@gmod/bam 8.10.0 → 8.11.0

package/dist/streamBam.js

@@ -0,0 +1,227 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.streamBamRecords = streamBamRecords;
+const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const record_ts_1 = __importDefault(require("./record.js"));
+const sam_ts_1 = require("./sam.js");
+const util_ts_1 = require("./util.js");
+/** compressed bytes per read; ~15 BGZF blocks, so ~8MB decompressed */
+const DEFAULT_WINDOW_SIZE = 1 << 20;
+/**
+ * Window reads in flight at once. Four, matching the browser's per-host
+ * connection cap of six with room left for whatever else the page is fetching,
+ * and holding 4MB of compressed bytes at the default window size.
+ */
+const DEFAULT_READ_AHEAD = 4;
+/**
+ * A window's blocks, inflated on the pool when there is one.
+ *
+ * The pool's own interface is what a window already has to hand: the raw
+ * compressed bytes and the {@link scanBgzfBlocks} listing the loop needed
+ * anyway to find the window's edge. It splits the blocks across its workers and
+ * hands them back individually, which concatenate to exactly what `unzip` of
+ * the same range returns — the blocks of a BGZF stream are independent, which
+ * is what makes any of this parallel.
+ *
+ * One block is not worth a round trip, the same threshold `unzipChunkSlice`
+ * uses. `pool` being undefined is the ordinary case, not a failure: node has no
+ * workers, and `getSharedWorkerPool` resolves to undefined there.
+ */
+async function inflate(compressed, blocks, blocksEnd, pool) {
+    if (pool && blocks.length > 1) {
+        const { blocks: inflated } = await pool.decompressBlocks(compressed, blocks);
+        return (0, util_ts_1.concatUint8Array)(inflated);
+    }
+    return (0, bgzf_filehandle_1.unzip)(compressed.subarray(0, blocksEnd));
+}
+/**
+ * Reads every record in a BAM, in file order, without an index.
+ *
+ * For BAMs that no index can address: unsorted, or name-sorted as they come off
+ * the sequencer. {@link BamFile} answers `chr:start-end` by seeking to the
+ * chunks an index names, which a file in neither order has none of.
+ *
+ * Yields records a batch at a time, one batch per window read, rather than one
+ * record per `yield`. A whole-file walk over a 1GB BAM is tens of millions of
+ * records, and an async generator pays a promise per yield — batching moves
+ * that cost to once per few thousand records and lets the caller's inner loop
+ * be synchronous:
+ *
+ * ```js
+ * for await (const records of streamBamRecords({ bamPath: 'reads.bam' })) {
+ *   for (const record of records) {
+ *     // ...
+ *   }
+ * }
+ * ```
+ *
+ * Deliberately a standalone function and not a `BamFile` method: it shares the
+ * record parser and header parser but none of the index, chunk or cache
+ * machinery, so a consumer who only streams does not pay for `BAI`/`CSI` in
+ * their bundle.
+ *
+ * Records are views into the window they were decompressed from, as everywhere
+ * else in this library. Holding one record from a batch retains that whole
+ * window (see {@link StreamBamOptions.windowSize}), so copy out the fields you
+ * want rather than keeping a sparse selection of records from a large file.
+ */
+async function* streamBamRecords({ bamFilehandle, bamPath, bamUrl, recordClass, renameRefSeqs = n => n, signal, onHeader, bgzfWorkerPool, windowSize = DEFAULT_WINDOW_SIZE, readAhead = DEFAULT_READ_AHEAD, }) {
+    const bam = (0, util_ts_1.resolveFilehandle)(bamFilehandle, bamPath, bamUrl);
+    if (!bam) {
+        throw new Error('no bam source: pass bamFilehandle, bamPath, or bamUrl');
+    }
+    const RecordClass = (recordClass ?? record_ts_1.default);
+    const readLen = Math.max(windowSize, bgzf_filehandle_1.MAX_BGZF_BLOCK_SIZE);
+    const depth = Math.max(1, Math.floor(readAhead));
+    let filePosition = 0;
+    // trailing bytes of the last window that did not complete a BGZF block, and
+    // that did not complete a BAM record, respectively. Both boundaries fall
+    // wherever they fall, so each window starts by finishing the last one's
+    // remainder.
+    let blockCarry;
+    let recordCarry;
+    let sawHeader = false;
+    // 1-based, as readBamFeatures' virtual-offset ids are
+    let recordIndex = 0;
+    const pool = await bgzfWorkerPool;
+    // Several windows are in flight at once, consumed in the order they were
+    // asked for. Depth is what makes this worth doing: with one read outstanding
+    // the wait for a window can only overlap the CPU spent on the window before
+    // it, which is a fraction of a round trip — measured at no gain at all, where
+    // depth 4 hides most of the latency instead. See {@link
+    // StreamBamOptions.readAhead}.
+    const queue = [];
+    let nextReadPosition = 0;
+    let exhausted = false;
+    // Widened to `depth` only once a read has come back full-length, i.e. once
+    // the file is known to be longer than one window. Opening at full depth
+    // would fetch a BAM smaller than a window in four requests, three of them
+    // answered 416, which is the common case for a small file and looks like a
+    // bug from the network tab. The ramp costs one round trip of depth on a file
+    // big enough to want it, out of however many windows it takes.
+    let allowed = 1;
+    const topUp = () => {
+        while (!exhausted && queue.length < allowed) {
+            queue.push(bam.read(readLen, nextReadPosition, { signal }));
+            nextReadPosition += readLen;
+        }
+    };
+    // Reads nobody will consume — queued past EOF, or still out when the caller
