@gmod/bam 7.1.19 → 7.1.21
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.
- package/README.md +22 -13
- package/dist/bai.d.ts +2 -2
- package/dist/bai.js +1 -0
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +2 -1
- package/dist/bamFile.js +15 -6
- package/dist/bamFile.js.map +1 -1
- package/dist/chunk.d.ts +1 -1
- package/dist/chunk.js +5 -0
- package/dist/chunk.js.map +1 -1
- package/dist/csi.js +4 -6
- package/dist/csi.js.map +1 -1
- package/dist/htsget.d.ts +1 -1
- package/dist/htsget.js +15 -9
- package/dist/htsget.js.map +1 -1
- package/dist/indexFile.d.ts +2 -2
- package/dist/indexFile.js +2 -0
- package/dist/indexFile.js.map +1 -1
- package/dist/nullFilehandle.d.ts +4 -4
- package/dist/nullIndex.d.ts +4 -4
- package/dist/record.d.ts +11 -14
- package/dist/record.js +119 -117
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +2 -2
- package/dist/util.js +4 -7
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.js +2 -0
- package/dist/virtualOffset.js.map +1 -1
- package/esm/bai.d.ts +2 -2
- package/esm/bai.js +2 -1
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +2 -1
- package/esm/bamFile.js +15 -6
- package/esm/bamFile.js.map +1 -1
- package/esm/chunk.d.ts +1 -1
- package/esm/chunk.js +5 -0
- package/esm/chunk.js.map +1 -1
- package/esm/csi.js +4 -6
- package/esm/csi.js.map +1 -1
- package/esm/htsget.d.ts +1 -1
- package/esm/htsget.js +12 -9
- package/esm/htsget.js.map +1 -1
- package/esm/indexFile.d.ts +2 -2
- package/esm/indexFile.js +2 -0
- package/esm/indexFile.js.map +1 -1
- package/esm/nullFilehandle.d.ts +4 -4
- package/esm/nullIndex.d.ts +4 -4
- package/esm/record.d.ts +11 -14
- package/esm/record.js +119 -117
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +2 -2
- package/esm/util.js +4 -7
- package/esm/util.js.map +1 -1
- package/esm/virtualOffset.js +2 -0
- package/esm/virtualOffset.js.map +1 -1
- package/package.json +28 -32
- package/src/bai.ts +5 -7
- package/src/bamFile.ts +3 -1
- package/src/chunk.ts +1 -1
- package/src/htsget.ts +18 -14
- package/src/indexFile.ts +3 -2
- package/src/nullFilehandle.ts +4 -4
- package/src/nullIndex.ts +4 -4
- package/src/record.ts +137 -140
- package/src/util.ts +11 -11
- package/CHANGELOG.md +0 -530
package/README.md
CHANGED
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@@ -1,6 +1,5 @@
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[](https://npmjs.org/package/@gmod/bam)
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-
[](https://github.com/GMOD/bam-js/actions?query=branch%3Amaster+workflow%3APush+)
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[](https://github.com/GMOD/bam-js/actions?query=branch%3Amain+workflow%3APush+)
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## Install
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@@ -11,25 +10,26 @@ $ npm install --save @gmod/bam
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## Usage
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```typescript
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// or import {BamFile} from '@gmod/bam'
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import { BamFile } from '@gmod/bam'
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const t = new BamFile({
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bamPath: 'test.bam',
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})
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// note: it's required to first run getHeader before any getRecordsForRange
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const header = await t.getHeader()
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// this would get same records as samtools view ctgA:1-50000
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const records = await t.getRecordsForRange('ctgA', 0, 50000)
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```
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The `bamPath` argument only works on nodejs. In the browser, you should pass
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`bamFilehandle` with a generic-filehandle2 e.g. `RemoteFile`
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```typescript
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import { RemoteFile } from 'generic-filehandle2'
