false);\n}\n\n// =====================================================================\n// Lookup / mutation helpers\n// =====================================================================\n\n/** Find an entry by name+number, or undefined. */\nexport function findEntry(file: AbifFile, name: string, number: number): AbifEntry | undefined {\n  return file.entries.find(e => e.tagName === name && e.tagNumber === number);\n}\n\n/** Find all entries with the given tag name. */\nexport function findEntries(file: AbifFile, name: string): AbifEntry[] {\n  return file.entries.filter(e => e.tagName === name);\n}\n\n/**\n * Replace the payload of an existing entry, or append a new one.\n * elementType/elementSize/elementCount must be supplied for new entries.\n *\n * This is the required way to mutate an entry read from a file — it clears `.raw`\n * on replacement so writeAbif() never reuses a now-stale on-disk shape. Setting\n * `entry.payload`/`elementType`/`elementSize`/`elementCount` directly instead\n * leaves `.raw` behind and can corrupt the written directory record.\n */\nexport function upsertEntry(\n  file: AbifFile,\n  name: string,\n  number: number,\n  payload: Uint8Array,\n  defaults: { elementType: number; elementSize: number; elementCount: number },\n): void {\n  if (payload.byteLength !== defaults.elementCount * defaults.elementSize) {\n    throw new Error(`upsertEntry ${name}${number}: payload length ${payload.byteLength} != count*size`);\n  }\n  const existing = findEntry(file, name, number);\n  if (existing) {\n    existing.elementType = defaults.elementType;\n    existing.elementSize = defaults.elementSize;\n    existing.elementCount = defaults.elementCount;\n    existing.payload = payload;\n    // `raw` describes the entry's shape as read from disk; once mutated it no longer applies —\n    // clearing it forces writeAbif() to place this entry fresh rather than reuse a stale record\n    // (e.g. a same-length content edit would otherwise silently keep the old elementCount/dataSize).\n    existing.raw = undefined;\n  } else {\n    file.entries.push({\n      tagName: name,\n      tagNumber: number,\n      elementType: defaults.elementType,\n      elementSize: defaults.elementSize,\n      elementCount: defaults.elementCount,\n      payload,\n      dataHandle: 0,\n    });\n  }\n}\n\n/** Re-export for users who want to interpret raw tag bytes themselves. */\nexport { tagNameFromInt32 };\n","/**\n * High-level typed view over an AbifFile.\n *\n * Reading helpers that interpret the raw payloads of well-known tags. For\n * mutation helpers (setSequence, setConfidences, ...) see ./setters.\n */\n\nimport { findEntry } from './abif-format';\nimport { asciiString, asDataView } from './bytes';\nimport { AbifDataChannelRole, AbifFile } from './types';\n\n/** Get DATA<n> as a signed-int16 array, or undefined. */\nexport function getDataChannel(file: AbifFile, n: number): Int16Array | undefined {\n  const e = findEntry(file, 'DATA', n);\n  if (!e) return undefined;\n  if (e.elementSize !== 2) {\n    throw new Error(`DATA${n}: expected elementSize=2, got ${e.elementSize}`);\n  }\n  const arr = new Int16Array(e.elementCount);\n  const view = asDataView(e.payload);\n  for (let i = 0; i < e.elementCount; i++) {\n    arr[i] = view.getInt16(i * 2, false);\n  }\n  return arr;\n}\n\n/**\n * Dye order, 4 ASCII chars (e.g. \"GATC\"). Defaults to \"GATC\" if FWO_ absent.\n *\n * GATC is the dye order produced by modern ABI 3730/3500 instruments and the\n * dominant default in the wild. Older \"ACGT\" defaults caused channel\n * mis-mapping on files where FWO_ is missing or malformed.\n */\nexport function getFwo(file: AbifFile): string {\n  const e = findEntry(file, 'FWO_', 1);\n  if (!e) return 'GATC';\n  // Read only the declared elements — payload may carry trailing padding beyond elementCount.\n  return asciiString(e.payload.subarray(0, e.elementCount));\n}\n\n/**\n * Whether an FWO_ string is a genuine dye order: a permutation of A/C/G/T with all\n * four bases distinct. `\"GATC\"` passes; `\"AAAA\"` (regex-valid but degenerate) does\n * not — mapping four channels through it would collapse them onto one base.\n */\nexport function isFwoPermutation(fwo: string): boolean {\n  return /^[ACGT]{4}$/.test(fwo) && new Set(fwo).size === 4;\n}\n\n/**\n * Fact: the file carries a second dye-trace block, DATA9..12 (all four tags), in\n * addition to DATA1..4. Reports presence only — it does NOT say which block is\n * raw and which is analyzed/processed; that convention isn't stored in the file.\n */\nexport function hasData9To12Block(file: AbifFile): boolean {\n  return !!(\n    findEntry(file, 'DATA', 9) &&\n    findEntry(file, 'DATA', 10) &&\n    findEntry(file, 'DATA', 11) &&\n    findEntry(file, 'DATA', 12)\n  );\n}\n\n/**\n * Spec-defined role of a DATA<n> tag, limited to the numbers the ABIF spec names:\n *\n *   - `'trace'`     — dye-signal channels: DATA1..4 (raw dyes 1-4), DATA9..12\n *                     (analyzed dyes 1-4), and the two optional 5th-dye blocks\n *                     DATA105 (raw dye 5) and DATA205 (analyzed dye 5).\n *   - `'telemetry'` — DATA5..8: instrument run telemetry (voltage, current,\n *                     power, temperature), one value per scan — NOT dye signal.\n *   - `'other'`     — any other DATA number. The spec does not enumerate higher\n *                     extra-dye tags (106/206/…), so we don't claim a role for them.\n *\n * A fact from the ABIF specification, not an inference about content.