@fishka/seqio 0.1.0

package/dist/abif/index.d.ts

@@ -0,0 +1,370 @@
+/**
+ * Low-level ABIF file model: a flat list of directory entries with raw
+ * payloads. Lossless round-trip is preserved: every entry (including unknown
+ * vendor tags) is kept as a raw payload, so a subsequent writeAbif() reproduces
+ * the same meaning.
+ */
+interface AbifFile {
+    /** ABIF version, e.g. 101 for v1.01. */
+    version: number;
+    /** Directory entries in the original on-disk order. */
+    entries: AbifEntry[];
+    /** MacBinary preamble offset (128 if present, 0 otherwise). Preserved for diagnostics. */
+    macBinaryOffset: number;
+}
+interface AbifEntry {
+    /** 4-character tag name, e.g. "DATA", "PBAS". */
+    tagName: string;
+    /** Tag number, e.g. 1 or 2 for PBAS1 / PBAS2. */
+    tagNumber: number;
+    /** ABIF element type code (1=byte, 2=char, 3=word, 4=short, 5=long, 7=float,
+     *  8=double, 10=date, 11=time, 13=bool, 18=pString, 19=cString,
+     *  1023=tdir, ≥1024=user-defined). */
+    elementType: number;
+    /** Bytes per element. */
+    elementSize: number;
+    /** Number of elements. */
+    elementCount: number;
+    /** Raw payload bytes (length === elementCount * elementSize). */
+    payload: Uint8Array;
+    /** Opaque dataHandle field, usually 0. Preserved for round-trip. */
+    dataHandle: number;
+}
+interface ChannelSignals {
+    A: number[];
+    C: number[];
+    G: number[];
+    T: number[];
+}
+/** Per-base chromatogram view. */
+interface Chromatogram {
+    /** Per-base peak position in sample points (from PLOC). */
+    positions: number[];
+    /** Four channels of signal values, aligned with sample points. */
+    signals: ChannelSignals;
+    /** Per-base Phred-like quality scores (0..100), from PCON. */
+    confidences?: number[];
+    /** Average peak spacing (samples per base), from SPAC. */
+    samplingRate?: number;
+}
+/** Basecalls extracted from PBAS/PCON/PLOC under the chosen version. */
+interface AbifBaseCalls {
+    /** Called bases (uppercase). */
+    sequence: string;
+    /** Per-base Q-score / confidence (PCON). */
+    confidences: number[];
+    /** Per-base peak positions in sample points (PLOC). */
+    positions: number[];
+    /** Which PBAS version was selected (1 or 2). */
+    pbasVersion: number;
+}
+/** Optional metadata extracted from well-known tags. */
+interface AbifMetadata {
+    sampleName?: string;
+    laneNumber?: number;
+    tube?: string;
+    machineName?: string;
+    machineModel?: string;
+    runDate?: string;
+    runTime?: string;
+    samplingRate?: number;
+    comments: string[];
+}
+/** Full chromatogram bundle: all DATA channels, plus FWO_-aware A/C/G/T views. */
+interface AbifChromatogramBundle {
+    /** FWO_ value (e.g. "GATC"). */
+    baseOrder: string;
+    /** All DATA tags by tagNumber → trace. */
+    dataChannels: Record<number, number[]>;
+    /** Basecalled traces (DATA9..12) mapped to A/C/G/T by FWO_. */
+    basecalled: ChannelSignals;
+    /** Raw traces (DATA1..4) mapped to A/C/G/T by FWO_. */
+    raw: ChannelSignals;
+}
+/** Rich result from {@link parseAbif} — everything the typical viewer needs. */
+interface ParsedAbif {
+    fileName: string;
+    fileSize: number;
+    abifVersion: number;
+    macBinaryOffset: number;
+    dirEntryCount: number;
+    metadata: AbifMetadata;
+    chromatogram: AbifChromatogramBundle;
+    baseCalls?: AbifBaseCalls;
+    /** All directory entries with their decoded payloads (best-effort by type). */
+    entries: AbifDirEntry[];
+}
+/** A directory entry with a typed decoded value alongside the raw payload. */
+interface AbifDirEntry {
+    /** 4-character tag name, e.g. "DATA". */
+    tag: string;
+    tagNumber: number;
+    elementType: number;
+    elementTypeName: string;
+    elementSize: number;
+    elementCount: number;
+    dataSize: number;
+    dataOffset: number;
+    inline: boolean;
+    decoded: AbifDecodedValue;
+    preview: string;
+}
+type AbifDecodedValue = {
+    kind: 'number';
+    value: number;
+} | {
+    kind: 'numbers';
+    value: number[];
+} | {
+    kind: 'string';
+    value: string;
+} | {
+    kind: 'bools';
+    value: boolean[];
+} | {
+    kind: 'date';
+    value: {
+        year: number;
+        month: number;
+        day: number;
+    };
+} | {
+    kind: 'time';
+    value: {
+        hour: number;
+        minute: number;
+        second: number;
+        hsec: number;
+    };
+} | {
+    kind: 'bytes';
+    value: Uint8Array;
+} | {
+    kind: 'unknown';
+    value: Uint8Array;
+};
+
+declare function tagNameFromInt32(n: number): string;
+
+/**
+ * Low-level ABIF reader/writer.