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import { BamFile } from '@gmod/bam'
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const bam = new BamFile({
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bamFilehandle: new RemoteFile('yourfile.bam'), // or a full http url
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baiFilehandle: new RemoteFile('yourfile.bam.bai'), // or a full http url
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@@ -46,14 +46,14 @@ Since 1.0.41 we support usage of the htsget protocol
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Here is a small code snippet for this
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```typescript
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import { HtsgetFile } from '@gmod/bam'
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const ti = new HtsgetFile({
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baseUrl: 'http://htsnexus.rnd.dnanex.us/v1/reads',
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trackId: 'BroadHiSeqX_b37/NA12878',
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})
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await ti.getHeader()
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const records = await ti.getRecordsForRange(1, 2000000, 2000001)
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const records = await ti.getRecordsForRange('1', 2000000, 2000001)
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```
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Our implementation makes some assumptions about how the protocol is implemented,
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@@ -65,8 +65,8 @@ so let us know if it doesn't work for your use case
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The BAM class constructor accepts arguments
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- `bamPath`/`bamUrl`/`bamFilehandle` - a
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class object with a read method
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- `bamPath`/`bamUrl`/`bamFilehandle` - a local file path, remote URL string, or
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a class object with a read method
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- `csiPath`/`csiUrl`/`csiFilehandle` - a CSI index for the BAM file, required
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for long chromosomes greater than 2^29 in length
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- `baiPath`/`baiUrl`/`baiFilehandle` - a BAI index for the BAM file
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@@ -112,8 +112,8 @@ density across 16kb windows in the genome
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- `refName` - a string for the chrom to fetch from
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Returns number of features on refName, uses special pseudo-bin from the BAI/CSI
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index (e.g. bin 37450 from bai, returning n_mapped from SAM spec pdf) or
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refName not exist in sample
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index (e.g. bin 37450 from bai, returning n_mapped from SAM spec pdf) or 0 if
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refName does not exist in the sample
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### async hasRefSeq(refName: string)
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@@ -201,3 +201,12 @@ console.log(records[0].getDoubleStart())
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## License
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MIT © [Colin Diesh](https://github.com/cmdcolin)
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## Publishing
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[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub
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Actions.
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```bash
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npm version patch # or minor/major
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```
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package/dist/bai.d.ts
CHANGED
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import Chunk from './chunk.ts';
