npm - @gmod/bam - Versions diffs - 7.8.2 → 7.9.0 - Mend

@gmod/bam 7.8.2 → 7.9.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (41) hide show

package/esm/bamFile.d.ts CHANGED Viewed

@@ -23,14 +23,17 @@ interface ChunkEntry<T> {
 }
 export declare const DEFAULT_MAX_CACHE_BYTES: number;
 declare class ChunkFeatureCache<T> {
-    maxBytes: number;
+    private _maxBytes;
     private entries;
     private bytes;
     constructor(maxBytes: number);
+    get maxBytes(): number;
+    set maxBytes(maxBytes: number);
     get size(): number;
     get byteSize(): number;
     get(key: string): ChunkEntry<T> | undefined;
     set(key: string, entry: ChunkEntry<T>): void;
+    private evict;
     delete(key: string): void;
     clear(): void;
     [Symbol.iterator](): MapIterator<[string, ChunkEntry<T>]>;

package/esm/bamFile.js CHANGED Viewed

@@ -9,10 +9,13 @@ import { parseHeaderText } from "./sam.js";
 import { appendInRange, parseRefSeqs } from "./util.js";
 export const BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
-// Ceiling on the header read. A million contigs is roughly 10MB of compressed
-// @SQ lines and ref-seq table, so anything past this is a corrupt header
-// claiming a huge n_ref rather than a real one, and growing the read further
-// just downloads the file.
+// Ceiling on GROWING the header read. A million contigs is roughly 10MB of
+// compressed @SQ lines and ref-seq table, so a read that has doubled past this
+// is chasing a corrupt header claiming a huge n_ref rather than a real one, and
+// growing further just downloads the file. It does not cap the FIRST read: that
+// length comes from the index's firstDataLine, which is a real offset rather
+// than a guess, so a header that genuinely runs past this still gets its one
+// exact read. See getHeaderPre.
 const maxHeaderReadLen = 32 * 1024 * 1024;
 function resolveFilehandle(filehandle, path, url) {
     return (filehandle ??
@@ -59,11 +62,21 @@ export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
 // nothing on the transport that matters and only widens peak memory.
 const MAX_CONCURRENT_CHUNK_READS = 6;
 class ChunkFeatureCache {
-    maxBytes;
+    _maxBytes;
     entries = new Map();
     bytes = 0;
     constructor(maxBytes) {
-        this.maxBytes = maxBytes;
+        this._maxBytes = maxBytes;
+    }
+    get maxBytes() {
+        return this._maxBytes;
+    }
+    // Accessor rather than a plain field so lowering the budget frees memory now.
+    // As a field, a caller trimming the cache under memory pressure got nothing
+    // back until the next chunk read happened to call set().
+    set maxBytes(maxBytes) {
+        this._maxBytes = maxBytes;
+        this.evict();
     }
     get size() {
         return this.entries.size;
@@ -84,11 +97,14 @@ class ChunkFeatureCache {
         this.delete(key);
         this.entries.set(key, entry);
         this.bytes += entry.bytes;
-        // Evict from the least-recently-used end. The size > 1 guard means a single
-        // chunk larger than the whole budget is still kept: the caller needs it for
-        // the query in flight, and dropping it would only force a re-decompress.
+        this.evict();
+    }
+    // Evict from the least-recently-used end. The size > 1 guard means a single
+    // chunk larger than the whole budget is still kept: the caller needs it for
+    // the query in flight, and dropping it would only force a re-decompress.
+    evict() {
         const lru = this.entries.keys();
-        while (this.bytes > this.maxBytes && this.entries.size > 1) {
+        while (this.bytes > this._maxBytes && this.entries.size > 1) {
             this.delete(lru.next().value);
         }
     }
@@ -171,16 +187,21 @@ export default class BamFile {
         let readLen = indexData.firstDataLine === undefined
             ? blockLen
             : indexData.firstDataLine.blockPosition + blockLen;
+        // do/while, so the index-derived length is always read once and only the
+        // doubling is bounded. Testing readLen before the first read instead meant
+        // a BAM whose header genuinely exceeds maxHeaderReadLen — millions of
+        // contigs — was rejected without a single byte being fetched, and reported
+        // as 'Insufficient data for reference sequences' when the data was there.
         let samHeader;
-        let atEof = false;
-        while (samHeader === undefined && !atEof && readLen <= maxHeaderReadLen) {
+        let atEof;
+        do {
             const buffer = await this.bam.read(readLen, 0, { signal: opts.signal });
             // a short read means readLen ran past the end of the file, so there are
             // no more bytes to grow into
             atEof = buffer.length < readLen;
             samHeader = this.applyHeader(await unzip(buffer));
             readLen *= 2;
-        }
+        } while (samHeader === undefined && !atEof && readLen <= maxHeaderReadLen);
         if (samHeader === undefined) {
             throw new Error('Insufficient data for reference sequences');
         }
@@ -447,8 +468,12 @@ export default class BamFile {
                 const mateRecs = [];
                 for (let i = 0, l = features.length; i < l; i++) {
                     const feature = features[i];
-                    if (readNameCounts.get(feature.name) === 1 &&
-                        !readIds.has(feature.fileOffset)) {
+                    // fileOffset first: it is a number already on the record, where
+                    // `name` decodes a string per record. A mate chunk usually overlaps
+                    // the query region, so this skips the decode for every record the
+                    // caller is already holding.
+                    if (!readIds.has(feature.fileOffset) &&
+                        readNameCounts.get(feature.name) === 1) {
                         mateRecs.push(feature);
                     }
                 }