+ *
+ * Round-trip without loss: every directory entry (including unknown vendor
+ * tags) is preserved as a raw payload (Uint8Array). The high-level layer
+ * (view.ts, parser.ts) provides typed access on top of this.
+ *
+ * ABIF file layout:
+ *   [0..3]      "ABIF" magic
+ *   [4..5]      version (int16 BE; 101 = v1.01)
+ *   [6..33]     TdirEntry describing the directory itself
+ *   [34..127]   reserved (94 bytes, zero-filled)
+ *   [...]       directory block (N * 28-byte entries) and payload blocks
+ *
+ * TdirEntry (28 bytes, big-endian):
+ *   off  size  field
+ *     0   4    tagName        (ASCII)
+ *     4   4    tagNumber      (int32)
+ *     8   2    elementType    (int16)
+ *    10   2    elementSize    (int16)
+ *    12   4    elementCount   (int32)
+ *    16   4    dataSize       (int32; total payload bytes; spec says count*size)
+ *    20   4    dataOffset     (int32) OR inline data if dataSize <= 4
+ *    24   4    dataHandle     (int32; usually 0)
+ *
+ * Inline rule (per ABIF spec): when count*size <= 4 the payload bytes are
+ * stored directly in the dataOffset field (left-aligned, padded to 4 bytes).
+ *
+ * MacBinary preamble: some ABIF files (older Mac-origin) start with a 128-byte
+ * MacBinary header before the actual ABIF magic. We detect and skip it.
+ */
+
+declare const HEADER_SIZE = 128;
+declare const ENTRY_SIZE = 28;
+/**
+ * Parse an ABIF file from raw bytes.
+ *
+ * Accepts Uint8Array (works in Node and the browser). Node's Buffer extends
+ * Uint8Array, so `readAbif(buffer)` and `readAbif(new Uint8Array(arrayBuffer))`
+ * both work.
+ *
+ * Throws if the magic header is missing. Does NOT require any specific tags
+ * (PBAS, DATA, ...) to be present — raw pre-basecalled files are supported.
+ */
+declare function readAbif(bytes: Uint8Array): AbifFile;
+/**
+ * Serialize an AbifFile back to a Uint8Array.
+ *
+ * Layout produced: header (128 B) + directory (N*28 B) + payload block.
+ * External payloads are packed tightly in entry order. Inline payloads
+ * (count*size <= 4) live entirely inside their directory entry.
+ *
+ * The output is not bit-identical to the input if the original had a different
+ * physical layout (e.g. payloads before directory), but the *meaning*
+ * round-trips: readAbif(writeAbif(f)) reproduces the same entries structurally.
+ *
+ * MacBinary preamble is not preserved by writeAbif.
+ */
+declare function writeAbif(file: AbifFile): Uint8Array;
+/** Find an entry by name+number, or undefined. */
+declare function findEntry(file: AbifFile, name: string, number: number): AbifEntry | undefined;
+/** Find all entries with the given tag name. */
+declare function findEntries(file: AbifFile, name: string): AbifEntry[];
+/**
+ * Replace the payload of an existing entry, or append a new one.
+ * elementType/elementSize/elementCount must be supplied for new entries.
+ */
+declare function upsertEntry(file: AbifFile, name: string, number: number, payload: Uint8Array, defaults: {
+    elementType: number;
+    elementSize: number;
+    elementCount: number;
+}): void;
+
+/**
+ * High-level typed view over an AbifFile.