+    // broke out of the loop or a window threw. Each needs its rejection taken,
+    // or a failing read that arrives after we have stopped looking surfaces as
+    // an unhandled rejection.
+    const abandon = () => {
+        for (const p of queue.splice(0)) {
+            p.catch(() => undefined);
+        }
+    };
+    try {
+        topUp();
+        while (queue.length > 0) {
+            (0, util_ts_1.throwIfAborted)(signal);
+            const read = await queue.shift();
+            filePosition += read.length;
+            // A short read is the end of the file — the filehandles here return
+            // exactly what was asked for until then, and an empty buffer past it.
+            // The reads already queued behind it are past EOF; drop them rather than
+            // decompressing empty buffers.
+            if (read.length < readLen) {
+                exhausted = true;
+                abandon();
+            }
+            else {
+                allowed = depth;
+            }
+            topUp();
+            const compressed = blockCarry
+                ? (0, util_ts_1.concatUint8Array)([blockCarry, read])
+                : read;
+            if (compressed.length === 0) {
+                break;
+            }
+            const blocks = (0, bgzf_filehandle_1.scanBgzfBlocks)(compressed, 0, Number.POSITIVE_INFINITY);
+            const last = blocks.at(-1);
+            if (!last) {
+                throw new Error(`not a BGZF stream: no valid block at byte ${filePosition - compressed.length}`);
+            }
+            const blocksEnd = last.inputOffset + last.compressedSize;
+            // copied, not subarray'd: the remainder is carried across an await, and a
+            // view would pin the whole window it came from
+            blockCarry =
+                blocksEnd < compressed.length ? compressed.slice(blocksEnd) : undefined;
+            const decompressed = await inflate(compressed, blocks, blocksEnd, pool);
+            const bytes = recordCarry
+                ? (0, util_ts_1.concatUint8Array)([recordCarry, decompressed])
+                : decompressed;
+            const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
+            let blockStart = 0;
+            if (!sawHeader) {
+                if (bytes.length < 8 || dataView.getInt32(0, true) !== util_ts_1.BAM_MAGIC) {
+                    throw new Error('not a BAM file: bad magic');
+                }
+                const lText = dataView.getInt32(4, true);
+                const refs = (0, util_ts_1.parseRefSeqs)(bytes, 8 + lText, renameRefSeqs);
+                if (!refs) {
+                    // a header with enough contigs to span a window: keep the whole thing
+                    // and try again with more of it
+                    recordCarry = bytes;
+                    continue;
+                }
+                const headerText = new TextDecoder('utf8').decode(bytes.subarray(8, 8 + lText));
+                onHeader?.({
+                    headerText,
+                    samHeader: (0, sam_ts_1.parseHeaderText)(headerText),
+                    chrToIndex: refs.chrToIndex,
+                    indexToChr: refs.indexToChr,
+                });
+                sawHeader = true;
+                blockStart = refs.end;
+            }
+            const sink = [];
+            while (blockStart + 4 <= bytes.length) {
+                const blockSize = dataView.getInt32(blockStart, true);
+                const blockEnd = blockStart + 4 + blockSize - 1;
+                if (blockEnd >= bytes.length) {
+                    break;
+                }
+                sink.push(new RecordClass(bytes, blockStart, blockEnd, 
+                // An indexed read derives fileOffset from the record's BGZF virtual
+                // offset, which nothing here has: there is no index to seek back
+                // with. Its ordinal in the file is the other thing that identifies a
+                // record by position, and it is the same for a given file whatever
+                // the window size, so it is as stable as a virtual offset without
+                // pretending to be one.
+                //
+                // NOT the crc32 of the record bytes that readBamFeatures falls back
+                // to when it has no positions. That is a content hash, so the two
+                // byte-identical records in exact_duplicate.bam collide on it, and
+                // hashing every record costs ~40% of the walk (135ms of 340ms over
+                // out.bam) where a counter costs nothing. The fallback only fires on
+                // an unusual path there; here it would fire on every record.
+                recordIndex++, dataView));
+                blockStart = blockEnd + 1;
+            }
+            recordCarry =
+                blockStart < bytes.length ? bytes.slice(blockStart) : undefined;
+            if (sink.length > 0) {
+                yield sink;
+            }
+        }
+    }
+    finally {
+        abandon();
+    }
+    if (!sawHeader) {
+        throw new Error('Insufficient data for reference sequences');
+    }
+    if (blockCarry !== undefined) {
+        throw new Error(`truncated BAM: ${blockCarry.length} trailing bytes are not a complete BGZF block`);
+    }
+    if (recordCarry !== undefined) {
+        throw new Error(`truncated BAM: ${recordCarry.length} bytes left after the last complete record`);
+    }
+}
+//# sourceMappingURL=streamBam.js.map