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import IndexFile from './indexFile.ts';
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import { BaseOpts } from './util.ts';
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import { VirtualOffset } from './virtualOffset.ts';
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import type { BaseOpts } from './util.ts';
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import type { VirtualOffset } from './virtualOffset.ts';
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export interface IndexCovEntry {
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start: number;
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end: number;
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package/dist/bai.js
CHANGED
package/dist/bai.js.map
CHANGED
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@@ -1 +1 @@
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1
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{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;AAAA,mEAAyC;AAEzC,0DAA8B;AAC9B,kEAAsC;AACtC,
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+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;AAAA,mEAAyC;AAEzC,0DAA8B;AAC9B,kEAAsC;AACtC,uCAAyE;AACzE,yDAA8C;AAK9C,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,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,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,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IACjC,MAAM,CAA4B;IAEzC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,KAAgB;QAC3B,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,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,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,mEAAmE;YACnE,qEAAqE;YACrE,OAAO;YACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,MAAM,MAAM,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IAAI,CAAC,CAAA;gBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;gBACpD,WAAW,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;YACzB,CAAC;QACH,CAAC;QACD,MAAM,YAAY,GAAG,IAAI,mBAAQ,CAAwC;YACvE,OAAO,EAAE,CAAC;SACX,CAAC,CAAA;QAEF,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,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBAC/C,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,mEAAmE;YACnE,qEAAqE;YACrE,OAAO;YACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,MAAM,MAAM,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IAAI,CAAC,CAAA;gBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;gBACpD,WAAW,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;YACzB,CAAC;YAED,OAAO;gBACL,QAAQ;gBACR,WAAW;gBACX,KAAK;aACN,CAAA;QACH,CAAC;QAED,OAAO;YACL,GAAG,EAAE,IAAI;YACT,aAAa;YACb,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,OAAO,EAAE,CAAC,KAAa,EAAE,EAAE;gBACzB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;oBAC7B,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBAChC,IAAI,MAAM,EAAE,CAAC;wBACX,YAAY,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;oBACjC,CAAC;oBACD,OAAO,MAAM,CAAA;gBACf,CAAC;gBACD,OAAO,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAChC,CAAC;YACD,QAAQ;SACT,CAAA;IACH,CAAC;IAED,KAAK,CAAC,QAAQ,CACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,IAAe;QAEf,MAAM,CAAC,GAAG,KAAK,CAAA;QACf,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;QACjC,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAEvC,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;QACrC,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;QAC5E,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QACvD,MAAM,MAAM,GAAG,KAAK;YAClB,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;YACxB,CAAC,CAAC,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,MAAM,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAE,CAAC,aAAa,CAAA;QACpE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;QAC3D,CAAC;QACD,IAAI,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,aAAa,CAAA;QAClD,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC/C,MAAM,CAAC,CAAC,CAAC,GAAG;gBACV,KAAK,EAAE,WAAW,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,aAAa,GAAG,UAAU;gBACrD,KAAK,EAAE,CAAC,GAAG,CAAC;gBACZ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC;aACf,CAAA;YACD,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,aAAa,CAAA;QAChD,CAAC;QACD,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACtB,GAAG,CAAC;YACJ,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,EAAE,SAAS,IAAI,CAAC,CAAC,CAAC,GAAG,SAAS;SACvD,CAAC,CAAC,CAAA;IACL,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;QAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,uEAAuE;QACvE,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAEnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QAED,uCAAuC;QACvC,MAAM,eAAe,GAAG,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAC1C,MAAM,MAAM,GAAY,EAAE,CAAA;QAE1B,sEAAsE;QACtE,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,MAAM,SAAS,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAC/B,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;wBACjD,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAE,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,0EAA0E;QAC1E,2EAA2E;QAC3E,+DAA+D;QAC/D,MAAM,EAAE,WAAW,EAAE,GAAG,EAAE,CAAA;QAC1B,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAA;QAChC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;QAC7C,MAAM,MAAM,GAAG,WAAW,CAAC,MAAM,CAAC,CAAA;QAElC,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,MAAM,CAAC,CAAA;IACvC,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAiB,EAAE;QAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;QAChD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACrC,OAAO,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IAC1C,CAAC;CACF;AAtPD,sBAsPC"}
|
package/dist/bamFile.d.ts
CHANGED
|
@@ -1,8 +1,8 @@
|
|
|
1
1
|
import QuickLRU from '@jbrowse/quick-lru';
|
|
2
2
|
import BAI from './bai.ts';
|
|
3
|
-
import Chunk from './chunk.ts';
|
|
4
3
|
import CSI from './csi.ts';
|
|
5
4
|
import BAMFeature from './record.ts';
|
|
5
|
+
import type Chunk from './chunk.ts';
|
|
6
6
|
import type { Bytes } from './record.ts';
|
|
7
7
|
import type { BamOpts, BaseOpts } from './util.ts';
|
|
8
8
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
@@ -20,6 +20,7 @@ export interface BamRecordLike {
|
|
|
20
20
|
export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
|
|
21
21
|
bytes: Bytes;
|
|
22
22
|
fileOffset: number;
|
|
23
|
+
dataView: DataView;
|
|
23
24
|
}) => T;
|
|
24
25
|
export declare const BAM_MAGIC = 21840194;
|
|
25
26
|
interface ChunkEntry<T> {
|
package/dist/bamFile.js
CHANGED
|
@@ -17,13 +17,21 @@ const util_ts_1 = require("./util.js");
|
|
|
17
17
|
exports.BAM_MAGIC = 21840194;
|
|
18
18
|
const blockLen = 1 << 16;
|
|
19
19
|
class BamFile {
|
|
20
|
+
renameRefSeq;
|
|
21
|
+
bam;
|
|
22
|
+
header;
|
|
23
|
+
chrToIndex;
|
|
24
|
+
indexToChr;
|
|
25
|
+
index;
|
|
26
|
+
htsget = false;
|
|
27
|
+
headerP;
|
|
28
|
+
// Cache for parsed features by chunk
|
|
29
|
+
// When a new chunk overlaps a cached chunk, we evict the cached one
|
|
30
|
+
chunkFeatureCache = new quick_lru_1.default({
|
|
31
|
+
maxSize: 100,
|
|
32
|
+
});
|
|
33
|
+
RecordClass;
|
|
20
34
|
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
|
|
21
|
-
this.htsget = false;
|
|
22
|
-
// Cache for parsed features by chunk
|
|
23
|
-
// When a new chunk overlaps a cached chunk, we evict the cached one
|
|
24
|
-
this.chunkFeatureCache = new quick_lru_1.default({
|
|
25
|
-
maxSize: 100,
|
|
26
|
-
});
|
|
27
35
|
this.renameRefSeq = renameRefSeqs;
|
|
28
36
|
this.RecordClass = (recordClass ?? record_ts_1.default);
|
|
29
37
|
if (bamFilehandle) {
|
|
@@ -339,6 +347,7 @@ class BamFile {
|
|
|
339
347
|
chunk.minv.dataPosition +
|
|
340
348
|
1
|
|
341
349
|
: (0, crc32_1.default)(ba.subarray(blockStart, blockEnd)) >>> 0,
|
|
350
|
+
dataView,
|
|
342
351
|
});
|
|
343
352
|
sink.push(feature);
|
|
344
353
|
}
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/chunk.d.ts
CHANGED
package/dist/chunk.js
CHANGED
|
@@ -2,6 +2,11 @@
|
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
// little class representing a chunk in the index
|
|
4
4
|
class Chunk {
|
|
5
|
+
minv;
|
|
6
|
+
maxv;
|
|
7
|
+
bin;
|
|
8
|
+
_fetchedSize;
|
|
9
|
+
buffer;
|
|
5
10
|
constructor(minv, maxv, bin, _fetchedSize) {
|
|
6
11
|
this.minv = minv;
|
|
7
12
|
this.maxv = maxv;
|
package/dist/chunk.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAIf;IACA;IACA;IACA;IANF,MAAM,CAA0B;IAEvC,YACS,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAQ;QACZ,SAAI,GAAJ,IAAI,CAAQ;QACZ,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AAlCD,wBAkCC"}