\n */\nexport function dataChannelRole(n: number): AbifDataChannelRole {\n  if (n >= 5 && n <= 8) return 'telemetry';\n  if ((n >= 1 && n <= 4) || (n >= 9 && n <= 12) || n === 105 || n === 205) return 'trace';\n  return 'other';\n}\n\n/**\n * Whether the file declares its sequence already reverse-complemented, from the\n * RevC1 flag (int16, non-zero = true). undefined when RevC1 is absent. Reported\n * as-is; the consumer decides how to act on it.\n */\nexport function getReverseComplemented(file: AbifFile): boolean | undefined {\n  const e = findEntry(file, 'RevC', 1);\n  if (!e) return undefined;\n  const view = asDataView(e.payload);\n  return e.payload.byteLength >= 2 ? view.getInt16(0, false) !== 0 : e.payload.some(b => b !== 0);\n}\n\n/**\n * Map from base letter (\"A\"|\"C\"|\"G\"|\"T\") to the DATA1..4 tag number that holds\n * its channel, using the dye order declared by FWO_. If FWO_=\"GATC\" then\n * G→1, A→2, T→3, C→4.\n *\n * This follows the file's own FWO_ declaration for the DATA1..4 block; it makes\n * no claim about whether that block is raw or processed.\n */\nexport function getChannelMap(file: AbifFile): Record<'A' | 'C' | 'G' | 'T', number> {\n  const fwo = getFwo(file);\n  if (!isFwoPermutation(fwo)) {\n    throw new Error(`FWO_ is not a permutation of A/C/G/T: \"${fwo}\"`);\n  }\n  return {\n    [fwo[0]]: 1,\n    [fwo[1]]: 2,\n    [fwo[2]]: 3,\n    [fwo[3]]: 4,\n  } as Record<'A' | 'C' | 'G' | 'T', number>;\n}\n\n/** Get PBAS sequence (prefer PBAS2 over PBAS1). undefined if neither present. */\nexport function getSequence(file: AbifFile): string | undefined {\n  return getSequenceForVersion(file, 2) ?? getSequenceForVersion(file, 1);\n}\n\n/**\n * Get PBAS<version> exactly as stored — no called/edited preference, unlike\n * {@link getSequence}. Used where each basecall version must be handled on its\n * own (e.g. cropping every version a file carries, not just the preferred one).\n */\nexport function getSequenceForVersion(file: AbifFile, version: number): string | undefined {\n  const e = findEntry(file, 'PBAS', version);\n  if (!e) return undefined;\n  // Bound by elementCount (payload may be padded) and drop trailing NULs, matching parseAbif.\n  return asciiString(e.payload.subarray(0, e.elementCount)).replace(/\\0+$/g, '');\n}\n\n/**\n * Get per-base Phred-like quality scores (0..255 byte values, typically 0..60\n * for Sanger). Prefers PCON2 over PCON1.\n *\n * PCON is declared in the ABIF spec as elementType=2 (char) but the byte\n * values ARE the Q-scores — we read raw bytes regardless of declared type.\n */\nexport function getConfidences(file: AbifFile): number[] | undefined {\n  return getConfidencesForVersion(file, 2) ?? getConfidencesForVersion(file, 1);\n}\n\n/**\n * Get PCON<version> exactly as stored — no called/edited preference, unlike\n * {@link getConfidences}. See {@link getSequenceForVersion} for why this exists.\n */\nexport function getConfidencesForVersion(file: AbifFile, version: number): number[] | undefined {\n  const e = findEntry(file, 'PCON', version);\n  if (!e) return undefined;\n  const out: number[] = new Array(e.elementCount);\n  for (let i = 0; i < e.elementCount; i++) out[i] = e.payload[i];\n  return out;\n}\n\n/**\n * Get peak scan positions (one per base). Prefers PLOC2 over PLOC1.\n *\n * Read as UNSIGNED int16: PLOC indexes into the sample trace and is always\n * non-negative, but values > 32767 (long traces) would wrap to negative\n * if interpreted as signed.\n */\nexport function getPositions(file: AbifFile): number[] | undefined {\n  return getPositionsForVersion(file, 2) ?? getPositionsForVersion(file, 1);\n}\n\n/**\n * Get PLOC<version> exactly as stored — no called/edited preference, unlike\n * {@link getPositions}. See {@link getSequenceForVersion} for why this exists.\n */\nexport function getPositionsForVersion(file: AbifFile, version: number): number[] | undefined {\n  const e = findEntry(file, 'PLOC', version);\n  if (!e) return undefined;\n  if (e.elementSize !== 2) {\n    throw new Error(`PLOC${version}: expected elementSize=2, got ${e.elementSize}`);\n  }\n  const view = asDataView(e.payload);\n  const out: number[] = new Array(e.elementCount);\n  for (let i = 0; i < e.elementCount; i++) out[i] = view.getUint16(i * 2, false);\n  return out;\n}\n\n/**\n * Get average peak spacing (samples per base), from SPAC/1.\n *\n * ABIF spec defines SPAC as float32 (elementType=7); some legacy files\n * mislabel it as long (type=5). Both are 4 bytes and on disk the payload\n * is always a 32-bit float, so we read as float regardless of declared type.\n *\n * Returns undefined if SPAC is absent or non-positive.\n */\nexport function getSamplingRate(file: AbifFile): number | undefined {\n  const e = findEntry(file, 'SPAC', 1);\n  if (!e || e.elementSize !== 4 || e.payload.byteLength < 4) return undefined;\n  const v = asDataView(e.payload).getFloat32(0, false);\n  return Number.isFinite(v) && v > 0 ? v : undefined;\n}\n","/**\n * Domain-layer operation: crop an ABIF file to a sample range.\n *\n * `{ start, end }` is a half-open sample range in the DATA9..12 (processed/analyzed)\n * domain — the only domain PLOC maps into (see AGENTS.md's \"raw vs processed\" note).\n * DATA9..12 are sliced exactly by that range. DATA1..4/5..8 (raw dye trace and\n * instrument telemetry) have no honest sample-for-sample correspondence to the\n * processed domain (the mapping is non-linear mobility correction, not stored in the\n * file), so they are never approximated: `rawTrace` keeps them whole and untouched,\n * or omits them, never a proportional slice.