@gmod/bam 7.8.2 → 7.9.1

package/esm/bamFile.js.map

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

@@ -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

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

@@ -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.d.ts

@@ -23,6 +23,13 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
     private setupP?;
+    /**
+     * The signal `setupP` was started under, while it is still in flight. The
+     * index is parsed once and shared by every query against the file, so without
+     * this the first query to arrive would own a read all the others depend on —
+     * see {@link parse}.
+     */
+    private setupSignal?;
     constructor({ filehandle, renameRefSeq, }: {
         filehandle: GenericFilehandle;
         renameRefSeq?: (a: string) => string;
@@ -36,7 +43,31 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
     protected abstract reg2bins(min: number, max: number): readonly (readonly [number, number])[];
     protected abstract getLowestChunk(refIndex: RefIndex, min: number): OffsetCoords | undefined;
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
-    parse(opts?: BaseOpts): Promise<TParsed>;
+    /**
+     * Parse the index, or join the parse already running.
+     *
+     * The index is downloaded and parsed once for the life of this object, so it
+     * is the one read here that is shared between queries — and therefore the one
+     * place a cancellation can leak from the query that asked for it to a query
+     * that did not. `_parse` hands `opts` straight to `filehandle.readFile`, so
+     * without this the first query to arrive owns a read every other query
+     * depends on: when it pans away, every concurrent query fails with its abort.
+     *
+     * A caller that joined someone else's parse and saw it fail because *they*
+     * aborted starts over rather than inheriting the failure — once, then
+     * propagates. Bounding it at one attempt is what jbrowse's
+     * `RemoteFileWithRangeCache.joinChunk` does with the same retry one layer
+     * down, and for the reason it gives: the pathological case becomes one
+     * duplicate parse rather than a recursion whose depth depends on how the
+     * aborts interleave.
+     *
+     * A retry rather than the reference count `_cachedChunkFeatures` uses, for
+     * the reason `@gmod/cram` gives for the same split in `CraiIndex`: the index
+     * is parsed once for the life of the object, so there is no repeated waste to
+     * recover, and this is a dozen lines against restructuring the memo.
+     */
+    parse(opts?: BaseOpts, retried?: boolean): Promise<TParsed>;
+    private startParse;
     lineCount(refId: number, opts?: BaseOpts): Promise<number>;
     hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
     estimatedBytesForRegions(regions: Region[], opts?: BaseOpts): Promise<number>;