package/esm/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/csi.js CHANGED Viewed

@@ -66,6 +66,20 @@ export default class CSI extends IndexFile {
         this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
         const maxBinNumber = this.maxBinNumber;
         const auxLength = dataView.getInt32(12, true);
+        // A tabix-only branch, which is why parseAuxData and the parseNameBytes it
+        // calls show as uncovered. CSI is shared between `samtools index -c` and
+        // `tabix -C`, and the aux block is how a tabix index carries what a reader
+        // of bgzipped TEXT needs: which columns hold ref/start/end, the comment
+        // character, lines to skip, and the reference names — which a BAM takes
+        // from its own header instead. So a BAM .csi sets l_aux to 0 and never
+        // reaches here (checked: 0 of the 19 .csi fixtures carry one).
+        //
+        // Kept rather than deleted for two reasons. CSI is exported from
+        // index.ts, so pointing it at a tabix index is reachable (@gmod/tabix is
+        // the right tool, but this would half-work and then silently not).
+        // More importantly parseNameBytes is marked SYNC: with its tabix-js
+        // counterpart, and dropping one side of a deliberately-paired pair of
+        // implementations is exactly what that marker exists to prevent.
         const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
         const refCount = dataView.getInt32(16 + auxLength, true);
         // SYNC: ~/src/gmod/tabix-js/src/csi.ts _parse — two-pass structure
@@ -166,6 +180,12 @@ export default class CSI extends IndexFile {
         for (; l <= this.depth; s -= 3, t += lshift(1, l * 3), l += 1) {
             const b = t + rshift(beg, s);
             const e = t + rshift(end, s);
+            // Unreachable as long as the clamp above stands, which is why it shows
+            // as uncovered: with end bounded to 2^(minShift + depth*3), level l
+            // spans at most 8^l - 1 bins, so the worst case is 8^depth - 1 + depth
+            // against a maxBinNumber of (8^(depth+1) - 1)/7, i.e. about 1.14 * 8^depth.
+            // Kept as a guard on the arithmetic rather than deleted — reg2bins is
+            // shared with tabix-js, whose callers reach it by other routes.
             if (e - b + bins.length > this.maxBinNumber) {
                 throw new Error(`query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
             }

package/esm/csi.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/index.d.ts CHANGED Viewed

