@gmod/bam 8.5.1 → 8.6.0

package/esm/record.d.ts

@@ -1,3 +1,5 @@
+import type { Mismatch, MismatchCallback, MismatchOptions } from './mismatches.ts';
+import type { PackedReference } from './reference.ts';
 export type NumericCigar = Uint32Array | Int32Array | number[];
 export default class BamRecord {
     fileOffset: number;
@@ -11,6 +13,7 @@ export default class BamRecord {
     private _cachedNumericCigar?;
     private _cachedNUMERIC_MD?;
     private _cachedSeqStart?;
+    private _reference?;
     constructor(byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView);
     get byteArray(): Uint8Array<ArrayBufferLike>;
     get flags(): number;
@@ -79,5 +82,47 @@ export default class BamRecord {
     get next_pos(): number;
     get template_length(): number;
     seqAt(idx: number): string | undefined;
+    /**
+     * Bind reference bases for this read to resolve its substitutions against,
+     * for a read with no MD tag. `BamFile` calls this for you when it was given a
+     * `fetchReferenceSequence`; call it yourself when you have the bases from
+     * somewhere else.
+     *
+     * **`ref` must cover the whole read**, and this throws if it does not. The
+     * reason is that records are cached and shared between queries (ADR 0006), so
+     * a binding that varied by query would make one query's reads answer out of
+     * another's region. A region covering the read is the same data whichever
+     * query fetched it, so binding it is safe; a partial one is not, and the
+     * per-call `forEachMismatch(cb, {ref})` is where that belongs.
+     */
+    setReference(ref: PackedReference | undefined): void;
+    /** the region {@link setReference} bound, if any */
+    get reference(): PackedReference | undefined;
+    /**
+     * Report each difference between this read and the reference —
+     * substitutions, insertions, deletions, reference skips and clips — without
+     * allocating an object per difference. This is the intended way to read a
+     * record's differences; deriving them from `CIGAR` and `MD` yourself takes
+     * rather more of the format to interpret correctly (see {@link Mismatch}).
+     *
+     * Substitutions come from the MD tag when the read has one, and otherwise
+     * from comparing SEQ against reference bases — which have to come from
+     * {@link setReference}, `opts.ref`, or the file's `fetchReferenceSequence`.
+     * With neither MD nor reference, indels and clips are still reported in full
+     * and substitutions are not reported at all: nothing in the record says where
+     * they are.
+     *
+     * @param callback called as
+     *   `(code, refPos, length, bases, qual, refBaseCode, clipLength)`
+     * @param opts optional reference window to restrict to, and an optional
+     *   per-call reference region; see {@link MismatchOptions}
+     */
+    forEachMismatch(callback: MismatchCallback, opts?: MismatchOptions): void;
+    /**
+     * The same differences {@link forEachMismatch} reports, as an array of
+     * {@link Mismatch} objects. Convenient; allocates one object per difference,
+     * so the callback form is the one to reach for on a hot path.
+     */
+    getMismatches(opts?: MismatchOptions): Mismatch[];
     toJSON(): Record<string, unknown>;
 }

