@fishka/seqio 0.5.0 → 0.6.1

package/dist/abif/index.d.mts

@@ -390,8 +390,23 @@ declare function findEntry(file: AbifFile, name: string, number: number): AbifEn
 /** 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.
+ * Insert a new entry at the slot that keeps the directory sorted by
+ * (tagName, tagNumber) — the order genuine ABI instruments emit and the ABIF
+ * spec prescribes. Readers that binary-search the directory (e.g. Chromas)
+ * silently miss a tag appended out of order — a re-basecalled file loses its
+ * quality bars because PCON2 is not found. Existing entries are never reordered,
+ * so an unmodified file still round-trips byte-exact; only the freshly added tag
+ * lands in its sorted place.
+ *
+ * Prefer {@link upsertEntry}; use this directly only to add an entry whose
+ * payload intentionally desyncs from `elementCount * elementSize` (e.g. copying
+ * a tolerated malformed record verbatim), which upsertEntry rejects.
+ */
+declare function insertEntrySorted(entries: AbifEntry[], entry: AbifEntry): void;
+/**
+ * Replace the payload of an existing entry, or insert a new one in sorted
+ * directory order. elementType/elementSize/elementCount must be supplied for
+ * new entries.
  *
  * This is the required way to mutate an entry read from a file — it clears `.raw`
  * on replacement so writeAbif() never reuses a now-stale on-disk shape. Setting
@@ -404,6 +419,55 @@ declare function upsertEntry(file: AbifFile, name: string, number: number, paylo
     elementCount: number;
 }): void;
 
+/**
+ * Domain-layer operation: crop an ABIF file to a sample range.
+ *
+ * `{ start, end }` is a half-open sample range in the DATA9..12 (processed/analyzed)
+ * domain — the only domain PLOC maps into (see AGENTS.md's "raw vs processed" note).
+ * DATA9..12 are sliced exactly by that range. DATA1..4/5..8 (raw dye trace and
+ * instrument telemetry) have no honest sample-for-sample correspondence to the
+ * processed domain (the mapping is non-linear mobility correction, not stored in the
+ * file), so they are never approximated: `rawTrace` keeps them whole and untouched,
+ * or omits them, never a proportional slice.
+ *
+ * Every basecall version the file carries (PBAS1/PCON1/PLOC1 "edited",
+ * PBAS2/PCON2/PLOC2 "called", or any vendor version) is cropped independently by its
+ * OWN PLOC — two versions are not guaranteed to share base positions or even length
+ * (edits insert/delete bases), so there is no shared coordinate to crop them together
+ * by. A version with no PLOC of its own cannot be cropped and is rejected rather than
+ * silently dropped or left un-cropped.
+ *
+ * Everything else (metadata, FWO_, SPAC, ...) is carried over untouched — this is a
+ * structural crop, not a re-derivation of run metadata for the new region.
+ *
+ * Reverse-complement is out of scope here; this function has no RC option.
+ *
+ * Returns a new, independently mutable AbifFile — the input is not mutated, and
+ * neither is the output if the input is later touched. Untouched entries are
+ * shallow-copied (a new AbifEntry object; the underlying payload bytes are shared,
+ * which is safe since nothing ever mutates payload bytes in place — only replaces
+ * them wholesale), so a later upsertEntry() on either file's copy of a shared tag
+ * can't reach into the other file's entries.
+ */
+
+interface CropAbifRange {
+    /** Inclusive start sample index into DATA9..12. */
+    start: number;
+    /** Exclusive end sample index into DATA9..12. */
+    end: number;
+}
+interface CropAbifOptions {
+    /**
+     * DATA1..4 (raw dye trace) and DATA5..8 (telemetry): 'full' keeps them whole and
+     * untouched (the exported file's raw trace no longer lines up sample-for-sample
+     * with the cropped DATA9..12/PLOC, by design — see the module doc comment);
+     * 'omit' drops them from the output entirely. Default 'omit'.
+     */
+    rawTrace?: 'full' | 'omit';
+}
+/** Crop an AbifFile to a DATA9..12 sample range. See the module doc comment for the model. */
+declare function cropAbif(file: AbifFile, range: CropAbifRange, options?: CropAbifOptions): AbifFile;
+
 /**
  * High-level "parse everything" wrapper around the raw + view layers.
  *
@@ -544,6 +608,12 @@ declare function getReverseComplemented(file: AbifFile): boolean | undefined;
 declare function getChannelMap(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 PBAS<version> exactly as stored — no called/edited preference, unlike
+ * {@link getSequence}. Used where each basecall version must be handled on its
+ * own (e.g. cropping every version a file carries, not just the preferred one).
+ */
+declare function getSequenceForVersion(file: AbifFile, version: number): string | undefined;
 /**
  * Get per-base Phred-like quality scores (0..255 byte values, typically 0..60
  * for Sanger). Prefers PCON2 over PCON1.
@@ -552,6 +622,11 @@ declare function getSequence(file: AbifFile): string | undefined;
  * values ARE the Q-scores — we read raw bytes regardless of declared type.
  */
 declare function getConfidences(file: AbifFile): number[] | undefined;
+/**
+ * Get PCON<version> exactly as stored — no called/edited preference, unlike
+ * {@link getConfidences}. See {@link getSequenceForVersion} for why this exists.
+ */
+declare function getConfidencesForVersion(file: AbifFile, version: number): number[] | undefined;
 /**
  * Get peak scan positions (one per base). Prefers PLOC2 over PLOC1.
  *
@@ -560,6 +635,11 @@ declare function getConfidences(file: AbifFile): number[] | undefined;
  * if interpreted as signed.
  */
 declare function getPositions(file: AbifFile): number[] | undefined;
+/**
+ * Get PLOC<version> exactly as stored — no called/edited preference, unlike
+ * {@link getPositions}. See {@link getSequenceForVersion} for why this exists.
+ */
+declare function getPositionsForVersion(file: AbifFile, version: number): number[] | undefined;
 /**
  * Get average peak spacing (samples per base), from SPAC/1.
  *
@@ -571,4 +651,4 @@ declare function getPositions(file: AbifFile): number[] | undefined;
  */
 declare function getSamplingRate(file: AbifFile): number | undefined;
 