@@ -3,6 +3,8 @@ export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from './bamFile.ts';
 export { default as CSI } from './csi.ts';
 export { default as BamRecord } from './record.ts';
 export { default as HtsgetFile } from './htsget.ts';
-export type { Bytes } from './record.ts';
+export type { NumericCigar } from './record.ts';
 export type { BamRecordClass, BamRecordLike } from './bamFile.ts';
+export type { BamOpts, BaseOpts } from './util.ts';
+export type { IndexCovEntry } from './bai.ts';
 export type { Fetcher } from 'generic-filehandle2';

package/esm/indexFile.js CHANGED Viewed

@@ -6,8 +6,11 @@ import { optimizeChunks } from "./util.js";
 export function memoizeByRefId(getIndices, maxSize = 5) {
     const cache = new QuickLRU({ maxSize });
     return (refId) => {
-        if (cache.has(refId)) {
-            return cache.get(refId);
+        // one lookup, not has()+get(): only truthy results are ever cached, so a
+        // miss and a cached value are already distinguishable
+        const cached = cache.get(refId);
+        if (cached !== undefined) {
+            return cached;
         }
         const result = getIndices(refId);
         if (result) {

package/esm/indexFile.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,oBAAoB,CAAA;AAEzC,OAAO,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAwB1C,uDAAuD;AACvD,6EAA6E;AAC7E,2CAA2C;AAC3C,MAAM,UAAU,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,KAAK,GAAG,IAAI,QAAQ,CAAY,EAAE,OAAO,EAAE,CAAC,CAAA;IAClD,OAAO,CAAC,KAAa,EAAE,EAAE;QACvB,yEAAyE;QACzE,sDAAsD;QACtD,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC/B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,OAAO,MAAM,CAAA;QACf,CAAC;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,MAAM,EAAE,CAAC;YACX,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC1B,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAgB,SAAS;IAG9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAElC,MAAM,CAAmB;IAEjC,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAwBD,KAAK,CAAC,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;QAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QACD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAC/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,MAAM,GAAY,EAAE,CAAA;QAC1B,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,MAAM,SAAS,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAC/B,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;wBACjD,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAE,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,cAAc,CAAC,MAAM,EAAE,IAAI,CAAC,cAAc,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,CAAA;IAC7D,CAAC;IAED,KAAK,CAAC,OAAiB,EAAE;QACvB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IACnC,CAAC;IAED,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,cAAc,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF"}

package/esm/record.d.ts CHANGED Viewed

@@ -1,9 +1,4 @@
 export type NumericCigar = Uint32Array | Int32Array | number[];
-export interface Bytes {
-    start: number;
-    end: number;
-    byteArray: Uint8Array;
-}
 export default class BamRecord {
     fileOffset: number;
     private _byteArray;
@@ -34,6 +29,22 @@ export default class BamRecord {
     get tags(): Record<string, unknown>;
     getTag(tagName: string): unknown;
     getTagRaw(tagName: string): unknown;
+    /**
+     * The value of `tagName`, or of `altName` if the record carries no `tagName` —
+     * resolved in ONE pass over the tag block instead of two.
+     *
+     * For the MM/Mm and ML/Ml alias pairs that modified-base callers emit, where
+     * `getTag(a) ?? getTag(b)` walks every tag on the record TWICE whenever
+     * neither is present, which is every read in a file without base
+     * modifications. jbrowse-components issues exactly that lookup per record on
+     * every render (extractModifications runs unconditionally), and on
+     * jb2bench's 1000x.shortread it was 12.9% of the whole query — more than the
+     * CIGAR, SEQ and MD reads the pileup actually uses, spent proving absence.
+     *
+     * `tagName` wins wherever it appears, so the result matches the two-lookup
+     * form even for a (malformed) record carrying both.
+     */
+    getTagAlt(tagName: string, altName: string): unknown;
     private _findTag;
     private _computeTags;
     isPaired(): boolean;