+ *
+ * Reading helpers that interpret the raw payloads of well-known tags. For
+ * mutation helpers (setSequence, setConfidences, ...) see ./setters.
+ */
+
+/** Get DATA<n> as a signed-int16 array, or undefined. */
+declare function getDataChannel(file: AbifFile, n: number): Int16Array | undefined;
+/**
+ * Dye order, 4 ASCII chars (e.g. "GATC"). Defaults to "GATC" if FWO_ absent.
+ *
+ * GATC is the dye order produced by modern ABI 3730/3500 instruments and the
+ * dominant default in the wild. Older "ACGT" defaults caused channel
+ * mis-mapping on files where FWO_ is missing or malformed.
+ */
+declare function getFwo(file: AbifFile): string;
+/**
+ * True when the file carries BOTH DATA1..4 and DATA9..12. Newer ABI-style
+ * instruments produce both: DATA1..4 is post-processed (mobility-corrected,
+ * baseline-subtracted, color-separated) and DATA9..12 is raw fluorescence.
+ * Older instruments produce only DATA1..4 (which IS the raw signal).
+ *
+ * Callers that re-process traces (basecallers) should detect this and bypass
+ * their own baseline-subtraction / color-matrix steps when DATA1..4 is
+ * already cleaned.
+ */
+declare function hasProcessedTraces(file: AbifFile): boolean;
+/**
+ * Map from base letter ("A"|"C"|"G"|"T") to the DATA tag number that holds
+ * its RAW fluorescence channel.
+ *
+ * ABIF stores up to 12 DATA tags. KB-basecaller-aware instruments (3130, 3500,
+ * ...) use DATA1..4 for processed traces and DATA9..12 for raw. Older / simpler
+ * instruments produce only DATA1..8 where DATA1..4 ARE the raw traces.
+ *
+ * This helper always returns the DATA1..4 mapping (the convention used by
+ * basecallers operating on raw signal). Use {@link hasProcessedTraces} to
+ * detect whether DATA1..4 has been pre-processed and bypass baseline/color
+ * steps accordingly.
+ *
+ * The dye-to-channel order within each block is given by FWO_. If
+ * FWO_="GATC" then G→1, A→2, T→3, C→4.
+ */
+declare function getRawChannelMap(file: AbifFile): Record<'A' | 'C' | 'G' | 'T', number>;
+/** Get PBAS sequence (prefer PBAS2 over PBAS1). undefined if neither present. */
+declare function getSequence(file: AbifFile): string | undefined;
+/**
+ * Get per-base Phred-like quality scores (0..255 byte values, typically 0..60
+ * for Sanger). Prefers PCON2 over PCON1.
+ *
+ * PCON is declared in the ABIF spec as elementType=2 (char) but the byte
+ * values ARE the Q-scores — we read raw bytes regardless of declared type.
+ */
+declare function getConfidences(file: AbifFile): number[] | undefined;
+/**
+ * Get peak scan positions (one per base). Prefers PLOC2 over PLOC1.
+ *
+ * Read as UNSIGNED int16: PLOC indexes into the sample trace and is always
+ * non-negative, but values > 32767 (long traces) would wrap to negative
+ * if interpreted as signed.
+ */
+declare function getPositions(file: AbifFile): number[] | undefined;
+/**
+ * Get average peak spacing (samples per base), from SPAC/1.
+ *
+ * ABIF spec defines SPAC as float32 (elementType=7); some legacy files
+ * mislabel it as long (type=5). Both are 4 bytes and on disk the payload
+ * is always a 32-bit float, so we read as float regardless of declared type.
+ *
+ * Returns undefined if SPAC is absent or non-positive.
+ */
+declare function getSamplingRate(file: AbifFile): number | undefined;
+
+/**
+ * Mutation helpers for AbifFile: write PBAS/PCON/PLOC/SPAC and ensure DATA9..12
+ * are present. Used by basecallers to author ABIF output.
+ */
+
+/** Set PBAS2 (replaces if present). */
+declare function setSequence(file: AbifFile, sequence: string): void;
+/** Set PCON2 (replaces if present). Values clamped to [0, 255]. */
+declare function setConfidences(file: AbifFile, q: ArrayLike<number>): void;
+/**
+ * Set PLOC2 (replaces if present).
