@gmod/bam 7.3.4 → 7.4.0

package/dist/record.js

@@ -5,15 +5,42 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const cigar_ts_1 = require("./cigar.js");
 const constants_ts_1 = __importDefault(require("./constants.js"));
-const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
-// precomputed pair orientation strings indexed by ((flags >> 4) & 0xF) | (isize > 0 ? 16 : 0)
-// bits 0-3 encode flag bits 0x10(reverse),0x20(mate reverse),0x40(read1),0x80(read2)
-// bit 4 encodes whether isize > 0
+const SEQRET = '=ACMGRSVTWYHKDBN';
+const SEQRET_DECODER = SEQRET.split('');
+const SEQRET_CODES = Uint8Array.from(SEQRET, c => c.charCodeAt(0));
+// 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.
+// Byte order within the u16 depends on host endianness.
+const LITTLE_ENDIAN = new Uint16Array(Uint8Array.of(1, 0).buffer)[0] === 1;
+const SEQRET_PAIR_CODES = new Uint16Array(256);
+const SEQRET_PAIR_STRINGS = new Array(256);
+for (let hi = 0; hi < 16; hi++) {
+    for (let lo = 0; lo < 16; lo++) {
+        const h = SEQRET_CODES[hi];
+        const l = SEQRET_CODES[lo];
+        SEQRET_PAIR_CODES[(hi << 4) | lo] = LITTLE_ENDIAN
+            ? h | (l << 8)
+            : (h << 8) | l;
+        SEQRET_PAIR_STRINGS[(hi << 4) | lo] =
+            SEQRET_DECODER[hi] + SEQRET_DECODER[lo];
+    }
+}
+// Read length at which building a byte buffer and calling TextDecoder once
+// overtakes plain string concatenation. Below it concat wins by 2-4x (rope
+// building is cheap and the decode has fixed overhead); above it the decoder
+// wins by 5-8x. Measured crossover is ~300bp, i.e. just past typical Illumina
+// read lengths.
+const SEQ_DECODER_THRESHOLD = 300;
+// 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);
+// bit 3 is whether this read is the leftmost of the pair. The read2 flag (0x80)
+// is deliberately not consulted — "not read1" is what decides the numbering, so
+// a record with neither flag set reads the same as read2.
 // prettier-ignore
 const PAIR_ORIENTATION_TABLE = [
-    'F F ', 'F R ', 'R F ', 'R R ', 'F2F1', 'F2R1', 'R2F1', 'R2R1',
     'F1F2', 'F1R2', 'R1F2', 'R1R2', 'F2F1', 'F2R1', 'R2F1', 'R2R1',
-    'F F ', 'R F ', 'F R ', 'R R ', 'F1F2', 'R1F2', 'F1R2', 'R1R2',
     'F2F1', 'R2F1', 'F2R1', 'R2R1', 'F1F2', 'R1F2', 'F1R2', 'R1R2',
 ];
 const ASCII_CIGAR_CODES = [
@@ -23,10 +50,19 @@ const textDecoder = new TextDecoder();
 // Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
 // Binary: 0b111001101 = 0x1CD
 const CIGAR_CONSUMES_REF_MASK = 0x1cd;
+function isNumericCigar(value) {
+    return (value instanceof Uint32Array ||
+        value instanceof Int32Array ||
+        Array.isArray(value));
+}
 // Decode a 'B' (array) tag value starting at `p` (the byte after type+subtype+
 // count). When the data is naturally aligned we return a typed-array view over
 // the underlying buffer (zero-copy); otherwise we copy element-by-element since
-// typed-array views require alignment. Shared by getTag and the full-tag parse.
+// typed-array views require alignment. The copy target is a plain array, not a
+// typed one: benchmarking the unaligned path found number[] fills faster below
+// ~10k elements and reads at least as fast at every size, so the only thing a
+// typed copy would buy is half the retained bytes. Shared by getTag and the
+// full-tag parse.
 function decodeBArrayTag(ba, dataView, p, Btype, limit) {
     const absOffset = ba.byteOffset + p;
     switch (Btype) {
@@ -317,7 +353,9 @@ class BamRecord {
     _computeTags() {
         const blockEnd = this._end;
         const ba = this._byteArray;
-        const tags = {};
+        // null prototype: tag names come from the file, so a read carrying a
+        // "constructor" or "toString" tag must not resolve to Object.prototype's
+        const tags = Object.create(null);
         let p = this.tagsStart;
         while (p < blockEnd) {
             const tag = String.fromCharCode(ba[p], ba[p + 1]);
@@ -414,6 +452,8 @@ class BamRecord {
         const absOffset = this._byteArray.byteOffset + p;
         if (absOffset % 4 === 0 && numCigarOps > 50) {
             const cigarView = new Uint32Array(this._byteArray.buffer, absOffset, numCigarOps);
+            // the view we need to sum is exactly what NUMERIC_CIGAR would build, so
+            // seed its cache rather than making it construct a second one
             this._cachedNumericCigar = cigarView;
             let lref = 0;
             for (let c = 0; c < numCigarOps; ++c) {
@@ -437,8 +477,10 @@ class BamRecord {
         const numCigarOps = flag_nc & 0xffff;
         const p = this.b0 + this.read_name_length;