package/esm/indexFile.js

@@ -1,13 +1,16 @@
 import QuickLRU from '@jbrowse/quick-lru';
-import { optimizeChunks } from "./util.js";
+import { optimizeChunks, throwIfAborted } from "./util.js";
 // SYNC: ~/src/gmod/tabix-js/src/util.ts memoizeByRefId
 // LRU-cache the result of getIndices(refId) so repeated lookups for the same
 // reference don't re-walk the index bytes.
 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) {
@@ -20,6 +23,13 @@ export default class IndexFile {
     filehandle;
     renameRefSeq;
     setupP;
+    /**
+     * The signal `setupP` was started under, while it is still in flight. The
+     * index is parsed once and shared by every query against the file, so without
+     * this the first query to arrive would own a read all the others depend on —
+     * see {@link parse}.
+     */
+    setupSignal;
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;
@@ -51,14 +61,66 @@ export default class IndexFile {
         }
         return optimizeChunks(chunks, this.getLowestChunk(ba, min));
     }
-    parse(opts = {}) {
-        if (!this.setupP) {
-            this.setupP = this._parse(opts).catch((e) => {
-                this.setupP = undefined;
+    /**
+     * Parse the index, or join the parse already running.
+     *
+     * The index is downloaded and parsed once for the life of this object, so it
+     * is the one read here that is shared between queries — and therefore the one
+     * place a cancellation can leak from the query that asked for it to a query
+     * that did not. `_parse` hands `opts` straight to `filehandle.readFile`, so
+     * without this the first query to arrive owns a read every other query
+     * depends on: when it pans away, every concurrent query fails with its abort.
+     *
+     * A caller that joined someone else's parse and saw it fail because *they*
+     * aborted starts over rather than inheriting the failure — once, then
+     * propagates. Bounding it at one attempt is what jbrowse's
+     * `RemoteFileWithRangeCache.joinChunk` does with the same retry one layer
+     * down, and for the reason it gives: the pathological case becomes one
+     * duplicate parse rather than a recursion whose depth depends on how the
+     * aborts interleave.
+     *
+     * A retry rather than the reference count `_cachedChunkFeatures` uses, for
+     * the reason `@gmod/cram` gives for the same split in `CraiIndex`: the index
+     * is parsed once for the life of the object, so there is no repeated waste to
+     * recover, and this is a dozen lines against restructuring the memo.
+     */
+    async parse(opts = {}, retried = false) {
+        throwIfAborted(opts.signal);
+        const pending = this.setupP;
+        if (!pending) {
+            return this.startParse(opts);
+        }
+        // read before awaiting: the owner is forgotten as soon as the parse settles
+        const ownerSignal = this.setupSignal;
+        try {
+            return await pending;
+        }
+        catch (e) {
+            if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
                 throw e;
-            });
+            }
+            return this.parse(opts, true);
         }
-        return this.setupP;
+    }
+    startParse(opts) {
+        const pending = this._parse(opts);
+        this.setupP = pending;
+        this.setupSignal = opts.signal;
+        // Drop a rejection rather than keeping it, so one transient failure does not
+        // poison the index for the lifetime of the file. Both branches are
+        // identity-checked so a retry started after this settles is not cleared by
+        // the attempt it already replaced.
+        pending.then(() => {
+            if (this.setupP === pending) {
+                this.setupSignal = undefined;
+            }
+        }, () => {
+            if (this.setupP === pending) {
+                this.setupP = undefined;
+                this.setupSignal = undefined;
+            }
+        });
+        return pending;
     }
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);

package/esm/indexFile.js.map

@@ -1 +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,IAAI,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;YACrB,OAAO,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QACzB,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"}
+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,oBAAoB,CAAA;AAEzC,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAwB1D,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;IACjC;;;;;OAKG;IACK,WAAW,CAAc;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;;;;;;;;;;;;;;;;;;;;;;OAsBG;IACH,KAAK,CAAC,KAAK,CAAC,OAAiB,EAAE,EAAE,OAAO,GAAG,KAAK;QAC9C,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAC3B,MAAM,OAAO,GAAG,IAAI,CAAC,MAAM,CAAA;QAC3B,IAAI,CAAC,OAAO,EAAE,CAAC;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QAC9B,CAAC;QAED,4EAA4E;QAC5E,MAAM,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACpC,IAAI,CAAC;YACH,OAAO,MAAM,OAAO,CAAA;QACtB,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,IAAI,OAAO,IAAI,CAAC,WAAW,EAAE,OAAO,IAAI,IAAI,CAAC,MAAM,EAAE,OAAO,EAAE,CAAC;gBAC7D,MAAM,CAAC,CAAA;YACT,CAAC;YACD,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;QAC/B,CAAC;IACH,CAAC;IAEO,UAAU,CAAC,IAAc;QAC/B,MAAM,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;QACjC,IAAI,CAAC,MAAM,GAAG,OAAO,CAAA;QACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,CAAA;QAC9B,6EAA6E;QAC7E,mEAAmE;QACnE,2EAA2E;QAC3E,mCAAmC;QACnC,OAAO,CAAC,IAAI,CACV,GAAG,EAAE;YACH,IAAI,IAAI,CAAC,MAAM,KAAK,OAAO,EAAE,CAAC;gBAC5B,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC9B,CAAC;QACH,CAAC,EACD,GAAG,EAAE;YACH,IAAI,IAAI,CAAC,MAAM,KAAK,OAAO,EAAE,CAAC;gBAC5B,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC9B,CAAC;QACH,CAAC,CACF,CAAA;QACD,OAAO,OAAO,CAAA;IAChB,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

@@ -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

@@ -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];