npm - @gmod/bam - Versions diffs - 8.10.0 → 8.11.1 - Mend

@gmod/bam 8.10.0 → 8.11.1

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

Files changed (35) hide show

package/README.md CHANGED Viewed

@@ -34,9 +34,26 @@ const bam = new BamFile({
 })
 ```
-Records come back unfiltered, and are shared between overlapping queries — treat
-them as read-only. Filter them yourself with the flag helpers and `getTag`,
-which decodes one tag instead of all of them:
+Over HTTP it is worth putting
+[`@gmod/range-cache-filehandle`](https://github.com/GMOD/range-cache-filehandle)
+underneath the filehandle. It caches what it reads in 256 KiB chunks and turns
+the chunks a read is missing into one request per contiguous run, so the
+scattered index and data reads a query makes arrive as a couple of fetches
+rather than dozens. `bamFilehandle` and `baiFilehandle` accept any
+generic-filehandle2 object, so it drops straight in:
+```typescript
+import { RemoteFileWithRangeCache } from '@gmod/range-cache-filehandle'
+const bam = new BamFile({
+  bamFilehandle: new RemoteFileWithRangeCache(url),
+  baiFilehandle: new RemoteFileWithRangeCache(`${url}.bai`),
+})
+```
+Records come back unfiltered, and overlapping queries share them — treat them as
+read-only. Filter them yourself with the flag helpers and `getTag`, which
+decodes one tag instead of all of them:
 ```typescript
 const records = (await bam.getRecordsForRange('chr1', 0, 100000)).filter(
@@ -44,6 +61,27 @@ const records = (await bam.getRecordsForRange('chr1', 0, 100000)).filter(
 )
 ```
+## Unsorted BAM
+A BAM that is unsorted, or still name-sorted as it came off the sequencer, has
+no index to query and so no `chr:start-end` to query it with. `streamBamRecords`
+walks one end to end instead, a batch of records at a time:
+```typescript
+import { streamBamRecords } from '@gmod/bam'
+for await (const records of streamBamRecords({ bamUrl: 'unsorted.bam' })) {
+  for (const record of records) {
+    // ...
+  }
+}
+```
+It reads the file a window at a time rather than all at once, so a 1GB BAM
+streams through in bounded memory. A standalone function rather than a `BamFile`
+method, so that streaming alone leaves `BAI`/`CSI` and the chunk cache out of
+your bundle. See [docs/api.md](docs/api.md) for `onHeader` and the window size.
 ## Mismatches
 `record.getMismatches()` gives every difference between a read and the reference
@@ -77,7 +115,7 @@ fields say, with that read walked through them:
 Substitutions need either an `MD` tag on the read or the reference bases, which
 is what `fetchReferenceSequence` is doing above — most aligners leave `MD` off,
-and it is called only if some read in the query needs it. Without it, a read
+and a query calls it only when one of its reads needs it. Without it, a read
 lacking `MD` still reports its indels and clips but no substitutions — nothing
 in the record says where they are. [docs/api.md](docs/api.md#mismatches) has the
 field meanings, and what to do about reads that run past the region you are
@@ -86,22 +124,22 @@ looking at.
 ## How a query flows
 A query turns the region into BGZF chunks through the index and decompresses
-each one in wasm. When nothing is cached yet, 70-90% of the time it takes to
-answer that query is spent decompressing. The rest is ordinary JS: records are
-views into their chunk's decompressed buffer, and their fields decode on access,
-so a query costs what you read off it. [docs/dataflow.md](docs/dataflow.md) has