         if (this._isCGTagPattern(p, numCigarOps)) {
-            return (this.tags.CG ??
-                new Uint32Array(0));
+            // getTag, not this.tags: the real CIGAR lives in one tag, so there's no
+            // reason to decode every other tag on the record to reach it
+            const cg = this.getTag('CG');
+            return isNumericCigar(cg) ? cg : new Uint32Array(0);
         }
         const absOffset = this._byteArray.byteOffset + p;
         if (absOffset % 4 === 0 && numCigarOps > 50) {
@@ -489,37 +531,65 @@ 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.
     get seq() {
         const len = this.seq_length;
-        const seqStart = this.seqStart;
-        const numeric = this._byteArray;
-        const buf = new Array(len);
-        let i = 0;
-        const fullBytes = len >> 1;
-        for (let j = 0; j < fullBytes; ++j) {
-            const sb = numeric[seqStart + j];
-            buf[i++] = SEQRET_DECODER[(sb & 0xf0) >> 4];
-            buf[i++] = SEQRET_DECODER[sb & 0x0f];
-        }
-        if (i < len) {
-            const sb = numeric[seqStart + fullBytes];
-            buf[i] = SEQRET_DECODER[(sb & 0xf0) >> 4];
-        }
-        return buf.join('');
-    }
-    // adapted from igv.js
-    // uses precomputed lookup table indexed by flag bits + isize sign.
-    // the BAM spec defines tlen as positive for the leftmost segment and
-    // negative for the rightmost, so tlen > 0 reliably indicates which
-    // read comes first without needing position-based correction
+        const ba = this._byteArray;
+        const p = this.seqStart;
+        const nPairs = len >> 1;
+        let seq;
+        if (len < SEQ_DECODER_THRESHOLD) {
+            seq = '';
+            for (let j = 0; j < nPairs; j++) {
+                seq += SEQRET_PAIR_STRINGS[ba[p + j]];
+            }
+            if (len & 1) {
+                seq += SEQRET_DECODER[(ba[p + nPairs] & 0xf0) >> 4];
+            }
+        }
+        else {
+            // round up to an even length so the Uint16Array view spans every pair; a
+            // trailing odd base is written as a single byte and trimmed on decode
+            const out = new Uint8Array((len + 1) & ~1);
+            const pairs = new Uint16Array(out.buffer);
+            for (let j = 0; j < nPairs; j++) {
+                pairs[j] = SEQRET_PAIR_CODES[ba[p + j]];
+            }
+            if (len & 1) {
+                out[len - 1] = SEQRET_CODES[(ba[p + nPairs] & 0xf0) >> 4];
+            }
+            seq = textDecoder.decode(out.subarray(0, len));
+        }
+        return seq;
+    }
+    // Must come out identical from either mate, or the two halves of one normal
+    // pair render as different orientations. The leftmost mate is therefore picked
+    // by a total order on (refId, pos) that both mates evaluate the same way, with
+    // a read1-first tie-break for equal loci.
+    //
+    // Deriving "leftmost" from template_length looks tempting — the spec makes
+    // tlen positive for the leftmost segment and negative for the rightmost — but
+    // aligners leave tlen at 0 whenever the insert size is unavailable, which
+    // includes every cross-reference pair. Both mates then read as "not leftmost"
+    // and disagree with each other.
     // (see also: gmod/cram-js src/cramFile/record.ts getPairOrientation)
     get pair_orientation() {
         const f = this.flags;
-        // unmapped (0x4) or mate unmapped (0x8) -> undefined
-        if (f & 0xc || this.ref_id !== this.next_refid) {
+        if (!(f & constants_ts_1.default.BAM_FPAIRED)) {
             return undefined;
         }
-        return PAIR_ORIENTATION_TABLE[((f >> 4) & 0xf) | (this.template_length > 0 ? 16 : 0)];
+        const refId = this.ref_id;
+        const mateRefId = this.next_refid;
+        const pos = this.start;
+        const matePos = this.next_pos;
+        const selfIsLeft = refId !== mateRefId
+            ? refId < mateRefId
+            : pos !== matePos
+                ? pos < matePos
+                : !!(f & constants_ts_1.default.BAM_FREAD1);
+        return PAIR_ORIENTATION_TABLE[((f >> 4) & 0x7) | (selfIsLeft ? 8 : 0)];
     }
     get bin_mq_nl() {
         return this._dataView.getInt32(this._start + 12, true);
@@ -542,7 +612,7 @@ class BamRecord {
     seqAt(idx) {
         if (idx < this.seq_length) {
             const sb = this._byteArray[this.seqStart + (idx >> 1)];
-            return idx % 2 === 0
+            return (idx & 1) === 0
                 ? SEQRET_DECODER[(sb & 0xf0) >> 4]
                 : SEQRET_DECODER[sb & 0x0f];
         }