package/esm/record.js CHANGED Viewed

@@ -27,6 +27,39 @@ for (let hi = 0; hi < 16; hi++) {
 // wins by 5-8x. Measured crossover is ~300bp, i.e. just past typical Illumina
 // read lengths.
 const SEQ_DECODER_THRESHOLD = 300;
+// Four bases per entry, indexed by a PAIR of SEQ bytes, so the sub-threshold
+// path halves its concat count: 1.5-1.6x on a short-read query end to end
+// (shortreads_300x 46.5 -> 30.5 ms over 53.6k reads, volvox 4.8 -> 2.9 ms).
+//
+// Built lazily, and only once the short path has been taken enough times to pay
+// for it. Filling 65536 entries costs ~6 ms and retains ~2 MB, so building on
+// first use is a LOSS on a file that decodes only a handful of short reads:
+// long-read fixtures with a short-read tail measured 1.4x slower that way
+// (ecoli_nanopore has 27 sub-300bp reads out of 480, chm1 has 5 of 204). The
+// counter is module-global on purpose — the table is shared, so what has to
+// amortize is the total number of short decodes in the process, not per file.
+const SEQRET_QUAD_WARMUP = 1024;
+let seqretShortCalls = 0;
+let SEQRET_QUAD_STRINGS;
+// The 4-base table, or undefined while still warming up (caller falls back to
+// the 2-base table).
+function seqretQuads() {
+    if (SEQRET_QUAD_STRINGS === undefined) {
+        if (++seqretShortCalls < SEQRET_QUAD_WARMUP) {
+            return undefined;
+        }
+        const quads = new Array(65536);
+        for (let a = 0; a < 256; a++) {
+            const sa = SEQRET_PAIR_STRINGS[a];
+            const base = a << 8;
+            for (let b = 0; b < 256; b++) {
+                quads[base | b] = sa + SEQRET_PAIR_STRINGS[b];
+            }
+        }
+        SEQRET_QUAD_STRINGS = quads;
+    }
+    return SEQRET_QUAD_STRINGS;
+}
 // Precomputed pair orientation strings, indexed by
 //   ((flags >> 4) & 0x7) | (selfIsLeft ? 8 : 0)
 // bits 0-2 are flag bits 0x10 (self reverse), 0x20 (mate reverse), 0x40 (read1);
@@ -172,6 +205,11 @@ function decodeBArrayTag(ba, dataView, p, Btype, limit) {
     }
 }
 // Byte span of a 'B' tag's element payload, for advancing the cursor past it.
+// Returns -1 for a subtype outside the spec's cCsSiIf, whose element width is
+// unknowable. Guessing one byte per element (which is what falling through to
+// `limit` did) doesn't skip the tag, it lands the cursor mid-value and decodes
+// the whole rest of the record's tag list out of garbage — where an unknown
+// top-level type has always stopped the walk instead. Same choice here.
 function bArrayByteLength(Btype, limit) {
     if (Btype === 0x69 || Btype === 0x49 || Btype === 0x66) {
         return limit << 2;
@@ -179,9 +217,12 @@ function bArrayByteLength(Btype, limit) {
     else if (Btype === 0x73 || Btype === 0x53) {
         return limit << 1;
     }
-    else {
+    else if (Btype === 0x63 || Btype === 0x43) {
         return limit;
     }
+    else {
+        return -1;
+    }
 }
 // Cursor position just past a tag's value — i.e. the start of the next tag —
 // given the value starts at `p`. For null-terminated Z/H this steps over the
@@ -207,6 +248,11 @@ function tagValueEnd(ba, dataView, type, p, blockEnd) {
         case 0x5a: // 'Z'
         case 0x48: {
             // 'H'
+            // Stays a plain byte loop. Swapping in Uint8Array.indexOf past a short
+            // inline probe is 2.7x faster on long-read MD (mean 9083 bytes on
+            // jb2bench's 200x.longread) but ~1.13x slower on short-read Z values,
+            // which are 4-13 bytes and are what the dominant case is made of. Measured
+            // both ways against the realistic corpus — see ADR 0012.
             let q = p;
             while (q < blockEnd && ba[q] !== 0) {
                 q++;
@@ -217,7 +263,12 @@ function tagValueEnd(ba, dataView, type, p, blockEnd) {