package/esm/record.js

@@ -1,8 +1,8 @@
 import { CIGAR_REF_SKIP, CIGAR_SOFT_CLIP } from "./cigar.js";
 import Constants from "./constants.js";
-const SEQRET = '=ACMGRSVTWYHKDBN';
-const SEQRET_DECODER = SEQRET.split('');
-const SEQRET_CODES = Uint8Array.from(SEQRET, c => c.charCodeAt(0));
+import { forEachMismatchNumeric } from "./mismatches.js";
+import { referenceCovers } from "./reference.js";
+import { SEQRET_CODES, SEQRET_DECODER } from "./seqAlphabet.js";
 // Both bases of a SEQ byte, precomputed for all 256 bytes so decoding advances a
 // byte at a time. Two forms because `seq` has two strategies (see below): packed
 // ASCII codes for a single Uint16Array store, and the 2-char string to append.
@@ -320,6 +320,7 @@ export default class BamRecord {
     _cachedNumericCigar;
     _cachedNUMERIC_MD;
     _cachedSeqStart;
+    _reference;
     // Positional rather than an options object, because every argument is
     // unpacked into a field immediately and nothing keeps the wrapper. The
     // options form allocated two throwaway objects for each of the ~200k records
@@ -811,6 +812,71 @@ export default class BamRecord {
             return undefined;
         }
     }
+    /**
+     * Bind reference bases for this read to resolve its substitutions against,
+     * for a read with no MD tag. `BamFile` calls this for you when it was given a
+     * `fetchReferenceSequence`; call it yourself when you have the bases from
+     * somewhere else.
+     *
+     * **`ref` must cover the whole read**, and this throws if it does not. The
+     * reason is that records are cached and shared between queries (ADR 0006), so
+     * a binding that varied by query would make one query's reads answer out of
+     * another's region. A region covering the read is the same data whichever
+     * query fetched it, so binding it is safe; a partial one is not, and the
+     * per-call `forEachMismatch(cb, {ref})` is where that belongs.
+     */
+    setReference(ref) {
+        if (ref !== undefined && !referenceCovers(ref, this.start, this.end)) {
+            throw new Error(`reference region ${ref.start}-${ref.start + ref.length} does not cover the record at ${this.start}-${this.end}. Records are shared between queries, so only a region covering the whole read can be bound to one; pass a partial region per call instead, as forEachMismatch(cb, {ref})`);
+        }
+        this._reference = ref;
+    }
+    /** the region {@link setReference} bound, if any */
+    get reference() {
+        return this._reference;
+    }
+    /**
+     * Report each difference between this read and the reference —
+     * substitutions, insertions, deletions, reference skips and clips — without
+     * allocating an object per difference. This is the intended way to read a
+     * record's differences; deriving them from `CIGAR` and `MD` yourself takes
+     * rather more of the format to interpret correctly (see {@link Mismatch}).
+     *
+     * Substitutions come from the MD tag when the read has one, and otherwise
+     * from comparing SEQ against reference bases — which have to come from
+     * {@link setReference}, `opts.ref`, or the file's `fetchReferenceSequence`.
+     * With neither MD nor reference, indels and clips are still reported in full
+     * and substitutions are not reported at all: nothing in the record says where
+     * they are.
+     *
+     * @param callback called as
+     *   `(code, refPos, length, bases, qual, refBaseCode, clipLength)`
+     * @param opts optional reference window to restrict to, and an optional
+     *   per-call reference region; see {@link MismatchOptions}
+     */
+    forEachMismatch(callback, opts) {
+        forEachMismatchNumeric(this.NUMERIC_CIGAR, this.NUMERIC_SEQ, this.seq_length, this.NUMERIC_MD, this.qual, opts?.ref ?? this._reference, this.start, opts?.start ?? Number.NEGATIVE_INFINITY, opts?.end ?? Number.POSITIVE_INFINITY, callback);
+    }
+    /**
+     * The same differences {@link forEachMismatch} reports, as an array of
+     * {@link Mismatch} objects. Convenient; allocates one object per difference,
+     * so the callback form is the one to reach for on a hot path.
+     */
+    getMismatches(opts) {
+        const out = [];
+        this.forEachMismatch((code, refPos, length, bases, qual, refBaseCode, clipLength) => {
+            out.push({
+                code,
+                refPos,
+                length,
+                bases,
+                qual,
+                refBaseCode,
+                clipLength,
+            });
+        }, opts);
+        return out;
+    }
     // Most public BamRecord fields are getters on the prototype, so
     // Object.keys(this) wouldn't include them — JSON.stringify needs an explicit
     // list. Returns the meaningful BAM-spec fields. Return type is widened so

package/esm/record.js.map

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package/esm/reference.d.ts

@@ -0,0 +1,45 @@
+/**
+ * A region of reference sequence in BAM's own 4-bit alphabet, so the mismatch
+ * walk can compare it against a read's already-packed `NUMERIC_SEQ` a byte —
+ * two bases — at a time, instead of unpacking a nibble and reading a string
+ * character per base. Only the rare byte that differs gets unpacked.
+ *
+ * Two packings, because a read's sequence parity and its reference parity need
+ * not agree: `even[i]` holds region bases (2i, 2i+1), `odd[i]` holds
+ * (2i-1, 2i). The walk picks whichever lines the reference pair up with the
+ * read's byte boundary. Together they cost one byte per base, the same as the
+ * region string they replace.
+ *
+ * Build one with {@link packReference}, per region rather than per read: a
+ * pileup's reads all resolve against the same region, and packing is the only
+ * per-base pass in the whole walk.
+ */
+export interface PackedReference {
+    /** 0-based reference coordinate of the first base */
+    start: number;
+    /** length in bases, i.e. of the string this was packed from */
+    length: number;
+    even: Uint8Array;
+    odd: Uint8Array;
+}
+/**
+ * The 4-bit codes back to ASCII, for reporting a mismatch's reference base.
+ * Always the uppercase spelling: packing is case-insensitive, so a soft-masked
+ * reference reports `A` where the raw string would have said `a`.
+ */
+export declare const CHAR_CODE_FROM_NIBBLE: Uint8Array<ArrayBuffer>;
+/**
+ * Pack a region of reference sequence for {@link PackedReference}.
+ *
+ * @param seq the reference bases, case-insensitive
+ * @param start the 0-based reference coordinate `seq[0]` sits at
+ */
+export declare function packReference(seq: string, start?: number): PackedReference;
+/**
+ * The single reference base at region-relative index `i`, for the ends of an
+ * odd-length run. Callers bound `i` to the region themselves — reading past the
+ * end would report a base the region does not have.
+ */
+export declare function referenceNibble(ref: PackedReference, i: number): number;
+/** whether `ref` covers every base of the 0-based half-open span [start, end) */
+export declare function referenceCovers(ref: PackedReference, start: number, end: number): boolean;

