@fishka/seqio 0.1.0

package/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

package/README.md

@@ -0,0 +1,62 @@
+# @fishka/seqio
+
+Sequencing I/O — parsers and writers for bioinformatics file formats.
+
+Currently supports:
+
+- **ABIF** (`.ab1` / `.abi`) — chromatogram traces produced by ABI Sanger / fragment analysis instruments. Lossless round-trip, browser- and Node-compatible.
+
+Planned: SCF, FASTA, FASTQ.
+
+## Install
+
+```sh
+npm install @fishka/seqio
+```
+
+## Use
+
+### Quick parse (typed view + metadata)
+
+```ts
+import { parseAbif } from '@fishka/seqio/abif';
+// or: import { parseAbif } from '@fishka/seqio';
+
+const result = parseAbif(uint8ArrayOrArrayBuffer, 'sample.ab1');
+
+result.baseCalls?.sequence;       // "ACGT..."
+result.baseCalls?.confidences;    // [40, 38, 41, ...]
+result.baseCalls?.positions;      // [13, 25, 38, ...] sample-point peaks
+result.chromatogram.basecalled.A; // raw int16 trace for the A channel
+result.metadata.sampleName;       // SMPL tag
+result.metadata.samplingRate;     // SPAC tag (falls back to PLOC-derived spacing)
+```
+
+### Low-level (entry-by-entry, round-trip)
+
+```ts
+import { readAbif, writeAbif, findEntry, upsertEntry } from '@fishka/seqio/abif';
+import { setSequence, setConfidences, setPositions, setAveragePeakSpacing } from '@fishka/seqio/abif';
+
+const file = readAbif(bytes);
+setSequence(file, 'ACGT...');
+setConfidences(file, [40, 38, 41, ...]);
+setPositions(file, [13, 25, 38, ...]);
+setAveragePeakSpacing(file, 12.5, 'my-basecaller');
+const out = writeAbif(file);
+```
+
+## Features
+
+- Browser- and Node-compatible (Uint8Array + DataView, no Node Buffer dependency).
+- Lossless round-trip: every directory entry preserved as raw payload.
+- MacBinary preamble support.
+- BioPython-compatible declared-vs-computed dataSize clamp.
+- PLOC read/written as unsigned int16 (preserves traces > 32k scans).
+- SPAC accepts both float32 (spec) and long (legacy) element types.
+- PCON/PLOC version fallback when PBAS2 ships without matching PCON2/PLOC2.
+- `ensureRawDataChannels()` helper for older DATA1..8-only files.
+
+## License
+
+MIT

package/dist/abif/index.d.mts

@@ -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 };