@gmod/bam 7.6.1 → 7.6.2

package/README.md

@@ -1,10 +1,12 @@
 [![NPM version](https://img.shields.io/npm/v/@gmod/bam.svg?style=flat-square)](https://npmjs.org/package/@gmod/bam)
 ![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/bam-js/publish.yml?branch=main)
 
+Parser for BAM files and their BAI/CSI indexes.
+
 ## Install
 
 ```bash
-$ npm install --save @gmod/bam
+npm install @gmod/bam
 ```
 
 ## Usage
@@ -12,90 +14,104 @@ $ npm install --save @gmod/bam
 ```typescript
 import { BamFile } from '@gmod/bam'
 
-const t = new BamFile({
-  bamPath: 'test.bam',
-})
-
-// note: it's required to first run getHeader before any getRecordsForRange
-const header = await t.getHeader()
+const bam = new BamFile({ bamPath: 'test.bam' })
 
-// this would get same records as samtools view ctgA:1-50000
-const records = await t.getRecordsForRange('ctgA', 0, 50000)
+// same records as `samtools view test.bam ctgA:1-50000`
+const records = await bam.getRecordsForRange('ctgA', 0, 50000)
 ```
 
-The `bamPath` argument only works on nodejs. In the browser, you should pass
-`bamFilehandle` with a generic-filehandle2 e.g. `RemoteFile`
+Coordinates are 0-based half-open (not the same as `samtools view` inputs).
+`bamPath` reads a local file, so it is node-only; in the browser pass a
+filehandle or URL instead:
 
 ```typescript
-import { RemoteFile } from 'generic-filehandle2'
 import { BamFile } from '@gmod/bam'
 
 const bam = new BamFile({
-  bamFilehandle: new RemoteFile('yourfile.bam'), // or a full http url
-  baiFilehandle: new RemoteFile('yourfile.bam.bai'), // or a full http url
+  bamUrl: 'https://example.com/yourfile.bam',
+  baiUrl: 'https://example.com/yourfile.bam.bai',
 })
 ```
 
-Input are 0-based half-open coordinates (note: not the same as samtools view
-coordinate inputs!)
-
 ## Usage with htsget
 
-Since 1.0.41 we support usage of the htsget protocol
-
-Here is a small code snippet for this
-
 ```typescript
 import { HtsgetFile } from '@gmod/bam'
 
-const ti = new HtsgetFile({
+const bam = new HtsgetFile({
   baseUrl: 'http://htsnexus.rnd.dnanex.us/v1/reads',
   trackId: 'BroadHiSeqX_b37/NA12878',
 })
-await ti.getHeader()
-const records = await ti.getRecordsForRange('1', 2000000, 2000001)
+const records = await bam.getRecordsForRange('1', 2000000, 2000001)
 ```
 
-Let us know if it doesn't work for your use case.
+htsget fetches the server's range as-is, so `viewAsPairs`, `pairAcrossChr` and
+`maxInsertSize` are ignored.
 
-Caveat: htsget `getRecordsForRange` does not honor `viewAsPairs`,
-`pairAcrossChr`, or `maxInsertSize`. The range is fetched from the server as-is.
+For a server that requires authentication, pass a `fetch` that adds the bearer
+token the spec calls for:
 
-## Documentation
-
-### BAM constructor
-
-The BAM class constructor accepts arguments
-
-- `bamPath`/`bamUrl`/`bamFilehandle` - a local file path, remote URL string, or
-  a class object with a read method
-- `csiPath`/`csiUrl`/`csiFilehandle` - a CSI index for the BAM file, required
-  for long chromosomes greater than 2^29 in length
-- `baiPath`/`baiUrl`/`baiFilehandle` - a BAI index for the BAM file
-- `recordClass` - a custom class extending BamRecord to use for records (see
-  Custom BamRecord class section below)
-
-Note: filehandles implement the Filehandle interface from generic-filehandle2.
-The `path` and `url` arguments are convenience wrappers for `LocalFile` and
-`RemoteFile`.
-
-### async getRecordsForRange(refName, start, end, opts)
+```typescript
+const bam = new HtsgetFile({
+  baseUrl: 'https://htsget.example.com/reads',
+  trackId: 'NA12878',
+  fetch: (url, init) => {
+    const headers = new Headers(init?.headers)
+    headers.set('authorization', `Bearer ${token}`)
+    return fetch(url, { ...init, headers })
+  },
+})
+```
 
-Note: requires calling `getHeader` first.
+Your `fetch` is called for the ticket request and for the data-block urls the
+ticket points at, so only attach credentials to hosts you trust — data blocks
+may live on a third-party host, and the spec has servers put whatever those
+need in each url's own `headers` field, which is applied either way.
 