|
package/dist/csi.js
CHANGED
|
@@ -18,12 +18,10 @@ function rshift(num, bits) {
|
|
|
18
18
|
return Math.floor(num / 2 ** bits);
|
|
19
19
|
}
|
|
20
20
|
class CSI extends indexFile_ts_1.default {
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
this.minShift = 0;
|
|
26
|
-
}
|
|
21
|
+
maxBinNumber = 0;
|
|
22
|
+
depth = 0;
|
|
23
|
+
minShift = 0;
|
|
24
|
+
setupP;
|
|
27
25
|
async lineCount(refId, opts) {
|
|
28
26
|
const indexData = await this.parse(opts);
|
|
29
27
|
return indexData.indices(refId)?.stats?.lineCount || 0;
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,mEAAyC;AAEzC,0DAA8B;AAC9B,kEAAsC;AACtC,uCAKkB;AAClB,yDAA6D;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,mEAAyC;AAEzC,0DAA8B;AAC9B,kEAAsC;AACtC,uCAKkB;AAClB,yDAA6D;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAChC,YAAY,GAAG,CAAC,CAAA;IAChB,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEb,MAAM,CAA4B;IAEzC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GACV,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EACnC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,IAAA,wBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAA8B;QACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,IAAI,UAAU,CAAA;QACd,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAEzC,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;YAC1C,oDAAoD;QACtD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,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;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,CAAA;oBACT,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,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;oBACjD,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,YAAY,GAAG,IAAI,mBAAQ,CAAwC;YACvE,OAAO,EAAE,CAAC;SACX,CAAC,CAAA;QAEF,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,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,cAAc,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,cAAc,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACjD,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACpE,IAAI,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|
package/dist/htsget.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import BamFile from './bamFile.ts';
|
|
2
|
-
import BamRecord from './record.ts';
|
|
3
2
|
import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
|
|
3
|
+
import type BamRecord from './record.ts';
|
|
4
4
|
import type { BamOpts, BaseOpts } from './util.ts';
|
|
5
5
|
export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends BamFile<T> {
|
|
6
6
|
private baseUrl;
|
package/dist/htsget.js
CHANGED
|
@@ -32,11 +32,16 @@ var __importStar = (this && this.__importStar) || (function () {
|
|
|
32
32
|
return result;
|
|
33
33
|
};
|
|
34
34
|
})();
|
|
35
|
+
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
36
|
+
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
37
|
+
};
|
|
35
38
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
36
39
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
37
40
|
const bamFile_ts_1 = __importStar(require("./bamFile.js"));
|
|
41
|
+
const chunk_ts_1 = __importDefault(require("./chunk.js"));
|
|
38
42
|
const sam_ts_1 = require("./sam.js");
|
|
39
43
|
const util_ts_1 = require("./util.js");
|
|
44
|
+
const virtualOffset_ts_1 = require("./virtualOffset.js");
|
|
40
45
|
async function concat(arr, opts) {
|
|
41
46
|
const res = await Promise.all(arr.map(async (chunk) => {
|
|
42
47
|
const { url, headers } = chunk;
|
|
@@ -52,11 +57,10 @@ async function concat(arr, opts) {
|
|
|
52
57
|
}
|
|
53
58
|
else {
|
|
54
59
|
// remove referer header, it is not even allowed to be specified
|
|
55
|
-
|
|
56
|
-
const { referer, ...rest } = headers;
|
|
60
|
+
const { referer: _referer, ...rest } = headers ?? {};
|
|
57
61
|
const res = await fetch(url, {
|
|
58
62
|
...opts,
|
|
59
|
-
headers:
|
|
63
|
+
headers: rest,
|
|
60
64
|
});
|
|
61
65
|
if (!res.ok) {
|
|
62
66
|
throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
|
|
@@ -67,6 +71,8 @@ async function concat(arr, opts) {
|
|
|
67
71
|
return (0, util_ts_1.concatUint8Array)(await Promise.all(res.map(elt => (0, bgzf_filehandle_1.unzip)(elt))));
|
|
68
72
|
}
|
|
69
73