\n *\n * Every basecall version the file carries (PBAS1/PCON1/PLOC1 \"edited\",\n * PBAS2/PCON2/PLOC2 \"called\", or any vendor version) is cropped independently by its\n * OWN PLOC — two versions are not guaranteed to share base positions or even length\n * (edits insert/delete bases), so there is no shared coordinate to crop them together\n * by. A version with no PLOC of its own cannot be cropped and is rejected rather than\n * silently dropped or left un-cropped.\n *\n * Everything else (metadata, FWO_, SPAC, ...) is carried over untouched — this is a\n * structural crop, not a re-derivation of run metadata for the new region.\n *\n * Reverse-complement is out of scope here; this function has no RC option.\n *\n * Returns a new, independently mutable AbifFile — the input is not mutated, and\n * neither is the output if the input is later touched. Untouched entries are\n * shallow-copied (a new AbifEntry object; the underlying payload bytes are shared,\n * which is safe since nothing ever mutates payload bytes in place — only replaces\n * them wholesale), so a later upsertEntry() on either file's copy of a shared tag\n * can't reach into the other file's entries.\n */\n\nimport { findEntry } from './abif-format';\nimport { asciiBytes, asDataView } from './bytes';\nimport { AbifEntry, AbifFile } from './types';\nimport { getConfidencesForVersion, getPositionsForVersion, getSequenceForVersion, hasData9To12Block } from './view';\n\nexport interface CropAbifRange {\n  /** Inclusive start sample index into DATA9..12. */\n  start: number;\n  /** Exclusive end sample index into DATA9..12. */\n  end: number;\n}\n\nexport interface CropAbifOptions {\n  /**\n   * DATA1..4 (raw dye trace) and DATA5..8 (telemetry): 'full' keeps them whole and\n   * untouched (the exported file's raw trace no longer lines up sample-for-sample\n   * with the cropped DATA9..12/PLOC, by design — see the module doc comment);\n   * 'omit' drops them from the output entirely. Default 'omit'.\n   */\n  rawTrace?: 'full' | 'omit';\n}\n\n/** Crop an AbifFile to a DATA9..12 sample range. See the module doc comment for the model. */\nexport function cropAbif(file: AbifFile, range: CropAbifRange, options: CropAbifOptions = {}): AbifFile {\n  const { start, end } = range;\n  if (!Number.isInteger(start) || !Number.isInteger(end) || start < 0 || end <= start) {\n    throw new Error(`cropAbif: invalid range [${start}, ${end})`);\n  }\n  if (!hasData9To12Block(file)) {\n    throw new Error('cropAbif: no DATA9..12 block to crop — the range has nothing to apply to');\n  }\n  // The range's meaning is bounded by the processed trace itself: clamping a too-large `end`\n  // instead of rejecting it would let a kept base's PLOC point past the (now shorter) cropped\n  // DATA9..12 — a structurally inconsistent result. Bound by the shortest of the four channels,\n  // in case a malformed file's DATA9..12 lengths ever disagree.\n  const processedLength = Math.min(\n    entryElementCount(file, 9),\n    entryElementCount(file, 10),\n    entryElementCount(file, 11),\n    entryElementCount(file, 12),\n  );\n  if (end > processedLength) {\n    throw new Error(`cropAbif: range end ${end} exceeds the processed trace length ${processedLength}`);\n  }\n  const rawTrace = options.rawTrace ?? 'omit';\n\n  const entries: AbifEntry[] = [];\n  for (const e of file.entries) {\n    if (e.tagName === 'DATA' && e.tagNumber >= 9 && e.tagNumber <= 12) {\n      entries.push(cropDataEntry(e, start, end));\n    } else if (e.tagName === 'DATA' && e.tagNumber >= 1 && e.tagNumber <= 8) {\n      // Shallow-copy so a later upsertEntry() on the cropped file's copy (mutates in place)\n      // can never reach back and corrupt the input file's own entry object.\n      if (rawTrace === 'full') entries.push({ ...e });\n    } else if (e.tagName === 'PBAS' || e.tagName === 'PCON' || e.tagName === 'PLOC') {\n      // Handled per-version below, once per version rather than once per tag.\n    } else {\n      entries.push({ ...e });\n    }\n  }\n\n  for (const version of basecallVersionsIn(file)) {\n    entries.push(...cropBasecallVersion(file, version, start, end));\n  }\n\n  return {\n    version: file.version,\n    tdir: file.tdir,\n    entries,\n    macBinaryOffset: 0,\n    macBinaryHeader: undefined,\n    headerReserved: file.headerReserved,\n    // Orphan byte ranges belong to the pre-crop file's specific byte layout; carrying\n    // them into a structurally different (smaller) file would preserve meaningless bytes.\n    unreferencedRanges: [],\n  };\n}\n\n/** DATA<n>'s elementCount, or 0 if absent — used to bound the requested range up front. */\nfunction entryElementCount(file: AbifFile, n: number): number {\n  return findEntry(file, 'DATA', n)?.elementCount ?? 0;\n}\n\nfunction cropDataEntry(e: AbifEntry, start: number, end: number): AbifEntry {\n  if (e.elementSize !== 2) {\n    throw new Error(`cropAbif: DATA${e.tagNumber} expected elementSize=2, got ${e.elementSize}`);\n  }\n  // Callers only reach here once cropAbif has already validated end <= the processed trace length.