-- `refName` - a string for the chrom to fetch from
-- `start` - a 0-based half open start coordinate
-- `end` - a 0-based half open end coordinate
-- `opts.signal` - an AbortSignal to indicate stop processing
-- `opts.viewAsPairs` - re-dispatches requests to find mate pairs. default: false
-- `opts.pairAcrossChr` - control the viewAsPairs option behavior to pair across
-  chromosomes. default: false
-- `opts.maxInsertSize` - control the viewAsPairs option behavior to limit
-  distance within a chromosome to fetch. default: 200kb
+## Documentation
 
-Records come back unfiltered. Filter the returned array yourself — the flag
-helpers (`record.isSecondary()` and friends) and `record.getTag(name)` cover it,
-and `getTag` decodes just the one tag rather than every tag on the read:
+### BamFile constructor
+
+- `bamPath`/`bamUrl`/`bamFilehandle` - local path, remote URL, or a
+  generic-filehandle2 object
+- `baiPath`/`baiUrl`/`baiFilehandle` - BAI index. Defaults to the `.bai` sibling
+  of `bamPath`/`bamUrl`
+- `csiPath`/`csiUrl`/`csiFilehandle` - CSI index, required for chromosomes
+  longer than 2^29
+- `renameRefSeqs` - `(refName: string) => string` applied to header ref names
+- `recordClass` - custom class extending `BamRecord` (see below)
+- `maxCacheBytes` - budget for the parsed-chunk cache, in decompressed bytes.
+  default: 100MB
+
+The `path`/`url` forms are convenience wrappers for generic-filehandle2's
+`LocalFile` and `RemoteFile`.
+
+### HtsgetFile constructor
+
+- `baseUrl` - htsget reads endpoint, e.g. `https://htsget.example.com/reads`
+- `trackId` - id of the resource under `baseUrl`
+- `fetch` - `fetch` replacement for adding auth headers (see above)
+- `recordClass` - custom class extending `BamRecord` (see below)
+
+### async getRecordsForRange(refName, start, end, opts?)
+
+- `refName` - chromosome to fetch from
+- `start`/`end` - 0-based half-open coordinates
+- `opts.signal` - `AbortSignal` to stop processing
+- `opts.viewAsPairs` - re-dispatch requests to find mate pairs. default: false
+- `opts.pairAcrossChr` - let `viewAsPairs` pair across chromosomes. default:
+  false
+- `opts.maxInsertSize` - distance limit for `viewAsPairs` within a chromosome.
+  default: 200kb
+- `opts.onProgress` - `(bytesDownloaded, totalBytes?) => void`, called per BGZF
+  chunk for a determinate progress bar
+
+Returned records are cached and shared between overlapping queries, so treat
+them as read-only — attaching your own fields to a record mutates it for every
+other query holding it.
+
+Records come back unfiltered. 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(
@@ -105,34 +121,35 @@ const records = (await bam.getRecordsForRange('chr1', 0, 100000)).filter(
 
 ### async getHeader(opts?)
 
-Fetches the header from `BamFile` or `HtsgetFile`. Must be called before
-`getRecordsForRange`.
+Returns the parsed SAM header. Called automatically by the query methods and
+cached, so you only need it when you want the header itself.
+`getHeaderText(opts?)` returns the raw header string.
+
+### async indexCov(refName, start?, end?)
 
-### async indexCov(refName, start, end)
+Returns `{start, end, score}` features estimating read density over 16kb
+windows, derived from the BAI linear index. CSI has no linear index, so a
+CSI-indexed file returns `[]`.
 
-- `refName` - a string for the chrom to fetch from
-- `start` - a 0-based half open start coordinate (optional)
-- `end` - a 0-based half open end coordinate (optional)
+### async lineCount(refName)
 
-Returns features of the form {start, end, score} containing estimated feature
-density across 16kb windows in the genome. BAI-only: derived from the linear
-index, which CSI omits — calling on a CSI-indexed file returns `[]`.
+Number of records on `refName` from the index's pseudo-bin (bin 37450 in BAI,
+`n_mapped` in the SAM spec), or 0 if `refName` is absent.
 
-### async lineCount(refName: string)
+### async hasRefSeq(refName)
 
-- `refName` - a string for the chrom to fetch from
+Whether `refName` is present in the file.
 
-Returns number of features on refName, uses special pseudo-bin from the BAI/CSI
-index (e.g. bin 37450 from bai, returning n_mapped from SAM spec pdf) or 0 if
-refName does not exist in the sample
+### async estimatedBytesForRegions(regions, opts?)
 