|
class HtsgetFile extends bamFile_ts_1.default {
|
|
74
|
+
baseUrl;
|
|
75
|
+
trackId;
|
|
70
76
|
constructor(args) {
|
|
71
77
|
super({ htsget: true, recordClass: args.recordClass });
|
|
72
78
|
this.baseUrl = args.baseUrl;
|
|
@@ -84,11 +90,11 @@ class HtsgetFile extends bamFile_ts_1.default {
|
|
|
84
90
|
throw new Error(`HTTP ${result.status} fetching ${url}: ${await result.text()}`);
|
|
85
91
|
}
|
|
86
92
|
const data = await result.json();
|
|
87
|
-
const uncba = await concat(data.htsget.urls.slice(1),
|
|
88
|
-
|
|
89
|
-
minv: { dataPosition: 0, blockPosition: 0 },
|
|
90
|
-
maxv: { dataPosition: 0, blockPosition: 0 },
|
|
93
|
+
const uncba = await concat(data.htsget.urls.slice(1), {
|
|
94
|
+
signal: opts?.signal,
|
|
91
95
|
});
|
|
96
|
+
const zero = new virtualOffset_ts_1.VirtualOffset(0, 0);
|
|
97
|
+
const allRecords = await this.readBamFeatures(uncba, [], [], new chunk_ts_1.default(zero, zero, 0));
|
|
92
98
|
const records = [];
|
|
93
99
|
for (let i = 0, l = allRecords.length; i < l; i++) {
|
|
94
100
|
const feature = allRecords[i];
|
|
@@ -110,13 +116,13 @@ class HtsgetFile extends bamFile_ts_1.default {
|
|
|
110
116
|
throw new Error(`HTTP ${result.status} fetching ${url}: ${await result.text()}`);
|
|
111
117
|
}
|
|
112
118
|
const data = await result.json();
|
|
113
|
-
const uncba = await concat(data.htsget.urls, opts);
|
|
119
|
+
const uncba = await concat(data.htsget.urls, { signal: opts.signal });
|
|
114
120
|
const dataView = new DataView(uncba.buffer);
|
|
115
121
|
if (dataView.getInt32(0, true) !== bamFile_ts_1.BAM_MAGIC) {
|
|
116
122
|
throw new Error('Not a BAM file');
|
|
117
123
|
}
|
|
118
124
|
const headLen = dataView.getInt32(4, true);
|
|
119
|
-
const decoder = new TextDecoder(
|
|
125
|
+
const decoder = new TextDecoder();
|
|
120
126
|
const headerText = decoder.decode(uncba.subarray(8, 8 + headLen));
|
|
121
127
|
const samHeader = (0, sam_ts_1.parseHeaderText)(headerText);
|
|
122
128
|
// use the @SQ lines in the header to figure out the
|
package/dist/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,2DAAiD;AACjD,0DAA8B;AAC9B,qCAA0C;AAC1C,uCAA4C;AAC5C,yDAAkD;AAWlD,KAAK,UAAU,MAAM,CAAC,GAAkB,EAAE,IAAkB;IAC1D,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;YAC5B,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;YAC5C,CAAC;YACD,MAAM,GAAG,GAAG,MAAM,GAAG,CAAC,WAAW,EAAE,CAAA;YACnC,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;QAC5B,CAAC;aAAM,CAAC;YACN,gEAAgE;YAChE,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,IAAI,EAAE,CAAA;YACpD,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;gBAC3B,GAAG,IAAI;gBACP,OAAO,EAAE,IAAI;aACd,CAAC,CAAA;YACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;YACH,CAAC;YACD,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;QAChD,CAAC;IACH,CAAC,CAAC,CACH,CAAA;IAED,OAAO,IAAA,0BAAgB,EAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;AACxE,CAAC;AAED,MAAqB,UAEnB,SAAQ,oBAAU;IACV,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEvB,YAAY,IAIX;QACC,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;QACtD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,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,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,CAAC,CAAA;QAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;QACH,CAAC;QACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;YACpD,MAAM,EAAE,IAAI,EAAE,MAAM;SACrB,CAAC,CAAA;QAEF,MAAM,IAAI,GAAG,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpC,MAAM,UAAU,GAAG,MAAM,IAAI,CAAC,eAAe,CAC3C,KAAK,EACL,EAAE,EACF,EAAE,EACF,IAAI,kBAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CACzB,CAAA;QAED,MAAM,OAAO,GAAQ,EAAE,CAAA;QACvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAClD,MAAM,OAAO,GAAG,UAAU,CAAC,CAAC,CAAE,CAAA;YAC9B,IAAI,OAAO,CAAC,MAAM,KAAK,KAAK,EAAE,CAAC;gBAC7B,IAAI,OAAO,CAAC,KAAK,IAAI,GAAG,EAAE,CAAC;oBACzB,MAAK;gBACP,CAAC;qBAAM,IAAI,OAAO,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC;oBAC9B,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACvB,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAiB,EAAE;QACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;QACH,CAAC;QACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,CAAA;QACrE,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,sBAAS,EAAE,CAAC;YAC7C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QACD,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAE1C,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;QACjC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAC,CAAA;QACjE,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAChD,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;gBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;QACvC,CAAC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF;AAzGD,6BAyGC"}