-export { type AbifBaseCallRole, type AbifBaseCallVariant, type AbifBaseCalls, type AbifByteRange, type AbifChromatogramBundle, type AbifDataChannelRole, type AbifDecodedValue, type AbifDirEntry, type AbifDirectory, type AbifEntry, type AbifEntryRaw, type AbifFile, type AbifMetadata, type ChannelSignals, type Chromatogram, ENTRY_SIZE, HEADER_SIZE, type 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 };
+export { type AbifBaseCallRole, type AbifBaseCallVariant, type AbifBaseCalls, type AbifByteRange, type AbifChromatogramBundle, type AbifDataChannelRole, type AbifDecodedValue, type AbifDirEntry, type AbifDirectory, type AbifEntry, type AbifEntryRaw, type AbifFile, type AbifMetadata, type ChannelSignals, type Chromatogram, type CropAbifOptions, type CropAbifRange, ENTRY_SIZE, HEADER_SIZE, type ParsedAbif, averagePeakSpacing, channelMaxLength, cropAbif, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getConfidencesForVersion, getDataChannel, getFwo, getPositions, getPositionsForVersion, getReverseComplemented, getSamplingRate, getSequence, getSequenceForVersion, hasData9To12Block, hasSignals, insertEntrySorted, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif };

package/dist/abif/index.d.ts

@@ -390,8 +390,23 @@ declare function findEntry(file: AbifFile, name: string, number: number): AbifEn
 /** 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.
+ * Insert a new entry at the slot that keeps the directory sorted by
+ * (tagName, tagNumber) — the order genuine ABI instruments emit and the ABIF
+ * spec prescribes. Readers that binary-search the directory (e.g. Chromas)
+ * silently miss a tag appended out of order — a re-basecalled file loses its
+ * quality bars because PCON2 is not found. Existing entries are never reordered,
+ * so an unmodified file still round-trips byte-exact; only the freshly added tag
+ * lands in its sorted place.
+ *
+ * Prefer {@link upsertEntry}; use this directly only to add an entry whose
+ * payload intentionally desyncs from `elementCount * elementSize` (e.g. copying
+ * a tolerated malformed record verbatim), which upsertEntry rejects.
+ */
+declare function insertEntrySorted(entries: AbifEntry[], entry: AbifEntry): void;
+/**
+ * Replace the payload of an existing entry, or insert a new one in sorted
+ * directory order. elementType/elementSize/elementCount must be supplied for
+ * new entries.
  *
  * This is the required way to mutate an entry read from a file — it clears `.raw`
  * on replacement so writeAbif() never reuses a now-stale on-disk shape. Setting
@@ -404,6 +419,55 @@ declare function upsertEntry(file: AbifFile, name: string, number: number, paylo
     elementCount: number;
 }): void;
 
