@gmod/bam 8.9.0 → 8.11.0

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>;

package/esm/streamBam.js

@@ -0,0 +1,221 @@
+import { MAX_BGZF_BLOCK_SIZE, scanBgzfBlocks, unzip, } from '@gmod/bgzf-filehandle';
+import BAMFeature from "./record.js";
+import { parseHeaderText } from "./sam.js";
+import { BAM_MAGIC, concatUint8Array, parseRefSeqs, resolveFilehandle, throwIfAborted, } from "./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 concatUint8Array(inflated);
+    }
+    return 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.
+ */
+export async function* streamBamRecords({ bamFilehandle, bamPath, bamUrl, recordClass, renameRefSeqs = n => n, signal, onHeader, bgzfWorkerPool, windowSize = DEFAULT_WINDOW_SIZE, readAhead = DEFAULT_READ_AHEAD, }) {
+    const bam = resolveFilehandle(bamFilehandle, bamPath, bamUrl);
+    if (!bam) {
+        throw new Error('no bam source: pass bamFilehandle, bamPath, or bamUrl');
+    }
+    const RecordClass = (recordClass ?? BAMFeature);
+    const readLen = Math.max(windowSize, 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) {
+            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
+                ? concatUint8Array([blockCarry, read])
+                : read;
+            if (compressed.length === 0) {
+                break;
+            }
+            const blocks = 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
+                ? 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) !== BAM_MAGIC) {
+                    throw new Error('not a BAM file: bad magic');
+                }
+                const lText = dataView.getInt32(4, true);
+                const refs = 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: 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/esm/streamBam.js.map

@@ -0,0 +1 @@
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package/esm/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/esm/util.js

@@ -1,5 +1,12 @@
+import { LocalFile, RemoteFile } from 'generic-filehandle2';
 import Chunk from "./chunk.js";
 import { VirtualOffset } from "./virtualOffset.js";
+/** 'BAM\1' read as a little-endian int32 */
+export const BAM_MAGIC = 21840194;
+export function resolveFilehandle(filehandle, path, url) {
+    return (filehandle ??
+        (path ? new LocalFile(path) : url ? new 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/esm/util.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "8.9.0",
+  "version": "8.11.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",

package/src/bamFile.ts

@@ -1,7 +1,6 @@
 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.ts'
 import CSI from './csi.ts'
@@ -10,9 +9,11 @@ import BAMFeature from './record.ts'
 import { packReference, referenceCovers } from './reference.ts'
 import { parseHeaderText } from './sam.ts'
 import {
+  BAM_MAGIC,
   MAX_CONCURRENT_CHUNK_READS,
   appendInRange,
   parseRefSeqs,
+  resolveFilehandle,
   throwIfAborted,
 } from './util.ts'
 
@@ -77,8 +78,6 @@ export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (
   dataView: DataView,
 ) => T
 
-export const BAM_MAGIC = 21840194
-
 const blockLen = 1 << 16
 
 // Ceiling on GROWING the header read. A million contigs is roughly 10MB of
@@ -90,17 +89,6 @@ const blockLen = 1 << 16
 // exact read. See getHeaderPre.
 const maxHeaderReadLen = 32 * 1024 * 1024
 
-function resolveFilehandle(
-  filehandle?: GenericFilehandle,
-  path?: string,
-  url?: string,
-) {
-  return (
-    filehandle ??
-    (path ? new LocalFile(path) : url ? new RemoteFile(url) : undefined)
-  )
-}
-
 interface ChunkEntry<T> {
   // decompressed size of the chunk these features are views into
   bytes: number
@@ -308,9 +296,10 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
      * A `@gmod/bgzf-filehandle` worker pool to inflate this file's chunks on,
      * instead of inflating them on the calling thread.
      *
-     * BGZF decompression is 70-90% of a cold query (ADR 0003), and BGZF blocks
-     * are independently inflatable, so this is the one remaining lever of that
-     * size. Measured 2.7-4.1x on the pool's own fixtures.
+     * Inflating the BGZF blocks is 70-90% of the wall clock of a query that
+     * finds nothing cached (ADR 0003), and BGZF blocks are independently
+     * inflatable, so this is the one remaining lever of that size. Measured
+     * 2.7-4.1x on the pool's own fixtures.
      *
      * Accepts the promise `getSharedWorkerPool()` returns as well as a pool,
      * so a caller whose own construction is synchronous can hand the pending
@@ -926,8 +915,8 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     // does not even take an options argument, so every read under it runs to
     // completion and arrives here with the cancellation unnoticed. Without this
     // a fully abandoned chunk still gets inflated and decoded — measured at 6
-    // chunks for one 20kb query on out.bam — which is the dominant cost of a
-    // cold query (ADR 0003), spent on records nobody will ever look at.
+    // chunks for one 20kb query on out.bam — which is where an uncached query
+    // spends most of its time (ADR 0003), on records nobody will ever look at.
     //
     // Safe precisely because this is the SHARED signal, not a caller's: it
     // fires only once every waiter has given up, so there is never a live

package/src/htsget.ts

@@ -1,8 +1,13 @@
 import { unzip } from '@gmod/bgzf-filehandle'
 
-import BamFile, { BAM_MAGIC } from './bamFile.ts'
+import BamFile from './bamFile.ts'
 import Chunk from './chunk.ts'
-import { appendInRange, concatUint8Array, parseRefSeqs } from './util.ts'
+import {
+  BAM_MAGIC,
+  appendInRange,
+  concatUint8Array,
+  parseRefSeqs,
+} from './util.ts'
 import { VirtualOffset } from './virtualOffset.ts'
 
 import type {

package/src/index.ts

@@ -8,6 +8,12 @@ export { default as CSI } from './csi.ts'
 export { default as BamRecord } from './record.ts'
 export { default as HtsgetFile } from './htsget.ts'
 
+// 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.ts'
+export type { BamStreamHeader, StreamBamOptions } from './streamBam.ts'
+
 // 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
@@ -47,5 +53,10 @@ export type { PackedReference } from './reference.ts'
 // getRecordsForRange/indexCov can only name these if they come out of here.
 export type { BamOpts, BaseOpts } from './util.ts'
 export type { IndexCovEntry } from './bai.ts'
+// `blocksForRange` hands these back, so a caller sizing or describing a query
+// off them needs to be able to name them. Type-only: chunks come out of the
+// index, and nothing outside builds one.
+export type { default as Chunk } from './chunk.ts'
+export type { Offset, OffsetCoords } from './virtualOffset.ts'
 // for typing the HtsgetFile `fetch` option
 export type { Fetcher } from 'generic-filehandle2'