-### async hasRefSeq(refName: string)
+Compressed bytes the given `{refName, start, end}[]` would fetch — useful for
+warning before a large query.
 
-- `refName` - a string for the chrom to check
+### clearFeatureCache()
 
-Returns whether we have this refName in the sample
+Drops the parsed-chunk cache.
 
-### BamRecord properties
+### BamRecord
 
 ```typescript
 // Core alignment fields
@@ -142,24 +159,26 @@ record.start // 0-based start coordinate
 record.end // 0-based end coordinate
 record.name // QNAME
 record.seq // sequence string
-record.qual // Uint8Array of quality scores (null if unmapped)
+record.qual // Uint8Array of quality scores (null if SEQ is empty)
 record.CIGAR // CIGAR string e.g. "50M2I48M"
 record.flags // SAM flags integer
 record.mq // mapping quality (undefined if 255)
 record.strand // 1 or -1
 record.template_length // TLEN
 
+// Mate info
+record.next_refid
+record.next_pos
+
 // Auxiliary data
-record.tags // object with all aux tags e.g. {MD: "100", NM: 0}
-record.getTag('MD') // get a single tag (more efficient than record.tags when you only need one)
-record.getTagRaw('MD') // get tag as Uint8Array for string tags (avoids string conversion)
-record.NUMERIC_MD // MD tag as Uint8Array (for fast mismatch rendering)
-record.NUMERIC_CIGAR // Uint32Array of packed CIGAR operations
-record.NUMERIC_SEQ // Uint8Array of packed sequence (4-bit encoded)
+record.tags // all aux tags e.g. {MD: "100", NM: 0}
+record.getTag('MD') // one tag, without decoding the rest
+record.getTagRaw('MD') // string tag as Uint8Array, skipping string conversion
 
-// Mate info
-record.next_refid // mate reference id
-record.next_pos // mate position
+// Typed-array views, for rendering without allocating strings
+record.NUMERIC_MD // MD tag as Uint8Array
+record.NUMERIC_CIGAR // Uint32Array of packed CIGAR operations
+record.NUMERIC_SEQ // Uint8Array of 4-bit encoded sequence
 
 // Flag methods
 record.isPaired()
@@ -176,14 +195,12 @@ record.isDuplicate()
 record.isSupplementary()
 
 // Utility
-record.seqAt(idx) // get single base at position
-record.toJSON() // serialize record
+record.seqAt(idx) // single base at position
+record.toJSON()
 ```
 
 ### Custom BamRecord class
 
-You can provide your own BamRecord class to add custom properties or methods:
-
 ```typescript
 import { BamFile, BamRecord } from '@gmod/bam'
 
@@ -191,10 +208,6 @@ class CustomBamRecord extends BamRecord {
   get customProperty() {
     return `custom-${this.name}`
   }
-
-  getDoubleStart() {
-    return this.start * 2
-  }
 }
 
 const bam = new BamFile<CustomBamRecord>({
@@ -202,11 +215,9 @@ const bam = new BamFile<CustomBamRecord>({
   recordClass: CustomBamRecord,
 })
 
-await bam.getHeader()
-const records = await bam.getRecordsForRange('ctgA', 0, 50000)
 // records are typed as CustomBamRecord[]
+const records = await bam.getRecordsForRange('ctgA', 0, 50000)
 console.log(records[0].customProperty)
-console.log(records[0].getDoubleStart())
 ```
 
 ## License

package/dist/bamFile.d.ts

@@ -73,6 +73,19 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
             value: string;
         }[];
     }[] | undefined>;
+    /**
+     * Installs the header text and ref name/id maps from the start of a
+     * decompressed BAM stream, returning the parsed SAM header lines. Returns
+     * undefined if the stream is cut off partway through the ref-seq table, so
+     * the caller can retry with more data.
+     */
+    protected applyHeader(uncba: Uint8Array): {
+        tag: string;
+        data: {
+            tag: string;
+            value: string;
+        }[];
+    }[] | undefined;
     getHeader(opts?: BaseOpts): Promise<{
         tag: string;
         data: {