+ *
+ * Written as UNSIGNED int16 so positions up to 65535 are preserved on disk
+ * (signed int16 would wrap on traces with > 32k scans).
+ */
+declare function setPositions(file: AbifFile, positions: ArrayLike<number>): void;
+/**
+ * Set SPAC/1, SPAC/2, SPAC/3 — the standard ABIF "average peak spacing" trio
+ * that KB-basecaller writes and downstream tools (BioPython, Sequencher,
+ * KB-aware viewers) expect:
+ *
+ *   - SPAC/1 (float32) — average peak spacing used in last analysis.
+ *   - SPAC/2 (pString) — basecaller name / identifier.
+ *   - SPAC/3 (float32) — average peak spacing computed by the basecaller.
+ *
+ * Both float fields are written with the same value.
+ */
+declare function setAveragePeakSpacing(file: AbifFile, spacing: number, basecallerName: string): void;
+/**
+ * Mean consecutive peak-to-peak distance in scans, from a positions array.
+ * Returns 0 when fewer than 2 positions are present.
+ */
+declare function averagePeakSpacing(positions: ArrayLike<number>): number;
+/**
+ * Ensure DATA9..12 are present in the file. Many downstream consumers
+ * (BioPython-style readers, viewers) read the chromatogram signal from
+ * DATA9..12 by convention — these tags are the raw fluorescence on newer
+ * instruments. Older files that only carry DATA1..8 break those consumers
+ * with a "no signal" error after re-basecalling.
+ *
+ * We populate DATA9..12 by copying DATA1..4 (which on DATA1..8-only files IS
+ * the raw signal). The DATA1..4 tags are left untouched so any tool that
+ * reads them keeps working.
+ *
+ * No-op when DATA9..12 already exist.
+ */
+declare function ensureRawDataChannels(file: AbifFile): void;
+
+/**
+ * High-level "parse everything" wrapper around the raw + view layers.
+ *
+ * Returns a single ParsedAbif object with metadata, the FWO_-aware
+ * basecalled / raw channel split, basecalls, and decoded directory entries
+ * for diagnostics. Mirrors what typical viewers (chromatogram UIs, sample
+ * inspectors) need from a single file.
+ *
+ * For round-trip authoring (basecallers), prefer {@link readAbif} +
+ * setters from ./setters which operate directly on the raw AbifFile.
+ */
+
+/**
+ * Parse an ABIF file into a high-level view: metadata, channels, basecalls,
+ * and decoded directory entries.
+ *
+ * Accepts ArrayBuffer or Uint8Array (Buffer in Node works too — it extends
+ * Uint8Array). The `fileName` argument is informational only; it's preserved
+ * in the result.
+ */
+declare function parseAbif(input: ArrayBuffer | Uint8Array, fileName?: string): ParsedAbif;
+/** True when any channel has at least one signal value. */
+declare function hasSignals(s: ChannelSignals): boolean;
+/** Length of the longest channel in a ChannelSignals bundle. */
+declare function channelMaxLength(s: ChannelSignals): number;
+
+export { type AbifBaseCalls, type AbifChromatogramBundle, type AbifDecodedValue, type AbifDirEntry, type AbifEntry, type AbifFile, type AbifMetadata, type ChannelSignals, type Chromatogram, ENTRY_SIZE, HEADER_SIZE, type ParsedAbif, averagePeakSpacing, channelMaxLength, ensureRawDataChannels, findEntries, findEntry, getConfidences, getDataChannel, getFwo, getPositions, getRawChannelMap, getSamplingRate, getSequence, hasProcessedTraces, hasSignals, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif };

package/dist/abif/index.js

@@ -0,0 +1,2 @@
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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; spec says count*size)\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 count*size <= 4 the payload bytes are\n * 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 { 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.\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: ${bytes.byteLength} bytes`);\n  }\n\n  // MacBinary wrap support: skip 128 bytes if magic is at offset 128.\n  let macBinaryOffset = 0;\n  if (asciiString(subview(bytes, 0, 4)) !