package/dist/record.js.map

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package/dist/util.d.ts

@@ -54,10 +54,10 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
 export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
 export declare function filterReadFlag(flags: number, flagInclude: number, flagExclude: number): boolean;
 export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;
-export declare function filterCacheKey(filterBy?: FilterBy): string;
 interface Filterable {
     flags: number;
     tags: Record<string, unknown>;
+    getTag?(tag: string): unknown;
 }
 export declare function applyFilters<T extends Filterable>(records: T[], filterBy: FilterBy): T[];
 interface Positioned {

package/dist/util.js

@@ -12,7 +12,6 @@ exports.parseNameBytes = parseNameBytes;
 exports.concatUint8Array = concatUint8Array;
 exports.filterReadFlag = filterReadFlag;
 exports.filterTagValue = filterTagValue;
-exports.filterCacheKey = filterCacheKey;
 exports.applyFilters = applyFilters;
 exports.appendInRange = appendInRange;
 const chunk_ts_1 = __importDefault(require("./chunk.js"));
@@ -120,9 +119,11 @@ function parseRefSeqs(uncba, start, renameRefSeq) {
     if (start + 4 > uncba.length) {
         return undefined;
     }
-    const dataView = new DataView(uncba.buffer);
+    const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
     const nRef = dataView.getInt32(start, true);
-    const chrToIndex = {};
+    // null prototype: ref names come from the file, so a contig named
+    // "constructor" must not resolve to Object.prototype's
+    const chrToIndex = Object.create(null);
     const indexToChr = [];
     const decoder = new TextDecoder('utf8');
     let p = start + 4;
@@ -155,7 +156,7 @@ function parseNameBytes(namesBytes, renameRefSeq = s => s) {
     let currRefId = 0;
     let currNameStart = 0;
     const refIdToName = [];
-    const refNameToId = {};
+    const refNameToId = Object.create(null);
     for (let i = 0; i < namesBytes.length; i++) {
         if (!namesBytes[i]) {
             if (currNameStart < i) {
@@ -190,13 +191,11 @@ function filterTagValue(readVal, filterVal) {
         ? readVal === undefined
         : `${readVal}` !== `${filterVal}`;
 }
-function filterCacheKey(filterBy) {
-    if (!filterBy) {
-        return '';
-    }
-    const { flagInclude = 0, flagExclude = 0, tagFilter } = filterBy;
-    const tagPart = tagFilter ? `:${tagFilter.tag}=${tagFilter.value ?? '*'}` : '';
-    return `:f${flagInclude}x${flagExclude}${tagPart}`;
+// Read a single tag, preferring the targeted accessor. Reaching for `tags`
+// instead would decode every unrelated tag on the record (NM/AS/ms/de/… — often
+// ~10 per read) just to test one, which measured 2.6x the cost of getTag.
+function readTag(record, tag) {
+    return record.getTag ? record.getTag(tag) : record.tags[tag];
 }
 // Apply flagInclude/flagExclude/tagFilter to a list of records.
 function applyFilters(records, filterBy) {
@@ -205,7 +204,7 @@ function applyFilters(records, filterBy) {
     for (let i = 0, l = records.length; i < l; i++) {
         const r = records[i];
         if (!filterReadFlag(r.flags, flagInclude, flagExclude) &&
-            !(tagFilter && filterTagValue(r.tags[tagFilter.tag], tagFilter.value))) {
+            !(tagFilter && filterTagValue(readTag(r, tagFilter.tag), tagFilter.value))) {
             out.push(r);
         }
     }