|
package/dist/indexFile.d.ts
CHANGED
package/dist/indexFile.js
CHANGED
|
@@ -2,6 +2,8 @@
|
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
const util_ts_1 = require("./util.js");
|
|
4
4
|
class IndexFile {
|
|
5
|
+
filehandle;
|
|
6
|
+
renameRefSeq;
|
|
5
7
|
constructor({ filehandle, renameRefSeq = (n) => n, }) {
|
|
6
8
|
this.filehandle = filehandle;
|
|
7
9
|
this.renameRefSeq = renameRefSeq;
|
package/dist/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAAA,uCAA0C;AAY1C,MAA8B,SAAS;IAC9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAE1C,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAeD,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,IAAA,wBAAc,EAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AA1CD,4BA0CC"}
|
package/dist/nullFilehandle.d.ts
CHANGED
package/dist/nullIndex.d.ts
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import IndexFile from './indexFile.ts';
|
|
2
2
|
export default class NullIndex extends IndexFile {
|
|
3
|
-
lineCount(): Promise<
|
|
4
|
-
protected _parse(): Promise<
|
|
5
|
-
indexCov(): Promise<
|
|
6
|
-
blocksForRange(): Promise<
|
|
3
|
+
lineCount(): Promise<never>;
|
|
4
|
+
protected _parse(): Promise<never>;
|
|
5
|
+
indexCov(): Promise<never>;
|
|
6
|
+
blocksForRange(): Promise<never>;
|
|
7
7
|
}
|
package/dist/record.d.ts
CHANGED
|
@@ -3,25 +3,22 @@ export interface Bytes {
|
|
|
3
3
|
end: number;
|
|
4
4
|
byteArray: Uint8Array;
|
|
5
5
|
}
|
|
6
|
-
interface CIGAR_AND_LENGTH {
|
|
7
|
-
length_on_ref: number;
|
|
8
|
-
NUMERIC_CIGAR: Uint32Array | number[];
|
|
9
|
-
}
|
|
10
6
|
export default class BamRecord {
|
|
11
7
|
fileOffset: number;
|
|
12
|
-
private
|
|
8
|
+
private _byteArray;
|
|
9
|
+
private _start;
|
|
10
|
+
private _end;
|
|
13
11
|
private _dataView;
|
|
14
|
-
private _cachedFlags?;
|
|
15
|
-
private _cachedRefId?;
|
|
16
|
-
private _cachedStart?;
|
|
17
12
|
private _cachedEnd?;
|
|
18
13
|
private _cachedTags?;
|
|
19
|
-
private
|
|
14
|
+
private _cachedLengthOnRef?;
|
|
15
|
+
private _cachedNumericCigar?;
|
|
20
16
|
private _cachedNUMERIC_MD?;
|
|
21
17
|
private _cachedTagsStart?;
|
|
22
18
|
constructor(args: {
|
|
23
19
|
bytes: Bytes;
|
|
24
20
|
fileOffset: number;
|
|
21
|
+
dataView: DataView;
|
|
25
22
|
});
|
|
26
23
|
get byteArray(): Uint8Array<ArrayBufferLike>;
|
|
27
24
|
get flags(): number;
|
|
@@ -38,7 +35,7 @@ export default class BamRecord {
|
|
|
38
35
|
get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
|
|
39
36
|
get tags(): Record<string, unknown>;
|
|
40
37
|
getTag(tagName: string): unknown;
|
|
41
|
-
getTagRaw(tagName: string): string | number | number[] |
|
|
38
|
+
getTagRaw(tagName: string): string | number | Uint8Array<ArrayBufferLike> | number[] | Uint32Array<ArrayBufferLike> | Int32Array<ArrayBufferLike> | Int16Array<ArrayBufferLike> | Uint16Array<ArrayBufferLike> | Int8Array<ArrayBufferLike> | Float32Array<ArrayBufferLike> | undefined;
|
|
42
39
|
private _findTag;
|
|
43
40
|
private _computeTags;
|
|
44
41
|
isPaired(): boolean;
|
|
@@ -53,8 +50,9 @@ export default class BamRecord {
|
|
|
53
50
|
isFailedQc(): boolean;
|
|
54
51
|
isDuplicate(): boolean;
|
|
55
52
|
isSupplementary(): boolean;
|
|
56
|
-
|
|
57
|
-
private
|
|
53
|
+
private _isCGTagPattern;
|
|
54
|
+
private _computeLengthOnRef;
|
|
55
|
+
private _computeNumericCigar;
|
|
58
56
|
get length_on_ref(): number;
|
|
59
57
|
get NUMERIC_CIGAR(): number[] | Uint32Array<ArrayBufferLike>;
|
|
60
58
|
get CIGAR(): string;
|
|
@@ -72,6 +70,5 @@ export default class BamRecord {
|
|
|
72
70
|
get next_pos(): number;
|
|
73
71
|
get template_length(): number;
|
|
74
72
|
seqAt(idx: number): string | undefined;
|
|
75
|
-
toJSON(): Record<string,
|
|
73
|
+
toJSON(): Record<string, unknown>;
|
|
76
74
|
}
|
|
77
|
-
export {};
|