\n  const payload = new Uint8Array(e.payload.subarray(start * 2, end * 2));\n  return {\n    tagName: 'DATA',\n    tagNumber: e.tagNumber,\n    elementType: e.elementType,\n    elementSize: 2,\n    elementCount: end - start,\n    payload,\n    dataHandle: e.dataHandle,\n  };\n}\n\n/** Every PBAS tag number present, ascending (1 = edited, 2 = called, other = vendor). */\nfunction basecallVersionsIn(file: AbifFile): number[] {\n  const versions = new Set<number>();\n  for (const e of file.entries) {\n    if (e.tagName === 'PBAS') versions.add(e.tagNumber);\n  }\n  return Array.from(versions).sort((a, b) => a - b);\n}\n\n/** Crop one basecall version's PBAS/PCON/PLOC by its own PLOC, independent of any other version. */\nfunction cropBasecallVersion(file: AbifFile, version: number, start: number, end: number): AbifEntry[] {\n  const sequence = getSequenceForVersion(file, version);\n  if (sequence === undefined) return [];\n  const positions = getPositionsForVersion(file, version);\n  if (positions === undefined) {\n    throw new Error(`cropAbif: PBAS${version} has no PLOC${version} to crop by`);\n  }\n  if (positions.length !== sequence.length) {\n    throw new Error(\n      `cropAbif: PBAS${version}/PLOC${version} length mismatch (${sequence.length} vs ${positions.length})`,\n    );\n  }\n  const confidences = getConfidencesForVersion(file, version);\n  if (confidences !== undefined && confidences.length !== sequence.length) {\n    throw new Error(`cropAbif: PBAS${version}/PCON${version} length mismatch`);\n  }\n\n  const kept: number[] = [];\n  for (let i = 0; i < positions.length; i++) {\n    if (positions[i] >= start && positions[i] < end) kept.push(i);\n  }\n\n  const croppedSequence = kept.map(i => sequence[i]).join('');\n  const croppedPositions = kept.map(i => positions[i] - start);\n\n  const out: AbifEntry[] = [\n    {\n      tagName: 'PBAS',\n      tagNumber: version,\n      elementType: 2, // char\n      elementSize: 1,\n      elementCount: croppedSequence.length,\n      payload: asciiBytes(croppedSequence),\n      dataHandle: 0,\n    },\n    {\n      tagName: 'PLOC',\n      tagNumber: version,\n      elementType: 4, // short, but PLOC values are unsigned (see setPositions)\n      elementSize: 2,\n      elementCount: croppedPositions.length,\n      payload: encodeUnsignedShorts(croppedPositions),\n      dataHandle: 0,\n    },\n  ];\n  if (confidences !== undefined) {\n    const croppedConfidences = kept.map(i => confidences[i]);\n    out.push({\n      tagName: 'PCON',\n      tagNumber: version,\n      elementType: 2, // declared char; bytes ARE Q-scores, see getConfidencesForVersion\n      elementSize: 1,\n      elementCount: croppedConfidences.length,\n      payload: Uint8Array.from(croppedConfidences),\n      dataHandle: 0,\n    });\n  }\n  return out;\n}\n\nfunction encodeUnsignedShorts(values: readonly number[]): Uint8Array {\n  const buf = new Uint8Array(values.length * 2);\n  const view = asDataView(buf);\n  for (let i = 0; i < values.length; i++) {\n    view.setUint16(i * 2, Math.max(0, Math.min(0xffff, values[i])), false);\n  }\n  return buf;\n}\n","/**\n * High-level \"parse everything\" wrapper around the raw + view layers.\n *\n * Returns a single ParsedAbif object with metadata, the FWO_-aware\n * DATA1..4 / DATA9..12 channel split, basecalls, and decoded directory entries\n * for diagnostics. Mirrors what typical viewers (chromatogram UIs, sample\n * inspectors) need from a single file.\n *\n * For round-trip authoring (basecallers), prefer {@link readAbif} +\n * setters from ./setters which operate directly on the raw AbifFile.\n */\n\nimport { readAbif } from './abif-format';\nimport { asciiString, asDataView, subview } from './bytes';\nimport {\n  AbifBaseCalls,\n  AbifBaseCallVariant,\n  AbifChromatogramBundle,\n  AbifDecodedValue,\n  AbifDirEntry,\n  AbifEntry,\n  AbifMetadata,\n  ChannelSignals,\n  ParsedAbif,\n} from './types';\nimport { getFwo, isFwoPermutation } from './view';\n\nconst TYPE_NAMES: Record<number, string> = {\n  1: 'byte',\n  2: 'char',\n  3: 'word',\n  4: 'short',\n  5: 'long',\n  7: 'float',\n  8: 'double',\n  10: 'date',\n  11: 'time',\n  12: 'thumb',\n  13: 'bool',\n  18: 'pString',\n  19: 'cString',\n  1023: 'tdir',\n};\n\nfunction typeName(t: number): string {\n  return TYPE_NAMES[t] ?? (t >= 1024 ? `user${t}` : `type${t}`);\n}\n\nfunction previewNumbers(arr: number[], max = 10): string {\n  if (arr.length <= max) return `[${arr.join(', ')}]`;\n  return `[${arr.slice(0, max).join(', ')}, … +${arr.length - max}] (n=${arr.length})`;\n}\n\nfunction truncate(s: string, n = 80): string {\n  return s.length > n ? s.slice(0, n) + '…' : s;\n}\n\nfunction previewBytes(bytes: Uint8Array): string {\n  const slice = bytes.subarray(0, 16);\n  const hex = Array.from(slice, b => b.toString(16).padStart(2, '0')).join(' ');\n  return `${bytes.byteLength}B [${hex}${bytes.byteLength > 16 ? ' …' : ''}]`;\n}\n\n/** Coerce a decoded value to a number array, treating a single scalar as a one-element array. */\nfunction asNumbers(d: AbifDecodedValue): number[] | undefined {\n  if (d.kind === 'numbers') return d.value;\n  if (d.kind === 'number') return [d.value];\n  return undefined;\n}\n\n/**\n * Decode a run of fixed-width numbers, bounded by BOTH the element count and the\n * actual payload length — so a malformed entry whose declared elementSize/dataSize\n * disagrees with the type's real width can never drive a read past the buffer.\n */\nfunction decodeNumeric(\n  byteLength: number,\n  elementCount: number,\n  size: number,\n  read: (offset: number) => number,\n): AbifDecodedValue {\n  const n = Math.max(0, Math.min(elementCount, Math.floor(byteLength / size)));\n  const arr: number[] = [];\n  for (let i = 0; i < n; i++) arr.push(read(i * size));\n  return arr.length === 1 ? { kind: 'number', value: arr[0] } : { kind: 'numbers', value: arr };\n}\n\n/**\n * Decode a payload best-effort by ABIF element type.