-the diagram and walks it through.
-Those decompressed chunks are then kept, so overlapping and adjacent queries
-reuse them instead of inflating again — up to 1GB per file, dropped after three
-idle minutes. A consumer holding one file per track should bound them together
-with a shared `cacheBudget` rather than shrinking each file's own ceiling:
-[docs/caching.md](docs/caching.md).
+each one in wasm. With nothing cached yet, decompression takes 70-90% of the
+time that query needs. The rest is ordinary JS: records are views into their
+chunk's decompressed buffer, and their fields decode on access, so a query costs
+what you read off it. [docs/dataflow.md](docs/dataflow.md) has the diagram and
+walks it through.
+The file then holds on to those decompressed chunks, so overlapping and adjacent
+queries reuse them instead of inflating again — up to 1GB per file, dropped
+after three idle minutes. A consumer holding one file per track should bound
+them together with a shared `cacheBudget` rather than shrinking each file's own
+ceiling: [docs/caching.md](docs/caching.md).
 ## Decompressing on a worker pool
-BGZF blocks are independently inflatable, so that decompression can be spread
-across threads — measured 2.7-4.1x on the pool's own fixtures.
+BGZF blocks inflate independently, so that decompression can spread across
+threads — measured 2.7-4.1x on the pool's own fixtures.
 ```typescript
 import { getSharedWorkerPool } from '@gmod/bgzf-filehandle'
@@ -113,8 +151,8 @@ const bam = new BamFile({
 })
 ```
-Safe to pass unconditionally: `getSharedWorkerPool()` is `undefined` under node,
-or anywhere Workers cannot be created, which keeps the in-process path. No
+Safe to pass unconditionally: `getSharedWorkerPool()` returns `undefined` under
+node, or anywhere the host forbids Workers, which keeps the in-process path. No
 cross-origin isolation needed. bam-js never creates a pool on its own — the
 thread budget belongs to the consumer. Worker counts, lifecycle and benchmarks:
 [bgzf-filehandle's worker pool docs](https://github.com/GMOD/bgzf-filehandle/blob/main/docs/worker-pool.md).
@@ -131,8 +169,8 @@ const bam = new HtsgetFile({
 const records = await bam.getRecordsForRange('1', 2000000, 2000001)
 ```
-htsget fetches the server's range as-is, so the mate-pairing options are
-ignored. Pass a `fetch` to add auth:
+htsget fetches the server's range as-is, so it ignores the mate-pairing options.
+Pass a `fetch` to add auth:
 ```typescript
 const bam = new HtsgetFile({
@@ -146,16 +184,16 @@ const bam = new HtsgetFile({
 })
 ```
-That `fetch` is called for the ticket request _and_ for the data-block urls the
-ticket points at, which may live on a third-party host — so only attach
-credentials to hosts you trust.
+That `fetch` serves the ticket request _and_ the data-block urls the ticket
+points at, which may live on a third-party host — so only attach credentials to
+hosts you trust.
 ## Docs
 - [docs/api.md](docs/api.md) — every constructor option, method and `BamRecord`
   field, plus custom record classes
 - [docs/cigar-and-md.md](docs/cigar-and-md.md) — what `CIGAR` and `MD` say, and
-  how mismatches are decoded from them
+  how the walk reads mismatches out of them
 - [docs/dataflow.md](docs/dataflow.md) — how a query flows, and where wasm sits
 - [docs/optimizations.md](docs/optimizations.md) — why each step of that path
   looks the way it does, and what measured it

