@gmod/bam 7.6.1 → 7.7.0

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/bai.d.ts

@@ -1,9 +1,9 @@
 import IndexFile from './indexFile.ts';
 import type { ParsedIndexBase, RefIndex } from './indexFile.ts';
 import type { BaseOpts } from './util.ts';
-import type { VirtualOffset } from './virtualOffset.ts';
 interface BaiRefIndex extends RefIndex {
-    linearIndex: VirtualOffset[];
+    linearBlockPositions: Float64Array;
+    linearDataPositions: Float64Array;
 }
 interface BaiParsed extends ParsedIndexBase<BaiRefIndex> {
     bai: true;
@@ -17,6 +17,9 @@ export default class BAI extends IndexFile<BaiParsed> {
     _parse(opts: BaseOpts): Promise<BaiParsed>;
     indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<IndexCovEntry[]>;
     protected reg2bins(min: number, max: number): readonly [readonly [0, 0], readonly [number, number], readonly [number, number], readonly [number, number], readonly [number, number], readonly [number, number]];
-    protected getLowestChunk(refIndex: BaiRefIndex, min: number): VirtualOffset | undefined;
+    protected getLowestChunk(refIndex: BaiRefIndex, min: number): {
+        blockPosition: number;
+        dataPosition: number;
+    } | undefined;
 }
 export {};

package/dist/bai.js

@@ -146,22 +146,32 @@ class BAI extends indexFile_ts_1.default {
             }
             const linearCount = dataView.getInt32(curr, true);
             curr += 4;
-            const linearIndex = new Array(linearCount);
+            const linearBlockPositions = new Float64Array(linearCount);
+            const linearDataPositions = new Float64Array(linearCount);
             for (let j = 0; j < linearCount; j++) {
-                linearIndex[j] = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
+                // a virtual offset is a 48-bit block position in the high bytes and a
+                // 16-bit data position in the low two
+                linearBlockPositions[j] =
+                    bytes[curr + 7] * 0x10000000000 +
+                        bytes[curr + 6] * 0x100000000 +
+                        bytes[curr + 5] * 0x1000000 +
+                        bytes[curr + 4] * 0x10000 +
+                        bytes[curr + 3] * 0x100 +
+                        bytes[curr + 2];
+                linearDataPositions[j] = (bytes[curr + 1] << 8) | bytes[curr];
                 curr += 8;
             }
-            (0, util_ts_1.clampChunkEnds)(Object.values(binIndex).flat(), linearIndex.map(v => v.blockPosition));
+            (0, util_ts_1.clampChunkEnds)(Object.values(binIndex).flat(), linearBlockPositions);
             return {
                 binIndex,
-                linearIndex,
+                linearBlockPositions,
+                linearDataPositions,
                 stats,
             };
         }
         return {
             bai: true,
             firstDataLine,
-            maxBlockSize: 1 << 16,
             indices: (0, indexFile_ts_1.memoizeByRefId)(getIndices),
             refCount,
         };
@@ -174,17 +184,18 @@ class BAI extends indexFile_ts_1.default {
         if (!seqIdx) {
             return [];
         }
-        const { linearIndex, stats } = seqIdx;
-        if (linearIndex.length === 0) {
+        const { linearBlockPositions, stats } = seqIdx;
+        const nintv = linearBlockPositions.length;
+        if (nintv === 0) {
             return [];
         }
-        const e = end === undefined ? (linearIndex.length - 1) * v : roundUp(end, v);
+        const e = end === undefined ? (nintv - 1) * v : roundUp(end, v);
         const s = start === undefined ? 0 : roundDown(start, v);
         const depths = range
             ? new Array((e - s) / v)
-            : new Array(linearIndex.length - 1);
-        const totalSize = linearIndex[linearIndex.length - 1].blockPosition;
-        if (e > (linearIndex.length - 1) * v) {
+            : new Array(nintv - 1);
+        const totalSize = linearBlockPositions[nintv - 1];
+        if (e > (nintv - 1) * v) {
             throw new Error('query outside of range of linear index');
         }
         // Scale the block-delta into a read count as we go, rather than building the
@@ -192,9 +203,9 @@ class BAI extends indexFile_ts_1.default {
         // multiply-then-divide order: hoisting lineCount/totalSize into a factor
         // reassociates the arithmetic and shifts scores by an ulp.
         const lineCount = stats?.lineCount ?? 0;
-        let currentPos = linearIndex[s / v].blockPosition;
+        let currentPos = linearBlockPositions[s / v];
         for (let i = s / v, j = 0; i < e / v; i++, j++) {
-            const nextPos = linearIndex[i + 1].blockPosition;
+            const nextPos = linearBlockPositions[i + 1];
             depths[j] = {
                 score: ((nextPos - currentPos) * lineCount) / totalSize,
                 start: i * v,
@@ -211,9 +222,14 @@ class BAI extends indexFile_ts_1.default {
     // contain alignments in the region. Linear index entries are monotonically
     // non-decreasing, so the first entry at minLin is the minimum.
     getLowestChunk(refIndex, min) {
-        const { linearIndex } = refIndex;
-        const nintv = linearIndex.length;
-        return linearIndex[Math.min(min >> BAI_LINEAR_SHIFT, nintv - 1)];
+        const { linearBlockPositions, linearDataPositions } = refIndex;
+        const i = Math.min(min >> BAI_LINEAR_SHIFT, linearBlockPositions.length - 1);
+        return i < 0
+            ? undefined
+            : {
+                blockPosition: linearBlockPositions[i],
+                dataPosition: linearDataPositions[i],
+            };
     }
 }
 exports.default = BAI;