\n *\n * Strings have trailing NULs stripped (cString/pString convention).\n * pString (type 18) is decoded as `length-prefix + chars`.\n */\nfunction decodePayload(elementType: number, elementCount: number, payload: Uint8Array): AbifDecodedValue {\n  const view = asDataView(payload);\n  switch (elementType) {\n    case 1: {\n      const arr = Array.from(payload.subarray(0, elementCount));\n      return { kind: 'numbers', value: arr };\n    }\n    case 2:\n    case 19: {\n      const s = asciiString(payload.subarray(0, elementCount)).replace(/\\0+$/g, '');\n      return { kind: 'string', value: s };\n    }\n    case 3:\n      return decodeNumeric(payload.byteLength, elementCount, 2, o => view.getUint16(o, false));\n    case 4:\n      return decodeNumeric(payload.byteLength, elementCount, 2, o => view.getInt16(o, false));\n    case 5:\n      return decodeNumeric(payload.byteLength, elementCount, 4, o => view.getInt32(o, false));\n    case 7:\n      return decodeNumeric(payload.byteLength, elementCount, 4, o => view.getFloat32(o, false));\n    case 8:\n      return decodeNumeric(payload.byteLength, elementCount, 8, o => view.getFloat64(o, false));\n    case 10: {\n      // A date needs 4 bytes; a short/truncated payload falls back to raw bytes rather than throwing.\n      if (payload.byteLength < 4) return { kind: 'unknown', value: payload };\n      const year = view.getInt16(0, false);\n      const month = view.getUint8(2);\n      const day = view.getUint8(3);\n      return { kind: 'date', value: { year, month, day } };\n    }\n    case 11: {\n      // A time needs 4 bytes; short payload → raw bytes, not a RangeError.\n      if (payload.byteLength < 4) return { kind: 'unknown', value: payload };\n      return {\n        kind: 'time',\n        value: {\n          hour: view.getUint8(0),\n          minute: view.getUint8(1),\n          second: view.getUint8(2),\n          hsec: view.getUint8(3),\n        },\n      };\n    }\n    case 13: {\n      const arr: boolean[] = [];\n      for (let i = 0; i < Math.min(elementCount, payload.byteLength); i++) arr.push(view.getUint8(i) !== 0);\n      return { kind: 'bools', value: arr };\n    }\n    case 18: {\n      // pString = length prefix + chars; an empty payload is just the empty string.\n      if (payload.byteLength < 1) return { kind: 'string', value: '' };\n      const len = view.getUint8(0);\n      const s = asciiString(subview(payload, 1, Math.min(len, Math.max(0, elementCount - 1))));\n      return { kind: 'string', value: s };\n    }\n    default:\n      return { kind: 'unknown', value: payload };\n  }\n}\n\nfunction previewDecoded(d: AbifDecodedValue, elementType: number): string {\n  switch (d.kind) {\n    case 'number':\n      return String(d.value);\n    case 'numbers':\n      return previewNumbers(d.value);\n    case 'string':\n      return truncate(JSON.stringify(d.value));\n    case 'bools':\n      return d.value.length === 1 ? String(d.value[0]) : `[${d.value.join(', ')}]`;\n    case 'date': {\n      const { year, month, day } = d.value;\n      return `${year}-${String(month).padStart(2, '0')}-${String(day).padStart(2, '0')}`;\n    }\n    case 'time': {\n      const { hour, minute, second } = d.value;\n      return `${String(hour).padStart(2, '0')}:${String(minute).padStart(2, '0')}:${String(second).padStart(2, '0')}`;\n    }\n    case 'bytes':\n      return `${typeName(elementType)} ${previewBytes(d.value)}`;\n    case 'unknown':\n      return `${typeName(elementType)} ${previewBytes(d.value)}`;\n  }\n}\n\n/**\n * Parse an ABIF file into a high-level view: metadata, channels, basecalls,\n * and decoded directory entries.\n *\n * This is the INTERPRETING layer — it makes convenience choices (FWO_ → \"GATC\"\n * fallback, derived samplingRate, preferred/upper-cased PBAS2 baseCalls). It is\n * not the raw structural truth: for that use {@link readAbif}, which reads the\n * directory verbatim (raw dataSize/offset/counts, tdir, inline bytes) and makes\n * no interpretation. `parseAbif` builds on top of it.\n *\n * Accepts ArrayBuffer or Uint8Array (Buffer in Node works too — it extends\n * Uint8Array). The `fileName` argument is informational only; it's preserved\n * in the result.\n */\nexport function parseAbif(input: ArrayBuffer | Uint8Array, fileName = ''): ParsedAbif {\n  const bytes = input instanceof Uint8Array ? input : new Uint8Array(input);\n  const file = readAbif(bytes);\n\n  const entries: AbifDirEntry[] = file.entries.map(e => {\n    // PCON is declared char (type 2) but its bytes ARE Q-scores; decode it as numbers so the\n    // diagnostic view keeps zeros the char decoder would strip (matches baseCalls.confidences).\n    const decoded =\n      e.tagName === 'PCON' && e.elementSize === 1\n        ? decodePayload(1, e.elementCount, e.payload) // type 1 = byte → { kind: 'numbers' }\n        : decodePayload(e.elementType, e.elementCount, e.payload);\n    // Prefer the real on-disk directory fields (present when read from a file) over\n    // reconciled/computed values, so the diagnostic view reflects the actual record.