package/dist/bamFile.d.ts CHANGED Viewed

@@ -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/dist/bamFile.js CHANGED Viewed

@@ -3,11 +3,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.DEFAULT_MAX_CACHE_BYTES = exports.BAM_MAGIC = void 0;
+exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.DEFAULT_MAX_CACHE_BYTES = void 0;
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const shared_read_cache_1 = require("@gmod/shared-read-cache");
 const crc32_1 = __importDefault(require("crc/calculators/crc32"));
-const generic_filehandle2_1 = require("generic-filehandle2");
 const bai_ts_1 = __importDefault(require("./bai.js"));
 const csi_ts_1 = __importDefault(require("./csi.js"));
 const nullFilehandle_ts_1 = __importDefault(require("./nullFilehandle.js"));
@@ -15,7 +14,6 @@ const record_ts_1 = __importDefault(require("./record.js"));
 const reference_ts_1 = require("./reference.js");
 const sam_ts_1 = require("./sam.js");
 const util_ts_1 = require("./util.js");
-exports.BAM_MAGIC = 21840194;
 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
@@ -25,10 +23,6 @@ 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 generic_filehandle2_1.LocalFile(path) : url ? new generic_filehandle2_1.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.
@@ -131,7 +125,7 @@ class BamFile {
             cacheKey: chunkCacheKey,
             fill: (chunk, signal) => this._readChunkFeatures(chunk, { signal }),
         });
-        const bamFh = resolveFilehandle(bamFilehandle, bamPath, bamUrl);
+        const bamFh = (0, util_ts_1.resolveFilehandle)(bamFilehandle, bamPath, bamUrl);
         if (bamFh) {
             this.bam = bamFh;
         }
@@ -142,9 +136,9 @@ class BamFile {
         else {
             throw new Error('no bam source: pass bamFilehandle, bamPath, bamUrl, or htsget: true');
         }
-        const csiFh = resolveFilehandle(csiFilehandle, csiPath, csiUrl);
-        const baiFh = resolveFilehandle(baiFilehandle, baiPath, baiUrl) ??
-            resolveFilehandle(undefined, bamPath ? `${bamPath}.bai` : undefined, bamUrl ? `${bamUrl}.bai` : undefined);
+        const csiFh = (0, util_ts_1.resolveFilehandle)(csiFilehandle, csiPath, csiUrl);
+        const baiFh = (0, util_ts_1.resolveFilehandle)(baiFilehandle, baiPath, baiUrl) ??
+            (0, util_ts_1.resolveFilehandle)(undefined, bamPath ? `${bamPath}.bai` : undefined, bamUrl ? `${bamUrl}.bai` : undefined);
         if (csiFh) {
             this.index = new csi_ts_1.default({ filehandle: csiFh });
         }
@@ -203,7 +197,7 @@ class BamFile {
      */
     applyHeader(uncba) {
         const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
-        if (dataView.getInt32(0, true) !== exports.BAM_MAGIC) {
+        if (dataView.getInt32(0, true) !== util_ts_1.BAM_MAGIC) {
             throw new Error('Not a BAM file');
         }
         const headLen = dataView.getInt32(4, true);
@@ -579,13 +573,15 @@ class BamFile {
             signal: opts.signal,
         });
         // The last chance to bail before the expensive part, and the reason it is
-        // worth having: honouring the signal is optional in the filehandle.
-        // `RemoteFile` hands it to `fetch`, but `LocalFile.read(length, position)`
-        // 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 where an uncached query
-        // spends most of its time (ADR 0003), on records nobody will ever look at.
+        // worth having: a filehandle can only honour the signal as far as its
+        // transport allows. `RemoteFile` hands it to `fetch` and is cancelled
+        // outright; `LocalFile` takes the signal and checks it either side of the
+        // read, but node's fs has no signal on `FileHandle.read`, so the read
+        // itself runs to completion whatever happens 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 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/dist/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/htsget.js CHANGED Viewed

@@ -1,43 +1,10 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-const bamFile_ts_1 = __importStar(require("./bamFile.js"));
+const bamFile_ts_1 = __importDefault(require("./bamFile.js"));
 const chunk_ts_1 = __importDefault(require("./chunk.js"));
 const util_ts_1 = require("./util.js");
 const virtualOffset_ts_1 = require("./virtualOffset.js");
@@ -73,7 +40,7 @@ function htsgetErrorMessage(text) {
  */
 function recordsOffset(uncba) {
     const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
-    if (uncba.byteLength < 8 || dataView.getInt32(0, true) !== bamFile_ts_1.BAM_MAGIC) {
+    if (uncba.byteLength < 8 || dataView.getInt32(0, true) !== util_ts_1.BAM_MAGIC) {
         return 0;
     }
     const refs = (0, util_ts_1.parseRefSeqs)(uncba, 8 + dataView.getInt32(4, true), n => n);