== 'ABIF') {\n    if (bytes.byteLength >= 128 + 4 && asciiString(subview(bytes, 128, 4)) === 'ABIF') {\n      macBinaryOffset = 128;\n    } else {\n      throw new Error('Not an ABIF file: missing \"ABIF\" magic.');\n    }\n  }\n  const base = macBinaryOffset;\n  const view = asDataView(bytes);\n\n  const version = view.getInt16(base + 4, false);\n\n  // Header bytes [base+6 .. base+34) are a TdirEntry describing the directory itself.\n  const dirEntry = decodeEntry(bytes, view, base + 6);\n  if (dirEntry.tagName !== 'tdir') {\n    throw new Error(`Expected \"tdir\" header entry, got \"${dirEntry.tagName}\"`);\n  }\n  if (dirEntry.elementSize !== ENTRY_SIZE) {\n    throw new Error(`Expected dir element size ${ENTRY_SIZE}, got ${dirEntry.elementSize}`);\n  }\n\n  const numEntries = dirEntry.elementCount;\n  // tdir.dataSize is always > 4 (28*N), so the dataOffset field is an external offset.\n  const dirOffset = view.getInt32(base + 6 + 20, false);\n  if (dirOffset < 0 || dirOffset + numEntries * ENTRY_SIZE > bytes.byteLength - base) {\n    throw new Error(\n      `Directory out of bounds: offset=${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));\n  }\n\n  return { version, entries, macBinaryOffset };\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 inline rule uses `elementCount * elementSize` (the structural size),\n *      not the declared `dataSize` field — they should agree, but the writer\n *      sometimes desynced them.\n *\n *   2. When the declared `dataSize` is smaller than `count*size`, trust the\n *      smaller value for payload reading. Some older instruments and edited\n *      files (e.g. BioPython A_forward.ab1) have `dataSize` set to the actual\n *      written size while `elementCount` was left at the original (larger)\n *      value, so reading the full count*size range would land in adjacent data.\n */\nfunction decodeEntry(bytes: Uint8Array, view: DataView, off: 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  const effectiveDataSize = Math.min(computedDataSize, Math.max(0, declaredDataSize));\n  // Inline is a structural property of the on-disk record: based on RAW count*size.\n  const inline = computedDataSize <= 4;\n  // For iteration we use the smaller of declared and computed, clamped to size\n  // boundaries, so we don't over-read past the real payload.\n  const elementCount =\n    elementSize > 0 && declaredDataSize >= 0 && declaredDataSize < computedDataSize\n      ? Math.floor(declaredDataSize / elementSize)\n      : rawElementCount;\n\n  let payload: Uint8Array;\n  if (inline) {\n    payload = new Uint8Array(subview(bytes, off + 20, effectiveDataSize));\n  } else {\n    const dataOffset = view.getInt32(off + 20, false);\n    if (dataOffset < 0 || dataOffset + effectiveDataSize > bytes.byteLength) {\n      throw new Error(\n        `Entry ${tagName}${tagNumber}: payload out of bounds (offset=${dataOffset}, size=${effectiveDataSize})`,\n      );\n    }\n    payload = new Uint8Array(subview(bytes, dataOffset, effectiveDataSize));\n  }\n\n  return { tagName, tagNumber, elementType, elementSize, elementCount, payload, dataHandle };\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. Inline payloads\n * (count*size <= 4) live entirely inside their directory entry.\n *\n * The output is not bit-identical to the input if the original had a different\n * physical layout (e.g. payloads before directory), but the *meaning*\n * round-trips: readAbif(writeAbif(f)) reproduces the same entries structurally.\n *\n * MacBinary preamble is not preserved by writeAbif.\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.\n  let payloadCursor = dirOffset + dirSize;\n  const externalOffsets: number[] = new Array(numEntries);\n  for (let i = 0; i < numEntries; i++) {\n    const e = file.entries[i];\n    const dataSize = e.elementCount * e.elementSize;\n    if (e.payload.byteLength !== dataSize) {\n      throw new Error(\n        `Entry ${e.tagName}${e.tagNumber}: payload length ${e.payload.byteLength} != dataSize ${dataSize}`,\n      );\n    }\n    if (dataSize > 4) {\n      externalOffsets[i] = payloadCursor;\n      payloadCursor += dataSize;\n    } else {\n      externalOffsets[i] = -1; // inline\n    }\n  }\n\n  const totalSize = payloadCursor;\n  const out = new Uint8Array(totalSize);\n  const outView = asDataView(out);\n\n  // Header: \"ABIF\" + version (int16 BE) + tdir entry + zeros.