\n    return {\n      tag: e.tagName,\n      tagNumber: e.tagNumber,\n      elementType: e.elementType,\n      elementTypeName: typeName(e.elementType),\n      elementSize: e.elementSize,\n      elementCount: e.elementCount,\n      rawElementCount: e.raw?.elementCount ?? e.elementCount,\n      dataSize: e.raw?.dataSize ?? e.elementCount * e.elementSize,\n      dataOffset: e.raw?.dataOffset ?? -1,\n      inline: e.raw?.inline ?? e.elementCount * e.elementSize <= 4,\n      decoded,\n      preview: previewDecoded(decoded, e.elementType),\n    };\n  });\n\n  // FWO_ → base order. Fall back to GATC unless FWO_ is a real permutation of A/C/G/T\n  // (a degenerate value like \"AAAA\" is regex-valid but would collapse channels).\n  let baseOrder = getFwo(file);\n  if (!isFwoPermutation(baseOrder)) baseOrder = 'GATC';\n\n  const dataChannels: Record<number, number[]> = {};\n  const data1To4: ChannelSignals = { A: [], C: [], G: [], T: [] };\n  const data9To12: ChannelSignals = { A: [], C: [], G: [], T: [] };\n  const metadata: AbifMetadata = { comments: [] };\n  const pbas: Record<number, string> = {};\n  const pcon: Record<number, number[]> = {};\n  const ploc: Record<number, number[]> = {};\n\n  const channelKey = (i: number): keyof ChannelSignals => baseOrder[i] as keyof ChannelSignals;\n\n  for (let idx = 0; idx < file.entries.length; idx++) {\n    const e = file.entries[idx];\n    const decoded = entries[idx].decoded;\n\n    if (e.tagName === 'DATA') {\n      // Accept single-element channels too (decodePayload collapses length-1 to a scalar).\n      const nums = asNumbers(decoded);\n      if (nums) {\n        dataChannels[e.tagNumber] = nums;\n        if (e.tagNumber >= 1 && e.tagNumber <= 4) data1To4[channelKey(e.tagNumber - 1)] = nums;\n        else if (e.tagNumber >= 9 && e.tagNumber <= 12) data9To12[channelKey(e.tagNumber - 9)] = nums;\n      }\n    } else if (e.tagName === 'PBAS' && decoded.kind === 'string') {\n      pbas[e.tagNumber] = decoded.value;\n    } else if (e.tagName === 'PCON') {\n      // PCON Q-scores are 1 byte each (elementType=2/char). Read them straight from the payload —\n      // a trailing zero is a valid score, but the char decoder strips trailing NULs and would drop it.\n      const nums = e.elementSize === 1 ? Array.from(e.payload.subarray(0, e.elementCount)) : asNumbers(decoded);\n      if (nums) pcon[e.tagNumber] = nums;\n    } else if (e.tagName === 'PLOC') {\n      // PLOC sample indices are always non-negative — reinterpret int16 as uint16.\n      const nums = asNumbers(decoded);\n      if (nums) ploc[e.tagNumber] = nums.map(v => (v < 0 ? v + 0x10000 : v));\n    } else if (e.tagName === 'SPAC') {\n      // ABIF spec defines SPAC as float (elementType=7). Some legacy files mislabel\n      // it as long (type=5); both are 4 bytes and the payload is always a float.\n      if (e.elementSize === 4 && e.payload.byteLength >= 4) {\n        const v = asDataView(e.payload).getFloat32(0, false);\n        if (Number.isFinite(v) && v > 0) metadata.samplingRate = v;\n      } else if (decoded.kind === 'number') {\n        metadata.samplingRate = decoded.value;\n      }\n    } else if (e.tagName === 'SMPL' && decoded.kind === 'string') {\n      metadata.sampleName = decoded.value;\n    } else if (e.tagName === 'LANE' && decoded.kind === 'number') {\n      metadata.laneNumber = decoded.value;\n    } else if (e.tagName === 'TUBE' && decoded.kind === 'string') {\n      metadata.tube = decoded.value;\n    } else if (e.tagName === 'MCHN' && decoded.kind === 'string') {\n      metadata.machineName = decoded.value;\n    } else if (e.tagName === 'MODL' && decoded.kind === 'string') {\n      metadata.machineModel = decoded.value;\n    } else if (e.tagName === 'RUND' && decoded.kind === 'date') {\n      const d = decoded.value;\n      metadata.runDate = `${d.year}-${String(d.month).padStart(2, '0')}-${String(d.day).padStart(2, '0')}`;\n    } else if (e.tagName === 'RUNT' && decoded.kind === 'time') {\n      const t = decoded.value;\n      metadata.runTime = `${String(t.hour).padStart(2, '0')}:${String(t.minute).padStart(2, '0')}:${String(t.second).padStart(2, '0')}`;\n    } else if (e.tagName === 'CMNT' && decoded.kind === 'string') {\n      metadata.comments.push(decoded.value);\n    } else if (e.tagName === 'RevC' && e.tagNumber === 1) {\n      // RevC1 (int16): file's own flag for whether the sequence is already\n      // reverse-complemented. Only tagNumber 1 is defined by the spec. Reported\n      // as-is; we draw no conclusion from it.\n      if (decoded.kind === 'number') metadata.reverseComplemented = decoded.value !== 0;\n      else if (decoded.kind === 'numbers') metadata.reverseComplemented = decoded.value.some(v => v !== 0);\n    }\n  }\n\n  // Every basecall version the file carries, exactly as stored — the source of\n  // truth. Per-version PCON/PLOC are kept strictly (no cross-version borrowing):\n  // a variant reports only what its own tag number holds.\n  const baseCallVariants: AbifBaseCallVariant[] = Object.keys(pbas)\n    .map(Number)\n    .sort((a, b) => a - b)\n    .map(\n      (v): AbifBaseCallVariant => ({\n        version: v,\n        role: v === 1 ? 'edited' : v === 2 ? 'called' : 'unknown',\n        // As stored: case is preserved (lower-case can encode masking/edits). The\n        // uppercased convenience view lives on `baseCalls`, not here.\n        sequence: pbas[v],\n        confidences: pcon[v] ?? [],\n        positions: ploc[v] ?? [],\n      }),\n    );\n\n  // Basecalls: prefer PBAS2 (called) over PBAS1 (edited) — a spec-role choice. Test key\n  // presence, not string truthiness, so an existing-but-empty PBAS2 is still honored.\n  let baseCalls: AbifBaseCalls | undefined;\n  const pbasVersion = 2 in pbas ? 2 : 1 in pbas ? 1 : Object.keys(pbas).map(Number)[0];\n  if (pbasVersion !