package/dist/htsget.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAE7C,8DAAkC;AAClC,0DAA8B;AAC9B,uCAKkB;AAClB,yDAAkD;AA2BlD,kEAAkE;AAClE,+EAA+E;AAC/E,iFAAiF;AACjF,SAAS,kBAAkB,CAAC,IAAY;IACtC,IAAI,MAAmC,CAAA;IACvC,IAAI,CAAC;QACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IAAC,MAAM,CAAC;QACP,yCAAyC;IAC3C,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,EAAE,MAAM,CAAA;IAC1B,OAAO,GAAG,EAAE,KAAK,KAAK,SAAS;QAC7B,CAAC,CAAC,IAAI;QACN,CAAC,CAAC,GAAG,CAAC,OAAO,KAAK,SAAS;YACzB,CAAC,CAAC,GAAG,CAAC,KAAK;YACX,CAAC,CAAC,GAAG,GAAG,CAAC,KAAK,KAAK,GAAG,CAAC,OAAO,EAAE,CAAA;AACtC,CAAC;AAED;;;;;;;;;;;GAWG;AACH,SAAS,aAAa,CAAC,KAAiB;IACtC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;IACD,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,mBAAS,EAAE,CAAC;QACrE,OAAO,CAAC,CAAA;IACV,CAAC;IACD,MAAM,IAAI,GAAG,IAAA,sBAAY,EAAC,KAAK,EAAE,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACxE,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CAAC,yCAAyC,CAAC,CAAA;IAC5D,CAAC;IACD,OAAO,IAAI,CAAC,GAAG,CAAA;AACjB,CAAC;AAED,KAAK,UAAU,OAAO,CAAC,OAAgB,EAAE,GAAW,EAAE,IAAkB;IACtE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACpC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,kBAAkB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,EAAE,CAC9E,CAAA;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,KAAK,UAAU,UAAU,CACvB,OAAgB,EAChB,EAAE,GAAG,EAAE,OAAO,EAAe,EAC7B,IAAkB;IAElB,0EAA0E;IAC1E,uDAAuD;IACvD,+CAA+C;IAC/C,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,IAAI,EAAE,CAAA;IACpD,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC;QACjC,CAAC,CAAC,MAAM,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC;QAC7B,CAAC,CAAC,MAAM,OAAO,CAAC,OAAO,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAC3D,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;AAChD,CAAC;AAED,KAAK,UAAU,cAAc,CAC3B,OAAgB,EAChB,GAAkB,EAClB,IAAkB;IAElB,2EAA2E;IAC3E,OAAO,IAAA,0BAAgB,EACrB,MAAM,OAAO,CAAC,GAAG,CACf,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,MAAM,UAAU,CAAC,OAAO,EAAE,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAC9D,CACF,CAAA;AACH,CAAC;AAED,MAAqB,UAEnB,SAAQ,oBAAU;IACV,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEf,OAAO,CAAS;IAExB,YAAY,IAiCX;QACC,KAAK,CAAC;YACJ,MAAM,EAAE,IAAI;YACZ,WAAW,EAAE,IAAI,CAAC,WAAW;YAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;YACjC,kBAAkB,EAAE,IAAI,CAAC,kBAAkB;YAC3C,sBAAsB,EAAE,IAAI,CAAC,sBAAsB;SACpD,CAAC,CAAA;QACF,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;IACpE,CAAC;IAED;;;OAGG;IACK,KAAK,CAAC,WAAW,CAAC,KAAa,EAAE,IAAe;QACtD,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,IAAI,KAAK,EAAE,CAAA;QACtD,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;QACtE,MAAM,MAAM,GAAiB,MAAM,GAAG,CAAC,IAAI,EAAE,CAAA;QAC7C,OAAO,cAAc,CAAC,IAAI,CAAC,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE;YACtD,MAAM,EAAE,IAAI,EAAE,MAAM;SACrB,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,WAAW,CAClC,iBAAiB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,EACzD,IAAI,CACL,CAAA;QACD,MAAM,IAAI,GAAG,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpC,MAAM,OAAO,GAAG,IAAI,CAAC,eAAe,CAClC,KAAK,CAAC,QAAQ,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,EACpC,EAAE,EACF,EAAE,EACF,IAAI,kBAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CACzB,CAAA;QACD,MAAM,MAAM,GAAG,IAAA,uBAAa,EAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;QACtD,MAAM,IAAI,CAAC,uBAAuB,CAAC,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;QAC5D,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,YAAY,CAAC,OAAiB,EAAE;QACpC,wEAAwE;QACxE,wDAAwD;QACxD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,yBAAyB,EAAE,IAAI,CAAC,CAAA;QACrE,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QACzC,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CAAC,2CAA2C,CAAC,CAAA;QAC9D,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;CACF;AAzGD,6BAyGC"}