package/dist/bamFile.js

@@ -15,6 +15,11 @@ const sam_ts_1 = require("./sam.js");
 const util_ts_1 = require("./util.js");
 exports.BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
+// Ceiling on the header read. A million contigs is roughly 10MB of compressed
+// @SQ lines and ref-seq table, so anything past this is a corrupt header
+// claiming a huge n_ref rather than a real one, and growing the read further
+// just downloads the file.
+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));
@@ -134,37 +139,52 @@ class BamFile {
             return undefined;
         }
         const indexData = await this.index.parse(opts);
-        // firstDataLine is not defined in cases where there is no data in the file
-        // (just bam header and nothing else)
-        const readLen = indexData.firstDataLine === undefined
-            ? undefined
+        // The records start at firstDataLine, so reading up to it plus the bgzf
+        // block straddling it covers the header. It is undefined when the index
+        // records no data at all (header-only BAM), and it undershoots when the
+        // index leaves offsets unset, so grow the read until the ref-seq table
+        // parses. Never readFile() here: on a remote BAM that is a whole-file
+        // download to read a header.
+        let readLen = indexData.firstDataLine === undefined
+            ? blockLen
             : indexData.firstDataLine.blockPosition + blockLen;
-        const buffer = readLen === undefined
-            ? await this.bam.readFile()
-            : await this.bam.read(readLen, 0);
-        let uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
+        let samHeader;
+        let atEof = false;
+        while (samHeader === undefined && !atEof && readLen <= maxHeaderReadLen) {
+            const buffer = await this.bam.read(readLen, 0, { signal: opts.signal });
+            // a short read means readLen ran past the end of the file, so there are
+            // no more bytes to grow into
+            atEof = buffer.length < readLen;
+            samHeader = this.applyHeader(await (0, bgzf_filehandle_1.unzip)(buffer));
+            readLen *= 2;
+        }
+        if (samHeader === undefined) {
+            throw new Error('Insufficient data for reference sequences');
+        }
+        return samHeader;
+    }
+    /**
+     * Installs the header text and ref name/id maps from the start of a
+     * decompressed BAM stream, returning the parsed SAM header lines. Returns
+     * undefined if the stream is cut off partway through the ref-seq table, so
+     * the caller can retry with more data.
+     */
+    applyHeader(uncba) {
         const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
         if (dataView.getInt32(0, true) !== exports.BAM_MAGIC) {
             throw new Error('Not a BAM file');
         }
         const headLen = dataView.getInt32(4, true);
-        this.header = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen));
-        // BAM files with many reference sequences may need more data than the
-        // initial read covers. If the first attempt comes up short, fall back to
-        // reading the whole file (the index's firstDataLine is just an
-        // optimization hint, not a guaranteed cap on the ref-seq table size).
-        const refSeqStart = headLen + 8;
-        let parsed = (0, util_ts_1.parseRefSeqs)(uncba, refSeqStart, this.renameRefSeq);
-        if (!parsed) {
-            uncba = await (0, bgzf_filehandle_1.unzip)(await this.bam.readFile());
-            parsed = (0, util_ts_1.parseRefSeqs)(uncba, refSeqStart, this.renameRefSeq);
-        }
-        if (!parsed) {
-            throw new Error('Insufficient data for reference sequences');
+        const parsed = (0, util_ts_1.parseRefSeqs)(uncba, headLen + 8, this.renameRefSeq);
+        let samHeader;
+        if (parsed) {
+            const headerText = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen));
+            this.header = headerText;
+            this.chrToIndex = parsed.chrToIndex;
+            this.indexToChr = parsed.indexToChr;
+            samHeader = (0, sam_ts_1.parseHeaderText)(headerText);
         }
-        this.chrToIndex = parsed.chrToIndex;
-        this.indexToChr = parsed.indexToChr;
-        return (0, sam_ts_1.parseHeaderText)(this.header);
+        return samHeader;
     }
     getHeader(opts) {
         if (!this.headerP) {

package/dist/bamFile.js.map

@@ -1 +1 @@
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package/dist/htsget.d.ts

@@ -2,14 +2,30 @@ import BamFile from './bamFile.ts';
 import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
 import type BamRecord from './record.ts';
 import type { BamOpts, BaseOpts } from './util.ts';
+import type { Fetcher } from 'generic-filehandle2';
 export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends BamFile<T> {
     private baseUrl;
     private trackId;
+    private fetchFn;
     constructor(args: {
         trackId: string;
         baseUrl: string;
         recordClass?: BamRecordClass<T>;
+        /**
+         * fetch implementation used for every request, so an `Authorization: Bearer
+         * <token>` header can be added for servers that require one. It is also
+         * called with the data-block urls from the ticket, which may point at
+         * third-party hosts, so only attach credentials to hosts you trust — the
+         * spec has servers put whatever a data block needs in that url's own
+         * `headers` field, which is applied either way.
+         */
+        fetch?: Fetcher;
     });
+    /**
+     * Requests a ticket and returns its data blocks decompressed and
+     * concatenated, which per the spec is a complete BAM stream.
+     */
+    private fetchTicket;
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
     getHeaderPre(opts?: BaseOpts): Promise<{
         tag: string;