package/dist/util.js.map

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

@@ -30,7 +30,7 @@ function reg2bins(beg, end) {
 export default class BAI extends IndexFile {
     async _parse(opts) {
         const bytes = await this.filehandle.readFile(opts);
-        const dataView = new DataView(bytes.buffer);
+        const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
         // check BAI magic numbers
         if (dataView.getUint32(0, true) !== BAI_MAGIC) {
             throw new Error('Not a BAI file');
@@ -151,19 +151,22 @@ export default class BAI extends IndexFile {
         if (e > (linearIndex.length - 1) * v) {
             throw new Error('query outside of range of linear index');
         }
+        // Scale the block-delta into a read count as we go, rather than building the
+        // entries and then rebuilding every one of them to apply the scale. Keep the
+        // multiply-then-divide order: hoisting lineCount/totalSize into a factor
+        // reassociates the arithmetic and shifts scores by an ulp.
+        const lineCount = stats?.lineCount ?? 0;
         let currentPos = linearIndex[s / v].blockPosition;
         for (let i = s / v, j = 0; i < e / v; i++, j++) {
+            const nextPos = linearIndex[i + 1].blockPosition;
             depths[j] = {
-                score: linearIndex[i + 1].blockPosition - currentPos,
+                score: ((nextPos - currentPos) * lineCount) / totalSize,
                 start: i * v,
                 end: i * v + v,
             };
-            currentPos = linearIndex[i + 1].blockPosition;
+            currentPos = nextPos;
         }
-        return depths.map(d => ({
-            ...d,
-            score: (d.score * (stats?.lineCount ?? 0)) / totalSize,
-        }));
+        return depths;
     }
     reg2bins(min, max) {
         return reg2bins(min, max);

package/esm/bai.js.map

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package/esm/bamFile.d.ts

@@ -1,4 +1,3 @@
-import QuickLRU from '@jbrowse/quick-lru';
 import BAI from './bai.ts';
 import CSI from './csi.ts';
 import BAMFeature from './record.ts';
@@ -26,8 +25,23 @@ export declare const BAM_MAGIC = 21840194;
 interface ChunkEntry<T> {
     minBlock: number;
     maxBlock: number;
+    bytes: number;
     features: T[];
 }
+export declare const DEFAULT_MAX_CACHE_BYTES: number;
+declare class ChunkFeatureCache<T> {
+    maxBytes: number;
+    private entries;
+    private bytes;
+    constructor(maxBytes: number);
+    get size(): number;
+    get byteSize(): number;
+    get(key: string): ChunkEntry<T> | undefined;
+    set(key: string, entry: ChunkEntry<T>): void;
+    delete(key: string): void;
+    clear(): void;
+    [Symbol.iterator](): MapIterator<[string, ChunkEntry<T>]>;
+}
 export default class BamFile<T extends BamRecordLike = BAMFeature> {
     renameRefSeq: (a: string) => string;
     bam: GenericFilehandle;
@@ -40,9 +54,9 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     index?: BAI | CSI;
     htsget: boolean;
     headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
-    chunkFeatureCache: QuickLRU<string, ChunkEntry<T>>;
+    chunkFeatureCache: ChunkFeatureCache<T>;
     private RecordClass;
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, }: {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
         bamUrl?: string;
@@ -55,6 +69,8 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         renameRefSeqs?: (a: string) => string;
         htsget?: boolean;
         recordClass?: BamRecordClass<T>;
+        /** budget for the parsed-chunk cache, in decompressed bytes */
+        maxCacheBytes?: number;
     });
     getHeaderPre(opts?: BaseOpts): Promise<{
         tag: string;
@@ -74,10 +90,13 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     private getSeqId;
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
     private evictOverlappingChunks;
-    private _fetchChunkFeaturesDirect;
+    private _fetchChunkFeatures;
     fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
-    _readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<T[]>;
-    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<T[]>;
+    _readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<{
+        features: T[];
+        bytes: number;
+    }>;
+    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): T[];
     hasRefSeq(seqName: string, opts?: BaseOpts): Promise<boolean>;
     lineCount(seqName: string, opts?: BaseOpts): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<never[] | import("./bai.ts").IndexCovEntry[]>;