package/dist/index.d.ts CHANGED Viewed

@@ -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/dist/index.js CHANGED Viewed

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.referenceNibble = exports.packReference = exports.CHAR_CODE_FROM_NIBBLE = exports.forEachMismatchNumeric = exports.MISMATCH_SUBST = exports.MISMATCH_SOFT_CLIP = exports.MISMATCH_REF_SKIP = exports.MISMATCH_INSERTION = exports.MISMATCH_HARD_CLIP = exports.MISMATCH_DELETION = exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.BAI = void 0;
+exports.referenceNibble = exports.packReference = exports.CHAR_CODE_FROM_NIBBLE = exports.forEachMismatchNumeric = exports.MISMATCH_SUBST = exports.MISMATCH_SOFT_CLIP = exports.MISMATCH_REF_SKIP = exports.MISMATCH_INSERTION = exports.MISMATCH_HARD_CLIP = exports.MISMATCH_DELETION = exports.streamBamRecords = exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.BAI = void 0;
 var bai_ts_1 = require("./bai.js");
 Object.defineProperty(exports, "BAI", { enumerable: true, get: function () { return __importDefault(bai_ts_1).default; } });
 var bamFile_ts_1 = require("./bamFile.js");
@@ -16,6 +16,11 @@ var record_ts_1 = require("./record.js");
 Object.defineProperty(exports, "BamRecord", { enumerable: true, get: function () { return __importDefault(record_ts_1).default; } });
 var htsget_ts_1 = require("./htsget.js");
 Object.defineProperty(exports, "HtsgetFile", { enumerable: true, get: function () { return __importDefault(htsget_ts_1).default; } });
+// 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.
+var streamBam_ts_1 = require("./streamBam.js");
+Object.defineProperty(exports, "streamBamRecords", { enumerable: true, get: function () { return streamBam_ts_1.streamBamRecords; } });
 // 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/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAIqB;AAHnB,2HAAA,6BAA6B,OAAA;AAC7B,qHAAA,uBAAuB,OAAA;AACvB,sHAAA,OAAO,OAAW;AAEpB,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc;AAE9B,gFAAgF;AAChF,gFAAgF;AAChF,qBAAqB;AACrB,+CAAiD;AAAxC,gHAAA,gBAAgB,OAAA;AAGzB,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,iDAQwB;AAPtB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,mHAAA,kBAAkB,OAAA;AAClB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,+GAAA,cAAc,OAAA;AACd,uHAAA,sBAAsB,OAAA;AAExB,8EAA8E;AAC9E,6EAA6E;AAC7E,oEAAoE;AACpE,+CAIuB;AAHrB,qHAAA,qBAAqB,OAAA;AACrB,6GAAA,aAAa,OAAA;AACb,+GAAA,eAAe,OAAA"}

package/dist/streamBam.d.ts ADDED Viewed

@@ -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>;