package/dist/streamBam.js.map

@@ -0,0 +1 @@
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package/dist/util.d.ts

@@ -1,6 +1,10 @@
 import Chunk from './chunk.ts';
 import { VirtualOffset } from './virtualOffset.ts';
 import type { OffsetCoords } from './virtualOffset.ts';
+import type { GenericFilehandle } from 'generic-filehandle2';
+/** 'BAM\1' read as a little-endian int32 */
+export declare const BAM_MAGIC = 21840194;
+export declare function resolveFilehandle(filehandle?: GenericFilehandle, path?: string, url?: string): GenericFilehandle | undefined;
 export interface BamOpts {
     viewAsPairs?: boolean;
     pairAcrossChr?: boolean;

package/dist/util.js

@@ -3,7 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MAX_CONCURRENT_CHUNK_READS = exports.throwIfAborted = void 0;
+exports.MAX_CONCURRENT_CHUNK_READS = exports.throwIfAborted = exports.BAM_MAGIC = void 0;
+exports.resolveFilehandle = resolveFilehandle;
 exports.chunksLikelyRead = chunksLikelyRead;
 exports.optimizeChunks = optimizeChunks;
 exports.parsePseudoBin = parsePseudoBin;
@@ -13,8 +14,15 @@ exports.minVirtualOffset = minVirtualOffset;
 exports.parseNameBytes = parseNameBytes;
 exports.concatUint8Array = concatUint8Array;
 exports.appendInRange = appendInRange;
+const generic_filehandle2_1 = require("generic-filehandle2");
 const chunk_ts_1 = __importDefault(require("./chunk.js"));
 const virtualOffset_ts_1 = require("./virtualOffset.js");
+/** 'BAM\1' read as a little-endian int32 */
+exports.BAM_MAGIC = 21840194;
+function resolveFilehandle(filehandle, path, url) {
+    return (filehandle ??
+        (path ? new generic_filehandle2_1.LocalFile(path) : url ? new generic_filehandle2_1.RemoteFile(url) : undefined));
+}
 // Re-exported so the internal import path stays './util.ts'. The
 // implementation moved to @gmod/shared-read-cache, which needs it anyway --
 // every consumer of that package was carrying an identical copy.

package/dist/util.js.map

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

@@ -48,7 +48,6 @@ export interface BamRecordLike {
  */
 export type ReferenceSequenceFetcher = (refName: string, start: number, end: number, opts?: BaseOpts) => Promise<string>;
 export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView) => T;
-export declare const BAM_MAGIC = 21840194;
 interface ChunkEntry<T> {
     bytes: number;
     features: T[];

package/esm/bamFile.js

@@ -1,15 +1,13 @@
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
 import { SharedReadCache } from '@gmod/shared-read-cache';
 import crc32 from 'crc/calculators/crc32';
-import { LocalFile, RemoteFile } from 'generic-filehandle2';
 import BAI from "./bai.js";
 import CSI from "./csi.js";
 import NullFilehandle from "./nullFilehandle.js";
 import BAMFeature from "./record.js";
 import { packReference, referenceCovers } from "./reference.js";
 import { parseHeaderText } from "./sam.js";
-import { MAX_CONCURRENT_CHUNK_READS, appendInRange, parseRefSeqs, throwIfAborted, } from "./util.js";
-export const BAM_MAGIC = 21840194;
+import { BAM_MAGIC, MAX_CONCURRENT_CHUNK_READS, appendInRange, parseRefSeqs, resolveFilehandle, throwIfAborted, } from "./util.js";
 const blockLen = 1 << 16;
 // 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
@@ -19,10 +17,6 @@ const blockLen = 1 << 16;
 // 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 ??
-        (path ? new LocalFile(path) : url ? new RemoteFile(url) : undefined));
-}
 /**
  * Whether a chunk's first record already lies past `chrId:..-max`, which means
  * every later chunk does too and none of them need to be read.