\n  out.set(asciiBytes('ABIF'), 0);\n  outView.setInt16(4, file.version, false);\n  // The tdir entry's dataOffset is the directory offset (explicit, not from\n  // the AbifEntry payload — the tdir is structural).\n  writeEntry(\n    {\n      tagName: 'tdir',\n      tagNumber: 1,\n      elementType: 1023,\n      elementSize: ENTRY_SIZE,\n      elementCount: numEntries,\n      payload: new Uint8Array(0),\n      dataHandle: 0,\n    },\n    out,\n    outView,\n    6,\n    /* externalOffset */ -1,\n    /* externalDataSize */ dirSize,\n    /* explicitDirOffset */ dirOffset,\n  );\n\n  // Directory entries.\n  for (let i = 0; i < numEntries; i++) {\n    const e = file.entries[i];\n    writeEntry(e, out, outView, dirOffset + i * ENTRY_SIZE, externalOffsets[i]);\n  }\n\n  // Payload block.\n  for (let i = 0; i < numEntries; i++) {\n    const off = externalOffsets[i];\n    if (off >= 0) {\n      out.set(file.entries[i].payload, off);\n    }\n  }\n\n  return out;\n}\n\nfunction writeEntry(\n  e: AbifEntry,\n  out: Uint8Array,\n  outView: DataView,\n  off: number,\n  externalOffset: number,\n  externalDataSize?: number,\n  explicitDirOffset?: number,\n): void {\n  if (e.tagName.length !== 4) {\n    throw new Error(`tagName must be 4 chars: \"${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.elementCount * e.elementSize;\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 ${payload.byteLength} != count*size`,\n    );\n  }\n  const existing = findEntry(file, name, number);\n  if (existing) {\n    existing.elementType = defaults.elementType;\n    existing.elementSize = defaults.elementSize;\n    existing.elementCount = defaults.elementCount;\n    existing.payload = payload;\n  } else {\n    file.entries.push({\n      tagName: name,\n      tagNumber: number,\n      elementType: defaults.elementType,\n      elementSize: defaults.elementSize,\n      elementCount: defaults.elementCount,\n      payload,\n      dataHandle: 0,\n    });\n  }\n}\n\n/** Re-export for users who want to interpret raw tag bytes themselves. */\nexport { tagNameFromInt32 };\n","/**\n * High-level typed view over an AbifFile.\n *\n * Reading helpers that interpret the raw payloads of well-known tags. For\n * mutation helpers (setSequence, setConfidences, ...) see ./setters.\n */\n\nimport { asciiString, asDataView } from './bytes';\nimport { findEntry } from './raw';\nimport { AbifFile } from './types';\n\n/** Get DATA<n> as a signed-int16 array, or undefined. */\nexport function getDataChannel(file: AbifFile, n: number): Int16Array | undefined {\n  const e = findEntry(file, 'DATA', n);\n  if (!e) return undefined;\n  if (e.elementSize !== 2) {\n    throw new Error(`DATA${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  return asciiString(e.payload);\n}\n\n/**\n * True when the file carries BOTH DATA1..4 and DATA9..12. Newer ABI-style\n * instruments produce both: DATA1..4 is post-processed (mobility-corrected,\n * baseline-subtracted, color-separated) and DATA9..12 is raw fluorescence.\n * Older instruments produce only DATA1..4 (which IS the raw signal).\n *\n * Callers that re-process traces (basecallers) should detect this and bypass\n * their own baseline-subtraction / color-matrix steps when DATA1..4 is\n * already cleaned.\n */\nexport function hasProcessedTraces(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 * Map from base letter (\"A\"|\"C\"|\"G\"|\"T\") to the DATA tag number that holds\n * its RAW fluorescence channel.\n *\n * ABIF stores up to 12 DATA tags. KB-basecaller-aware instruments (3130, 3500,\n * ...) use DATA1..4 for processed traces and DATA9..12 for raw. Older / simpler\n * instruments produce only DATA1..8 where DATA1..4 ARE the raw traces.\n *\n * This helper always returns the DATA1..4 mapping (the convention used by\n * basecallers operating on raw signal). Use {@link hasProcessedTraces} to\n * detect whether DATA1..4 has been pre-processed and bypass baseline/color\n * steps accordingly.