package/dist/bai.js.map

@@ -1 +1 @@
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+{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAA4E;AAC5E,yDAA8C;AAuB9C,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,4EAA4E;AAC5E,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAC3B,MAAM,mBAAmB,GAAG,CAAC,IAAI,gBAAgB,CAAA,CAAC,QAAQ;AAE1D,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAQD,4EAA4E;AAC5E,qEAAqE;AACrE,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,gBAAgB,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,gBAAgB,CAAC,CAAC;KAC5D,CAAA;AACZ,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAoB;IACnD,KAAK,CAAC,MAAM,CAAC,IAAc;QACzB,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,0BAA0B;QAC1B,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC3C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,aAAwC,CAAA;QAE5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAE9C,IAAI,IAAI,CAAC,CAAA;YAET,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;oBACX,CAAC;gBACH,CAAC;YACH,CAAC;YAED,mEAAmE;YACnE,kDAAkD;YAClD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,aAAa,GAAG,IAAA,0BAAgB,EAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,aAAa,CAAC,CAAA;YACzE,IAAI,IAAI,CAAC,GAAG,WAAW,CAAA;QACzB,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,KAAK,CAAA;YAET,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAE5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACxC,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;oBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,oBAAoB,GAAG,IAAI,YAAY,CAAC,WAAW,CAAC,CAAA;YAC1D,MAAM,mBAAmB,GAAG,IAAI,YAAY,CAAC,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,sEAAsE;gBACtE,sCAAsC;gBACtC,oBAAoB,CAAC,CAAC,CAAC;oBACrB,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,aAAa;wBAChC,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,WAAW;wBAC9B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,SAAS;wBAC5B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,OAAO;wBAC1B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,KAAK;wBACxB,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,CAAA;gBAClB,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,IAAI,CAAE,CAAA;gBAC/D,IAAI,IAAI,CAAC,C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package/dist/bamFile.d.ts

@@ -72,14 +72,27 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
             tag: string;
             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: {
             tag: string;
             value: string;
         }[];
-    }[] | undefined>;
+    }[]>;
     getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     private getSeqId;
     /**
@@ -100,7 +113,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         features: T[];
         bytes: number;
     }>;
-    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): T[];
+    readBamFeatures(ba: Uint8Array, cpositions: ArrayLike<number>, dpositions: ArrayLike<number>, chunk: Chunk): T[];
     hasRefSeq(seqName: string, opts?: BaseOpts): Promise<boolean>;
     lineCount(seqName: string, opts?: BaseOpts): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<never[] | import("./bai.ts").IndexCovEntry[]>;