package/esm/bamFile.js.map

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

@@ -1,7 +1,7 @@
 import { unzip } from '@gmod/bgzf-filehandle';
-import BamFile, { BAM_MAGIC } from "./bamFile.js";
+import BamFile from "./bamFile.js";
 import Chunk from "./chunk.js";
-import { appendInRange, concatUint8Array, parseRefSeqs } from "./util.js";
+import { BAM_MAGIC, appendInRange, concatUint8Array, parseRefSeqs, } from "./util.js";
 import { VirtualOffset } from "./virtualOffset.js";
 // Errors carry a JSON body naming the error type, e.g. {"htsget":
 // {"error":"InvalidAuthentication","message":"..."}}. Surface that rather than

package/esm/htsget.js.map

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

@@ -3,6 +3,8 @@ export { DEFAULT_CACHE_IDLE_TIMEOUT_MS, DEFAULT_MAX_CACHE_BYTES, default as BamF
 export { default as CSI } from './csi.ts';
 export { default as BamRecord } from './record.ts';
 export { default as HtsgetFile } from './htsget.ts';
+export { streamBamRecords } from './streamBam.ts';
+export type { BamStreamHeader, StreamBamOptions } from './streamBam.ts';
 export { MISMATCH_DELETION, MISMATCH_HARD_CLIP, MISMATCH_INSERTION, MISMATCH_REF_SKIP, MISMATCH_SOFT_CLIP, MISMATCH_SUBST, forEachMismatchNumeric, } from './mismatches.ts';
 export { CHAR_CODE_FROM_NIBBLE, packReference, referenceNibble, } from './reference.ts';
 export type { NumericCigar } from './record.ts';

package/esm/index.js

@@ -3,6 +3,10 @@ export { DEFAULT_CACHE_IDLE_TIMEOUT_MS, DEFAULT_MAX_CACHE_BYTES, default as BamF
 export { default as CSI } from "./csi.js";
 export { default as BamRecord } from "./record.js";
 export { default as HtsgetFile } from "./htsget.js";
+// The index-free whole-file walk, for BAMs an index cannot address. Kept out of
+// BamFile so that streaming it does not drag BAI/CSI and the chunk cache into a
+// consumer's bundle.
+export { streamBamRecords } from "./streamBam.js";
 // The mismatch walk, and the codes it reports differences as. The walk is
 // exported alongside `record.forEachMismatch` for callers holding BAM's packed
 // arrays without a record around them — a SAM parser, or a worker that was

package/esm/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EACL,6BAA6B,EAC7B,uBAAuB,EACvB,OAAO,IAAI,OAAO,GACnB,MAAM,cAAc,CAAA;AACrB,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA;AAEnD,gFAAgF;AAChF,gFAAgF;AAChF,qBAAqB;AACrB,OAAO,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAA;AAGjD,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,OAAO,EACL,iBAAiB,EACjB,kBAAkB,EAClB,kBAAkB,EAClB,iBAAiB,EACjB,kBAAkB,EAClB,cAAc,EACd,sBAAsB,GACvB,MAAM,iBAAiB,CAAA;AACxB,8EAA8E;AAC9E,6EAA6E;AAC7E,oEAAoE;AACpE,OAAO,EACL,qBAAqB,EACrB,aAAa,EACb,eAAe,GAChB,MAAM,gBAAgB,CAAA"}