\n *\n * The dye-to-channel order within each block is given by FWO_. If\n * FWO_=\"GATC\" then G→1, A→2, T→3, C→4.\n */\nexport function getRawChannelMap(file: AbifFile): Record<'A' | 'C' | 'G' | 'T', number> {\n  const fwo = getFwo(file);\n  if (!/^[ACGT]{4}$/.test(fwo)) {\n    throw new Error(`FWO_ malformed: \"${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  const e2 = findEntry(file, 'PBAS', 2);\n  if (e2) return asciiString(e2.payload);\n  const e1 = findEntry(file, 'PBAS', 1);\n  if (e1) return asciiString(e1.payload);\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 { hasProcessedTraces } 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 (hasProcessedTraces(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 * basecalled / raw 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 } from './view';\nimport {\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/**\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      const arr: number[] = [];\n      for (let i = 0; i < elementCount; i++) arr.push(view.getUint16(i * 2, false));\n      return arr.length === 1 ? { kind: 'number', value: arr[0] } : { kind: 'numbers', value: arr };\n    }\n    case 4: {\n      const arr: number[] = [];\n      for (let i = 0; i < elementCount; i++) arr.push(view.getInt16(i * 2, false));\n      return arr.length === 1 ? { kind: 'number', value: arr[0] } : { kind: 'numbers', value: arr };\n    }\n    case 5: {\n      const arr: number[] = [];\n      for (let i = 0; i < elementCount; i++) arr.push(view.getInt32(i * 4, false));\n      return arr.length === 1 ? { kind: 'number', value: arr[0] } : { kind: 'numbers', value: arr };\n    }\n    case 7: {\n      const arr: number[] = [];\n      for (let i = 0; i < elementCount; i++) arr.push(view.getFloat32(i * 4, false));\n      return arr.length === 1 ? { kind: 'number', value: arr[0] } : { kind: 'numbers', value: arr };\n    }\n    case 8: {\n      const arr: number[] = [];\n      for (let i = 0; i < elementCount; i++) arr.push(view.getFloat64(i * 8, false));\n      return arr.length === 1 ? { kind: 'number', value: arr[0] } : { kind: 'numbers', value: arr };\n    }\n    case 10: {\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      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 < elementCount; i++) arr.push(view.getUint8(i) !== 0);\n      return { kind: 'bools', value: arr };\n    }\n    case 18: {\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)} ${previewBytes(d.value)}`;\n  }\n}\n\n/**\n * Parse an ABIF file into a high-level view: metadata, channels, basecalls,\n * and decoded directory entries.\n *\n * Accepts ArrayBuffer or Uint8Array (Buffer in Node works too — it extends\n * Uint8Array). The `fileName` argument is informational only; it's preserved\n * in the result.\n */\nexport function parseAbif(input: ArrayBuffer | Uint8Array, fileName = ''): ParsedAbif {\n  const bytes = input instanceof Uint8Array ? input : new Uint8Array(input);\n  const file = readAbif(bytes);\n\n  const entries: AbifDirEntry[] = file.entries.map(e => {\n    const decoded = decodePayload(e.elementType, e.elementCount, e.payload);\n    return {\n      tag: e.tagName,\n      tagNumber: e.tagNumber,\n      elementType: e.elementType,\n      elementTypeName: typeName(e.elementType),\n      elementSize: e.elementSize,\n      elementCount: e.elementCount,\n      dataSize: e.elementCount * e.elementSize,\n      // Effective offset within the file is not tracked here (we already\n      // resolved it during read); inline detection uses the structural rule.\n      dataOffset: 0,\n      inline: e.elementCount * e.elementSize <= 4,\n      decoded,\n      preview: previewDecoded(decoded, e.elementType),\n    };\n  });\n\n  // FWO_ → base order.\n  let baseOrder = getFwo(file);\n  if (!