== undefined && pbas[pbasVersion] !== undefined) {\n    // Don't .trim(): keep length aligned with PCON/PLOC (trailing nulls already stripped).\n    const seq = pbas[pbasVersion].toUpperCase();\n    // Fall back to whichever PCON has a length matching the chosen PBAS — some\n    // files ship PCON only under one tagNumber even when PBAS exists under both.\n    // Fall back to whichever version's PCON/PLOC matches the chosen PBAS length — triggered when the\n    // preferred version's array is missing OR present-but-length-mismatched. Expose none rather than a\n    // broken array when nothing matches, so baseCalls stays self-consistent (baseCallVariants stays strict).\n    let confidences = pcon[pbasVersion] ?? [];\n    if (confidences.length !== seq.length) {\n      confidences =\n        Object.keys(pcon)\n          .map(Number)\n          .map(v => pcon[v])\n          .find(c => c.length === seq.length) ?? [];\n    }\n    let positions = ploc[pbasVersion] ?? [];\n    if (positions.length !== seq.length) {\n      positions =\n        Object.keys(ploc)\n          .map(Number)\n          .map(v => ploc[v])\n          .find(pp => pp.length === seq.length) ?? [];\n    }\n    baseCalls = { sequence: seq, confidences, positions, pbasVersion };\n  }\n\n  // SPAC fallback: derive from PLOC positions or DATA9 length when missing.\n  if (!Number.isFinite(metadata.samplingRate) || (metadata.samplingRate ?? 0) <= 0) {\n    const pos = baseCalls?.positions;\n    const data9Len = Math.max(data9To12.A.length, data9To12.C.length, data9To12.G.length, data9To12.T.length);\n    if (pos && pos.length > 1) {\n      metadata.samplingRate = (pos[pos.length - 1] - pos[0]) / (pos.length - 1);\n    } else if (baseCalls && baseCalls.sequence.length > 0 && data9Len > 0) {\n      metadata.samplingRate = data9Len / baseCalls.sequence.length;\n    }\n  }\n\n  const chromatogram: AbifChromatogramBundle = { baseOrder, dataChannels, data1To4, data9To12 };\n\n  return {\n    fileName,\n    fileSize: bytes.byteLength,\n    abifVersion: file.version,\n    macBinaryOffset: file.macBinaryOffset,\n    dirEntryCount: file.entries.length,\n    metadata,\n    chromatogram,\n    baseCalls,\n    baseCallVariants,\n    entries,\n  };\n}\n\n/** True when any channel has at least one signal value. */\nexport function hasSignals(s: ChannelSignals): boolean {\n  return s.A.length > 0 || s.C.length > 0 || s.G.length > 0 || s.T.length > 0;\n}\n\n/** Length of the longest channel in a ChannelSignals bundle. */\nexport function channelMaxLength(s: ChannelSignals): number {\n  return Math.max(s.A.length, s.C.length, s.G.length, s.T.length);\n}\n\n// Quiet unused-import for the AbifEntry type if it isn't reachable elsewhere.\nexport type { AbifEntry };\n","/**\n * Mutation helpers for AbifFile: write PBAS/PCON/PLOC/SPAC and ensure DATA9..12\n * are present. Used by basecallers to author ABIF output.\n */\n\nimport { findEntry, upsertEntry } from './abif-format';\nimport { asciiBytes, asDataView } from './bytes';\nimport { AbifFile } from './types';\nimport { hasData9To12Block } from './view';\n\n/** Set PBAS2 (replaces if present). */\nexport function setSequence(file: AbifFile, sequence: string): void {\n  upsertEntry(file, 'PBAS', 2, asciiBytes(sequence), {\n    elementType: 2, // char\n    elementSize: 1,\n    elementCount: sequence.length,\n  });\n}\n\n/** Set PCON2 (replaces if present). Values clamped to [0, 255]. */\nexport function setConfidences(file: AbifFile, q: ArrayLike<number>): void {\n  const buf = new Uint8Array(q.length);\n  for (let i = 0; i < q.length; i++) {\n    buf[i] = Math.max(0, Math.min(255, Math.round(q[i])));\n  }\n  upsertEntry(file, 'PCON', 2, buf, {\n    elementType: 2,\n    elementSize: 1,\n    elementCount: q.length,\n  });\n}\n\n/**\n * Set PLOC2 (replaces if present).\n *\n * Written as UNSIGNED int16 so positions up to 65535 are preserved on disk\n * (signed int16 would wrap on traces with > 32k scans).\n */\nexport function setPositions(file: AbifFile, positions: ArrayLike<number>): void {\n  const buf = new Uint8Array(positions.length * 2);\n  const view = asDataView(buf);\n  for (let i = 0; i < positions.length; i++) {\n    view.setUint16(i * 2, Math.max(0, Math.min(0xffff, positions[i])), false);\n  }\n  upsertEntry(file, 'PLOC', 2, buf, {\n    elementType: 4,\n    elementSize: 2,\n    elementCount: positions.length,\n  });\n}\n\n/**\n * Set SPAC/1, SPAC/2, SPAC/3 — the standard ABIF \"average peak spacing\" trio\n * that KB-basecaller writes and downstream tools (BioPython, Sequencher,\n * KB-aware viewers) expect:\n *\n *   - SPAC/1 (float32) — average peak spacing used in last analysis.\n *   - SPAC/2 (pString) — basecaller name / identifier.\n *   - SPAC/3 (float32) — average peak spacing computed by the basecaller.\n *\n * Both float fields are written with the same value.\n */\nexport function setAveragePeakSpacing(file: AbifFile, spacing: number, basecallerName: string): void {\n  const f1 = new Uint8Array(4);\n  asDataView(f1).setFloat32(0, spacing, false);\n  upsertEntry(file, 'SPAC', 1, f1, { elementType: 7, elementSize: 4, elementCount: 1 });\n\n  const nameBytes = asciiBytes(basecallerName);\n  const len = Math.min(255, nameBytes.length);\n  const p = new Uint8Array(1 + len);\n  p[0] = len;\n  p.set(nameBytes.subarray(0, len), 1);\n  upsertEntry(file, 'SPAC', 2, p, { elementType: 18, elementSize: 1, elementCount: 1 + len });\n\n  const f3 = new Uint8Array(4);\n  asDataView(f3).setFloat32(0, spacing, false);\n  upsertEntry(file, 'SPAC', 3, f3, { elementType: 7, elementSize: 4, elementCount: 1 });\n}\n\n/**\n * Mean consecutive peak-to-peak distance in scans, from a positions array.