package/esm/reference.js

@@ -0,0 +1,55 @@
+import { SEQRET } from "./seqAlphabet.js";
+// ASCII -> 4-bit code, case-insensitive. Anything outside the alphabet reads as
+// N, which mismatches every concrete base — what an unrecognized character does
+// when the comparison is done in ASCII.
+const NIBBLE_FROM_CHAR = new Uint8Array(256).fill(15);
+for (let i = 0; i < 16; i++) {
+    NIBBLE_FROM_CHAR[SEQRET.charCodeAt(i)] = i;
+    NIBBLE_FROM_CHAR[SEQRET.charCodeAt(i) | 0x20] = i;
+}
+/**
+ * The 4-bit codes back to ASCII, for reporting a mismatch's reference base.
+ * Always the uppercase spelling: packing is case-insensitive, so a soft-masked
+ * reference reports `A` where the raw string would have said `a`.
+ */
+export const CHAR_CODE_FROM_NIBBLE = new Uint8Array(16);
+for (let i = 0; i < 16; i++) {
+    CHAR_CODE_FROM_NIBBLE[i] = SEQRET.charCodeAt(i);
+}
+/**
+ * Pack a region of reference sequence for {@link PackedReference}.
+ *
+ * @param seq the reference bases, case-insensitive
+ * @param start the 0-based reference coordinate `seq[0]` sits at
+ */
+export function packReference(seq, start = 0) {
+    const n = seq.length;
+    const even = new Uint8Array((n >> 1) + 1);
+    const odd = new Uint8Array((n >> 1) + 1);
+    for (let i = 0; i < n; i++) {
+        const code = seq.charCodeAt(i);
+        const nibble = code < 256 ? NIBBLE_FROM_CHAR[code] : 15;
+        if (i & 1) {
+            even[i >> 1] |= nibble;
+            odd[(i + 1) >> 1] = nibble << 4;
+        }
+        else {
+            even[i >> 1] = nibble << 4;
+            odd[i >> 1] |= nibble;
+        }
+    }
+    return { start, length: n, even, odd };
+}
+/**
+ * The single reference base at region-relative index `i`, for the ends of an
+ * odd-length run. Callers bound `i` to the region themselves — reading past the
+ * end would report a base the region does not have.
+ */
+export function referenceNibble(ref, i) {
+    return (ref.even[i >> 1] >> ((1 - (i & 1)) << 2)) & 0xf;
+}
+/** whether `ref` covers every base of the 0-based half-open span [start, end) */
+export function referenceCovers(ref, start, end) {
+    return ref.start <= start && ref.start + ref.length >= end;
+}
+//# sourceMappingURL=reference.js.map

package/esm/reference.js.map

@@ -0,0 +1 @@
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package/esm/seqAlphabet.d.ts

@@ -0,0 +1,3 @@
+export declare const SEQRET = "=ACMGRSVTWYHKDBN";
+export declare const SEQRET_DECODER: string[];
+export declare const SEQRET_CODES: Uint8Array<ArrayBuffer>;

package/esm/seqAlphabet.js

@@ -0,0 +1,11 @@
+// BAM's 4-bit sequence alphabet (SAM spec §4.2, `seq`): nibble value -> base.
+//
+// Shared rather than duplicated because three modules need it for three
+// different shapes — `record.ts` builds pair/quad tables on top of it to decode
+// whole reads, `reference.ts` inverts it to pack a reference the same way, and
+// `mismatches.ts` reads single bases out of it — and a copy that drifted would
+// silently mis-decode one of them.
+export const SEQRET = '=ACMGRSVTWYHKDBN';
+export const SEQRET_DECODER = SEQRET.split('');
+export const SEQRET_CODES = Uint8Array.from(SEQRET, c => c.charCodeAt(0));
+//# sourceMappingURL=seqAlphabet.js.map

package/esm/seqAlphabet.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seqAlphabet.js","sourceRoot":"","sources":["../src/seqAlphabet.ts"],"names":[],"mappings":"AAAA,8EAA8E;AAC9E,EAAE;AACF,wEAAwE;AACxE,gFAAgF;AAChF,+EAA+E;AAC/E,+EAA+E;AAC/E,mCAAmC;AACnC,MAAM,CAAC,MAAM,MAAM,GAAG,kBAAkB,CAAA;AACxC,MAAM,CAAC,MAAM,cAAc,GAAG,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;AAC9C,MAAM,CAAC,MAAM,YAAY,GAAG,UAAU,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "8.5.1",
+  "version": "8.6.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",