package/esm/streamBam.d.ts

@@ -0,0 +1,101 @@
+import BAMFeature from './record.ts';
+import { parseHeaderText } from './sam.ts';
+import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
+import type { BgzfWorkerPool } from '@gmod/bgzf-filehandle';
+import type { GenericFilehandle } from 'generic-filehandle2';
+export interface BamStreamHeader {
+    /** the raw SAM header text, i.e. what `samtools view -H` prints */
+    headerText: string;
+    /** the same text parsed into `@HD`/`@SQ`/`@RG`… lines and their tags */
+    samHeader: ReturnType<typeof parseHeaderText>;
+    /** ref name to the `refId` records carry, from the binary ref-seq table */
+    chrToIndex: Record<string, number>;
+    /** the inverse, indexed by `refId` */
+    indexToChr: {
+        refName: string;
+        length: number;
+    }[];
+}
+export interface StreamBamOptions<T extends BamRecordLike = BAMFeature> {
+    bamFilehandle?: GenericFilehandle;
+    bamPath?: string;
+    bamUrl?: string;
+    recordClass?: BamRecordClass<T>;
+    renameRefSeqs?: (a: string) => string;
+    signal?: AbortSignal;
+    /**
+     * Fires once, before the first batch, with everything the ref-seq table and
+     * header text hold. A callback rather than a separate call, because the
+     * stream has to read the header anyway to find where the records start —
+     * making it a method would mean either reading the front of the file twice
+     * or holding state between two calls.
+     */
+    onHeader?: (header: BamStreamHeader) => void;
+    /**
+     * Worker pool to inflate each window on, as in {@link BamFile}. Without one
+     * the whole walk inflates on the calling thread, which on a large file is
+     * long enough to be worth keeping off whichever thread draws — pass
+     * `getSharedWorkerPool()` in a browser, or run the stream in a worker.
+     *
+     * Takes the promise as readily as the pool, since `getSharedWorkerPool()`
+     * returns one and awaiting an already-settled promise costs a microtask.
+     */
+    bgzfWorkerPool?: BgzfWorkerPool | Promise<BgzfWorkerPool | undefined>;
+    /**
+     * How many window reads to keep in flight at once. Defaults to
+     * {@link DEFAULT_READ_AHEAD}; 1 issues the next read only once the previous
+     * window has been handed to the caller.
+     *
+     * Depth is the whole point of it. One outstanding read overlaps a round trip
+     * with only the CPU spent on the window before it — 8% end to end over a
+     * local server with 20ms of latency — because the wait itself is still
+     * serial. Several outstanding turn N waits into roughly N/depth.
+     *
+     * Costs `depth` windows of compressed bytes held at once, and up to
+     * `depth - 1` wasted requests at EOF: a read's length is the only thing that
+     * says the file has ended, so the reads queued behind the last one have
+     * already gone out by the time it lands. A file that fits in a single window
+     * pays neither — the depth only opens up once a read comes back full.
+     */
+    readAhead?: number;
+    /**
+     * Compressed bytes to read per request. The default reads ~1MB at a time,
+     * which is a reasonable HTTP request size and bounds how much sits
+     * decompressed at once (~8MB, since BGZF blocks are capped at 64KB and
+     * compress ~8x). Values below one maximum-size block are raised to it, since
+     * a window that cannot hold a whole block can never make progress.
+     */
+    windowSize?: number;
+}
+/**
+ * Reads every record in a BAM, in file order, without an index.
+ *
+ * For BAMs that no index can address: unsorted, or name-sorted as they come off
+ * the sequencer. {@link BamFile} answers `chr:start-end` by seeking to the
+ * chunks an index names, which a file in neither order has none of.
+ *
+ * Yields records a batch at a time, one batch per window read, rather than one
+ * record per `yield`. A whole-file walk over a 1GB BAM is tens of millions of
+ * records, and an async generator pays a promise per yield — batching moves
+ * that cost to once per few thousand records and lets the caller's inner loop
+ * be synchronous:
+ *
+ * ```js
+ * for await (const records of streamBamRecords({ bamPath: 'reads.bam' })) {
+ *   for (const record of records) {
+ *     // ...
+ *   }
+ * }
+ * ```
+ *
+ * Deliberately a standalone function and not a `BamFile` method: it shares the
+ * record parser and header parser but none of the index, chunk or cache
+ * machinery, so a consumer who only streams does not pay for `BAI`/`CSI` in
+ * their bundle.
+ *
+ * Records are views into the window they were decompressed from, as everywhere
+ * else in this library. Holding one record from a batch retains that whole
+ * window (see {@link StreamBamOptions.windowSize}), so copy out the fields you
+ * want rather than keeping a sparse selection of records from a large file.
+ */
+export declare function streamBamRecords<T extends BamRecordLike = BAMFeature>({ bamFilehandle, bamPath, bamUrl, recordClass, renameRefSeqs, signal, onHeader, bgzfWorkerPool, windowSize, readAhead, }: StreamBamOptions<T>): AsyncGenerator<T[], void, undefined>;