\n * Returns 0 when fewer than 2 positions are present.\n */\nexport function averagePeakSpacing(positions: ArrayLike<number>): number {\n  if (positions.length < 2) return 0;\n  return (positions[positions.length - 1] - positions[0]) / (positions.length - 1);\n}\n\n/**\n * Ensure DATA9..12 are present in the file. Many downstream consumers\n * (BioPython-style readers, viewers) read the chromatogram signal from\n * DATA9..12 by convention — these tags are the raw fluorescence on newer\n * instruments. Older files that only carry DATA1..8 break those consumers\n * with a \"no signal\" error after re-basecalling.\n *\n * We populate DATA9..12 by copying DATA1..4 (which on DATA1..8-only files IS\n * the raw signal). The DATA1..4 tags are left untouched so any tool that\n * reads them keeps working.\n *\n * No-op when DATA9..12 already exist.\n */\nexport function ensureRawDataChannels(file: AbifFile): void {\n  if (hasData9To12Block(file)) return;\n  for (let i = 1; i <= 4; i++) {\n    const src = findEntry(file, 'DATA', i);\n    if (!src) continue;\n    const target = 8 + i;\n    if (findEntry(file, 'DATA', target)) continue;\n    file.entries.push({\n      tagName: 'DATA',\n      tagNumber: target,\n      elementType: src.elementType,\n      elementSize: src.elementSize,\n      elementCount: src.elementCount,\n      payload: new Uint8Array(src.payload),\n      dataHandle: 0,\n    });\n  }\n}\n"]}

package/dist/index.d.mts

@@ -1,4 +1,4 @@
-export { AbifBaseCallRole, AbifBaseCallVariant, AbifBaseCalls, AbifByteRange, AbifChromatogramBundle, AbifDataChannelRole, AbifDecodedValue, AbifDirEntry, AbifDirectory, AbifEntry, AbifEntryRaw, AbifFile, AbifMetadata, ChannelSignals, Chromatogram, ENTRY_SIZE, HEADER_SIZE, ParsedAbif, averagePeakSpacing, channelMaxLength, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getDataChannel, getFwo, getPositions, getReverseComplemented, getSamplingRate, getSequence, hasData9To12Block, hasSignals, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif } from './abif/index.mjs';
+export { AbifBaseCallRole, AbifBaseCallVariant, AbifBaseCalls, AbifByteRange, AbifChromatogramBundle, AbifDataChannelRole, AbifDecodedValue, AbifDirEntry, AbifDirectory, AbifEntry, AbifEntryRaw, AbifFile, AbifMetadata, ChannelSignals, Chromatogram, CropAbifOptions, CropAbifRange, ENTRY_SIZE, HEADER_SIZE, ParsedAbif, averagePeakSpacing, channelMaxLength, cropAbif, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getConfidencesForVersion, getDataChannel, getFwo, getPositions, getPositionsForVersion, getReverseComplemented, getSamplingRate, getSequence, getSequenceForVersion, hasData9To12Block, hasSignals, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif } from './abif/index.mjs';
 
 /**
  * FASTA / FASTQ / .qual text serialization.

package/dist/index.d.ts

@@ -1,4 +1,4 @@
-export { AbifBaseCallRole, AbifBaseCallVariant, AbifBaseCalls, AbifByteRange, AbifChromatogramBundle, AbifDataChannelRole, AbifDecodedValue, AbifDirEntry, AbifDirectory, AbifEntry, AbifEntryRaw, AbifFile, AbifMetadata, ChannelSignals, Chromatogram, ENTRY_SIZE, HEADER_SIZE, ParsedAbif, averagePeakSpacing, channelMaxLength, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getDataChannel, getFwo, getPositions, getReverseComplemented, getSamplingRate, getSequence, hasData9To12Block, hasSignals, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif } from './abif/index.js';
+export { AbifBaseCallRole, AbifBaseCallVariant, AbifBaseCalls, AbifByteRange, AbifChromatogramBundle, AbifDataChannelRole, AbifDecodedValue, AbifDirEntry, AbifDirectory, AbifEntry, AbifEntryRaw, AbifFile, AbifMetadata, ChannelSignals, Chromatogram, CropAbifOptions, CropAbifRange, ENTRY_SIZE, HEADER_SIZE, ParsedAbif, averagePeakSpacing, channelMaxLength, cropAbif, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getConfidencesForVersion, getDataChannel, getFwo, getPositions, getPositionsForVersion, getReverseComplemented, getSamplingRate, getSequence, getSequenceForVersion, hasData9To12Block, hasSignals, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif } from './abif/index.js';
 
 /**
  * FASTA / FASTQ / .qual text serialization.

package/dist/index.js

@@ -1,12 +1,12 @@
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c=i.raw?.elementCount??i.elementCount,u=Math.max(0,c),d=r.getInt32(n+6+20,false);if(d<0||d+u*x>e.byteLength-n)throw new Error(`Directory out of bounds: offset=${d}, entries=${u}, file=${e.byteLength-n}`);let s=[];for(let E=0;E<u;E++)s.push(B(e,r,n+d+E*x,n));let g=i.raw?.dataSize??u*x,S=n+d+u*x,b=Math.min(Math.max(0,g-u*x),Math.max(0,e.byteLength-S)),h={entryCount:u,rawEntryCount:c,elementType:i.elementType,tagNumber:i.tagNumber,entrySize:i.elementSize,dataSize:g,dataOffset:d,dataOffsetBytes:i.raw?.dataOffsetBytes??new Uint8Array(4),dataHandle:i.dataHandle,paddingBytes:new Uint8Array(N(e,S,b))},y=new Uint8Array(N(e,n+6+x,v-6-x)),A=t===128?new Uint8Array(N(e,0,128)):void 0,C=G(e,n,d,g,s,t);return {version:a,tdir:h,entries:s,macBinaryOffset:t,macBinaryHeader:A,headerReserved:y,unreferencedRanges:C}}function G(e,t,n,r,a,i){let c=e.byteLength,u=[];i===128&&u.push([0,128]),u.push([t,t+v]);let d=Math.max(a.length*x,Math.max(0,r));u.push([t+n,t+n+d]);for(let h of a)if(h.raw&&!h.raw.inline){let 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