+/**
+ * Domain-layer operation: crop an ABIF file to a sample range.
+ *
+ * `{ start, end }` is a half-open sample range in the DATA9..12 (processed/analyzed)
+ * domain — the only domain PLOC maps into (see AGENTS.md's "raw vs processed" note).
+ * DATA9..12 are sliced exactly by that range. DATA1..4/5..8 (raw dye trace and
+ * instrument telemetry) have no honest sample-for-sample correspondence to the
+ * processed domain (the mapping is non-linear mobility correction, not stored in the
+ * file), so they are never approximated: `rawTrace` keeps them whole and untouched,
+ * or omits them, never a proportional slice.
+ *
+ * Every basecall version the file carries (PBAS1/PCON1/PLOC1 "edited",
+ * PBAS2/PCON2/PLOC2 "called", or any vendor version) is cropped independently by its
+ * OWN PLOC — two versions are not guaranteed to share base positions or even length
+ * (edits insert/delete bases), so there is no shared coordinate to crop them together
+ * by. A version with no PLOC of its own cannot be cropped and is rejected rather than
+ * silently dropped or left un-cropped.
+ *
+ * Everything else (metadata, FWO_, SPAC, ...) is carried over untouched — this is a
+ * structural crop, not a re-derivation of run metadata for the new region.
+ *
+ * Reverse-complement is out of scope here; this function has no RC option.
+ *
+ * Returns a new, independently mutable AbifFile — the input is not mutated, and
+ * neither is the output if the input is later touched. Untouched entries are
+ * shallow-copied (a new AbifEntry object; the underlying payload bytes are shared,
+ * which is safe since nothing ever mutates payload bytes in place — only replaces
+ * them wholesale), so a later upsertEntry() on either file's copy of a shared tag
+ * can't reach into the other file's entries.
+ */
+
+interface CropAbifRange {
+    /** Inclusive start sample index into DATA9..12. */
+    start: number;
+    /** Exclusive end sample index into DATA9..12. */
+    end: number;
+}
+interface CropAbifOptions {
+    /**
+     * DATA1..4 (raw dye trace) and DATA5..8 (telemetry): 'full' keeps them whole and
+     * untouched (the exported file's raw trace no longer lines up sample-for-sample
+     * with the cropped DATA9..12/PLOC, by design — see the module doc comment);
+     * 'omit' drops them from the output entirely. Default 'omit'.
+     */
+    rawTrace?: 'full' | 'omit';
+}
+/** Crop an AbifFile to a DATA9..12 sample range. See the module doc comment for the model. */
+declare function cropAbif(file: AbifFile, range: CropAbifRange, options?: CropAbifOptions): AbifFile;
+
 /**
  * High-level "parse everything" wrapper around the raw + view layers.
  *
@@ -544,6 +608,12 @@ declare function getReverseComplemented(file: AbifFile): boolean | undefined;
 declare function getChannelMap(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 PBAS<version> exactly as stored — no called/edited preference, unlike
+ * {@link getSequence}. Used where each basecall version must be handled on its
+ * own (e.g. cropping every version a file carries, not just the preferred one).
+ */
+declare function getSequenceForVersion(file: AbifFile, version: number): string | undefined;
 /**
  * Get per-base Phred-like quality scores (0..255 byte values, typically 0..60
  * for Sanger). Prefers PCON2 over PCON1.
@@ -552,6 +622,11 @@ declare function getSequence(file: AbifFile): string | undefined;
  * values ARE the Q-scores — we read raw bytes regardless of declared type.
  */
 declare function getConfidences(file: AbifFile): number[] | undefined;
+/**
+ * Get PCON<version> exactly as stored — no called/edited preference, unlike
+ * {@link getConfidences}. See {@link getSequenceForVersion} for why this exists.
+ */
+declare function getConfidencesForVersion(file: AbifFile, version: number): number[] | undefined;
 /**
  * Get peak scan positions (one per base). Prefers PLOC2 over PLOC1.
  *
@@ -560,6 +635,11 @@ declare function getConfidences(file: AbifFile): number[] | undefined;
  * if interpreted as signed.
  */
 declare function getPositions(file: AbifFile): number[] | undefined;
+/**
+ * Get PLOC<version> exactly as stored — no called/edited preference, unlike
+ * {@link getPositions}. See {@link getSequenceForVersion} for why this exists.
+ */
+declare function getPositionsForVersion(file: AbifFile, version: number): number[] | undefined;
 /**
  * Get average peak spacing (samples per base), from SPAC/1.
  *
@@ -571,4 +651,4 @@ declare function getPositions(file: AbifFile): number[] | undefined;
  */
 declare function getSamplingRate(file: AbifFile): number | undefined;
 
-export { type AbifBaseCallRole, type AbifBaseCallVariant, type AbifBaseCalls, type AbifByteRange, type AbifChromatogramBundle, type AbifDataChannelRole, type AbifDecodedValue, type AbifDirEntry, type AbifDirectory, type AbifEntry, type AbifEntryRaw, type AbifFile, type AbifMetadata, type ChannelSignals, type Chromatogram, ENTRY_SIZE, HEADER_SIZE, type 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 };
+export { type AbifBaseCallRole, type AbifBaseCallVariant, type AbifBaseCalls, type AbifByteRange, type AbifChromatogramBundle, type AbifDataChannelRole, type AbifDecodedValue, type AbifDirEntry, type AbifDirectory, type AbifEntry, type AbifEntryRaw, type AbifFile, type AbifMetadata, type ChannelSignals, type Chromatogram, type CropAbifOptions, type CropAbifRange, ENTRY_SIZE, HEADER_SIZE, type ParsedAbif, averagePeakSpacing, channelMaxLength, cropAbif, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getConfidencesForVersion, getDataChannel, getFwo, getPositions, getPositionsForVersion, getReverseComplemented, getSamplingRate, getSequence, getSequenceForVersion, hasData9To12Block, hasSignals, insertEntrySorted, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif };

package/dist/abif/index.js

@@ -1,2 +1,2 @@
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