             // 'B'
             const Btype = ba[p];
             const limit = dataView.getInt32(p + 1, true);
-            return p + 5 + bArrayByteLength(Btype, limit);
+            const payload = bArrayByteLength(Btype, limit);
+            if (payload < 0) {
+                console.error('Unknown BAM B tag subtype', Btype);
+                return 0;
+            }
+            return p + 5 + payload;
         }
         default:
             console.error('Unknown BAM tag type', type);
@@ -382,6 +433,59 @@ export default class BamRecord {
     getTagRaw(tagName) {
         return this._findTag(tagName, true);
     }
+    /**
+     * The value of `tagName`, or of `altName` if the record carries no `tagName` —
+     * resolved in ONE pass over the tag block instead of two.
+     *
+     * For the MM/Mm and ML/Ml alias pairs that modified-base callers emit, where
+     * `getTag(a) ?? getTag(b)` walks every tag on the record TWICE whenever
+     * neither is present, which is every read in a file without base
+     * modifications. jbrowse-components issues exactly that lookup per record on
+     * every render (extractModifications runs unconditionally), and on
+     * jb2bench's 1000x.shortread it was 12.9% of the whole query — more than the
+     * CIGAR, SEQ and MD reads the pileup actually uses, spent proving absence.
+     *
+     * `tagName` wins wherever it appears, so the result matches the two-lookup
+     * form even for a (malformed) record carrying both.
+     */
+    getTagAlt(tagName, altName) {
+        if (this._cachedTags !== undefined) {
+            return this._cachedTags[tagName] ?? this._cachedTags[altName];
+        }
+        const a0 = tagName.charCodeAt(0);
+        const a1 = tagName.charCodeAt(1);
+        const b0 = altName.charCodeAt(0);
+        const b1 = altName.charCodeAt(1);
+        const blockEnd = this._end;
+        const ba = this._byteArray;
+        let p = this.tagsStart;
+        // where the alternate landed, if it turns up before the primary does
+        let altType = -1;
+        let altStart = 0;
+        let altEnd = 0;
+        while (p < blockEnd) {
+            const c0 = ba[p];
+            const c1 = ba[p + 1];
+            const type = ba[p + 2];
+            const valueStart = p + 3;
+            const end = tagValueEnd(ba, this._dataView, type, valueStart, blockEnd);
+            if (end === 0) {
+                break; // unknown type: can't compute how far to advance
+            }
+            if (c0 === a0 && c1 === a1) {
+                return decodeTagValue(ba, this._dataView, type, valueStart, end, false);
+            }
+            if (altType < 0 && c0 === b0 && c1 === b1) {
+                altType = type;
+                altStart = valueStart;
+                altEnd = end;
+            }
+            p = end;
+        }
+        return altType < 0
+            ? undefined
+            : decodeTagValue(ba, this._dataView, altType, altStart, altEnd, false);
+    }
     _findTag(tagName, raw) {
         const tag1 = tagName.charCodeAt(0);
         const tag2 = tagName.charCodeAt(1);
@@ -522,11 +626,18 @@ export default class BamRecord {
         }
         return lref;
     }
+    // Unmapped records are not special-cased here, unlike in
+    // _computeLengthOnRef. The spec says no assumptions can be made about an
+    // unmapped read's CIGAR, but "no assumptions" is not "no CIGAR": aligners
+    // emit placed unmapped mates that carry a real one, and htslib prints
+    // whatever is stored. Dropping it lost data the file had — paired.bam's
+    // SRR062635.1831187 at 20:74230 is FLAG 133 with 35M65S.
+    //
+    // Reference span stays 0 for them regardless, since that is a claim about