/^[ACGT]{4}$/.test(baseOrder)) baseOrder = 'GATC';\n\n  const dataChannels: Record<number, number[]> = {};\n  const basecalled: ChannelSignals = { A: [], C: [], G: [], T: [] };\n  const raw: 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' && decoded.kind === 'numbers') {\n      dataChannels[e.tagNumber] = decoded.value;\n      if (e.tagNumber >= 1 && e.tagNumber <= 4) raw[channelKey(e.tagNumber - 1)] = decoded.value;\n      else if (e.tagNumber >= 9 && e.tagNumber <= 12) basecalled[channelKey(e.tagNumber - 9)] = decoded.value;\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 stored as elementType=2 (char) — char codes ARE the values.\n      if (decoded.kind === 'numbers') pcon[e.tagNumber] = decoded.value;\n      else if (decoded.kind === 'string') {\n        pcon[e.tagNumber] = Array.from(decoded.value, c => c.charCodeAt(0));\n      }\n    } else if (e.tagName === 'PLOC' && decoded.kind === 'numbers') {\n      // PLOC sample indices are always non-negative — reinterpret int16 as uint16.\n      ploc[e.tagNumber] = decoded.value.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    }\n  }\n\n  // Basecalls: prefer PBAS2 (BioPython convention).\n  let baseCalls: AbifBaseCalls | undefined;\n  const pbasVersion = pbas[2] ? 2 : pbas[1] ? 1 : Object.keys(pbas).map(Number)[0];\n  if (pbasVersion !== undefined && pbas[pbasVersion]) {\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    let confidences = pcon[pbasVersion] ?? [];\n    if (confidences.length === 0) {\n      for (const v of Object.keys(pcon).map(Number)) {\n        if (pcon[v].length === seq.length) {\n          confidences = pcon[v];\n          break;\n        }\n      }\n    }\n    let positions = ploc[pbasVersion] ?? [];\n    if (positions.length === 0) {\n      for (const v of Object.keys(ploc).map(Number)) {\n        if (ploc[v].length === seq.length) {\n          positions = ploc[v];\n          break;\n        }\n      }\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      basecalled.A.length,\n      basecalled.C.length,\n      basecalled.G.length,\n      basecalled.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, basecalled, raw };\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    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"]}

package/dist/abif/index.mjs

@@ -0,0 +1,2 @@
+function y(e){let t="";for(let n=0;n<e.length;n++)t+=String.fromCharCode(e[n]);return t}function x(e){let t=new Uint8Array(e.length);for(let n=0;n<e.length;n++)t[n]=e.charCodeAt(n)&255;return t}function p(e){return new DataView(e.buffer,e.byteOffset,e.byteLength)}function C(e,t,n){return e.subarray(t,t+n)}function P(e){return String.fromCharCode(e>>>24&255,e>>>16&255,e>>>8&255,e&255)}var F=128,w=28;function U(e){if(e.byteLength<F)throw new Error(`ABIF too small: ${e.byteLength} bytes`);let t=0;if(y(C(e,0,4))!=="ABIF")if(e.byteLength>=132&&y(C(e,128,4))==="ABIF")t=128;else throw new Error('Not an ABIF file: missing "ABIF" magic.');let n=t,r=p(e),a=r.getInt16(n+4,false),i=k(e,r,n+6);if(i.tagName!=="tdir")throw new Error(`Expected "tdir" header entry, got "${i.tagName}"`);if(i.elementSize!==w)throw new Error(`Expected dir element size ${w}, got ${i.elementSize}`);let c=i.elementCount,m=r.getInt32(n+6+20,false);if(m<0||m+c*w>e.byteLength-n)throw new Error(`Directory out of bounds: 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oe(e,t){let n=new Uint8Array(t.length);for(let r=0;r<t.length;r++)n[r]=Math.max(0,Math.min(255,Math.round(t[r])));v(e,"PCON",2,n,{elementType:2,elementSize:1,elementCount:t.length});}function se(e,t){let n=new Uint8Array(t.length*2),r=p(n);for(let a=0;a<t.length;a++)r.setUint16(a*2,Math.max(0,Math.min(65535,t[a])),false);v(e,"PLOC",2,n,{elementType:4,elementSize:2,elementCount:t.length});}function le(e,t,n){let r=new Uint8Array(4);p(r).setFloat32(0,t,false),v(e,"SPAC",1,r,{elementType:7,elementSize:4,elementCount:1});let a=x(n),i=Math.min(255,a.length),c=new Uint8Array(1+i);c[0]=i,c.set(a.subarray(0,i),1),v(e,"SPAC",2,c,{elementType:18,elementSize:1,elementCount:1+i});let m=new Uint8Array(4);p(m).setFloat32(0,t,false),v(e,"SPAC",3,m,{elementType:7,elementSize:4,elementCount:1});}function ue(e){return e.length<2?0:(e[e.length-1]-e[0])/(e.length-1)}function me(e){if(!I(e))for(let t=1;t<=4;t++){let n=d(e,"DATA",t);if(!n)continue;let 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