+    // alignment rather than about the stored bytes, and the query filter reads
+    // it.
     _computeNumericCigar() {
         const flag_nc = this._dataView.getInt32(this._start + 16, true);
-        if (flag_nc & (Constants.BAM_FUNMAP << 16)) {
-            return new Uint32Array(0);
-        }
         const numCigarOps = flag_nc & 0xffff;
         const p = this.b0 + this.read_name_length;
         if (this._isCGTagPattern(p, numCigarOps)) {
@@ -557,14 +668,26 @@ export default class BamRecord {
         }
         return this._cachedNumericCigar;
     }
+    // Two appends per op, NOT `result += length + String.fromCharCode(op)`. The
+    // one-append form builds an intermediate cons string per op just to append it
+    // and drop it; appending each piece straight onto the rope is 1.23-1.35x
+    // faster on long reads, which is where this accessor dominates
+    // (chr22_nanopore_subset 51.2 -> 38.6 ms for 757 reads averaging 2171 ops,
+    // ultra-long-ont 13.2 -> 9.9 ms). Short reads carry 1-3 ops and land inside
+    // this box's noise band either way.
+    //
+    // ADR 0003 rejected two other rewrites of this loop — a precomputed 16-entry
+    // op-char table, and digits into a Uint8Array with one TextDecoder.decode —
+    // and both are still losers. Re-measured here: the op-char table is 1.13x
+    // SLOWER than String.fromCharCode even on top of this change, because V8
+    // already hands back an interned single-character string.
     get CIGAR() {
         const numeric = this.NUMERIC_CIGAR;
         let result = '';
         for (let i = 0, l = numeric.length; i < l; i++) {
             const packed = numeric[i];
-            const length = packed >> 4;
-            const opCode = ASCII_CIGAR_CODES[packed & 0xf];
-            result += length + String.fromCharCode(opCode);
+            result += packed >> 4;
+            result += String.fromCharCode(ASCII_CIGAR_CODES[packed & 0xf]);
         }
         return result;
     }
@@ -584,9 +707,10 @@ export default class BamRecord {
         const p = this.seqStart;
         return this._byteArray.subarray(p, p + this.num_seq_bytes);
     }
-    // Decode two bases per iteration off a 256-entry table. Building an array of
-    // 1-char strings and join()ing it — the obvious approach — is 3x slower at
-    // 100bp and 35x slower at 15kb.
+    // Decode four bases per iteration off the 65536-entry table (two off the
+    // 256-entry one until that table has warmed up). Building an array of 1-char
+    // strings and join()ing it — the obvious approach — is 3x slower at 100bp and
+    // 35x slower at 15kb.
     get seq() {
         const len = this.seq_length;
         const ba = this._byteArray;
@@ -594,9 +718,23 @@ export default class BamRecord {
         const nPairs = len >> 1;
         let seq;
         if (len < SEQ_DECODER_THRESHOLD) {
+            const quads = seqretQuads();
             seq = '';
-            for (let j = 0; j < nPairs; j++) {
-                seq += SEQRET_PAIR_STRINGS[ba[p + j]];
+            if (quads === undefined) {
+                for (let j = 0; j < nPairs; j++) {
+                    seq += SEQRET_PAIR_STRINGS[ba[p + j]];
+                }
+            }
+            else {
+                const nQuads = nPairs >> 1;
+                for (let j = 0; j < nQuads; j++) {
+                    const q = p + 2 * j;
+                    seq += quads[(ba[q] << 8) | ba[q + 1]];
+                }
+                // odd byte count: two more bases off the 2-base table
+                if (nPairs & 1) {
+                    seq += SEQRET_PAIR_STRINGS[ba[p + nPairs - 1]];
+                }
             }
             if (len & 1) {
                 seq += SEQRET_DECODER[(ba[p + nPairs] & 0xf0) >> 4];