@gmod/bam 7.1.8 → 7.1.9
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/CHANGELOG.md +4 -0
- package/dist/htsget.d.ts +5 -2
- package/dist/htsget.js +1 -1
- package/dist/htsget.js.map +1 -1
- package/esm/htsget.d.ts +5 -2
- package/esm/htsget.js +1 -1
- package/esm/htsget.js.map +1 -1
- package/package.json +1 -1
- package/src/htsget.ts +11 -3
package/CHANGELOG.md
CHANGED
package/dist/htsget.d.ts
CHANGED
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@@ -1,14 +1,17 @@
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1
1
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import BamFile from './bamFile.ts';
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2
2
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import Chunk from './chunk.ts';
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3
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+
import BamRecord from './record.ts';
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4
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+
import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
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5
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import type { BamOpts, BaseOpts } from './util.ts';
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4
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-
export default class HtsgetFile extends BamFile {
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6
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+
export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends BamFile<T> {
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private baseUrl;
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8
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private trackId;
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constructor(args: {
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trackId: string;
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baseUrl: string;
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12
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+
recordClass?: BamRecordClass<T>;
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10
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});
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11
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-
streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<
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14
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+
streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
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_readChunk({ chunk }: {
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chunk: Chunk;
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opts: BaseOpts;
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package/dist/htsget.js
CHANGED
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@@ -68,7 +68,7 @@ async function concat(arr, opts) {
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}
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class HtsgetFile extends bamFile_ts_1.default {
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constructor(args) {
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71
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-
super({ htsget: true });
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71
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+
super({ htsget: true, recordClass: args.recordClass });
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this.baseUrl = args.baseUrl;
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this.trackId = args.trackId;
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}
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package/dist/htsget.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,2DAAiD;
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1
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+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,2DAAiD;AAGjD,qCAA0C;AAC1C,uCAA4C;AAU5C,KAAK,UAAU,MAAM,CAAC,GAAkB,EAAE,IAA0B;IAClE,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,mBAAmB;YAEnB,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,CAAA;YACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;gBAC3B,GAAG,IAAI;gBACP,OAAO,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE;aACvC,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;IAKlB,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,CAAC,qBAAqB,CAC1B,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,MAAM,EAAE,CAAA;QACV,CAAC;aAAM,CAAC;YACN,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;YACH,CAAC;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;YAE3D,KAAK,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAC7B;gBACE,sCAAsC;gBACtC;oBACE,MAAM,EAAE,KAAK;oBACb,YAAY,EAAE,SAAS;oBACvB,GAAG,EAAE,CAAC;oBACN,SAAS;wBACP,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,cAAc;wBACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;oBACD,WAAW;wBACT,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,CAAC;wBACf,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;wBACrC,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,QAAQ;wBACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;iBACF;aACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;QACH,CAAC;IACH,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,EAAE,KAAK,EAAoC;QAC1D,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;YAClB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;QACpD,CAAC;QACD,OAAO;YACL,IAAI,EAAE,KAAK,CAAC,MAAM;YAClB,UAAU,EAAE,EAAE;YACd,UAAU,EAAE,EAAE;YACd,KAAK;SACN,CAAA;IACH,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,IAAI,CAAC,CAAA;QAClD,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,CAAC,MAAM,CAAC,CAAA;QACvC,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;AApID,6BAoIC"}
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package/esm/htsget.d.ts
CHANGED
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@@ -1,14 +1,17 @@
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1
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import BamFile from './bamFile.ts';
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import Chunk from './chunk.ts';
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import BamRecord from './record.ts';
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import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
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import type { BamOpts, BaseOpts } from './util.ts';
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export default class HtsgetFile extends BamFile {
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export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends BamFile<T> {
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private baseUrl;
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private trackId;
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constructor(args: {
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trackId: string;
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baseUrl: string;
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recordClass?: BamRecordClass<T>;
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});
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-
streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<
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streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
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_readChunk({ chunk }: {
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chunk: Chunk;
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opts: BaseOpts;
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package/esm/htsget.js
CHANGED
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@@ -33,7 +33,7 @@ async function concat(arr, opts) {
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}
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export default class HtsgetFile extends BamFile {
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constructor(args) {
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super({ htsget: true });
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super({ htsget: true, recordClass: args.recordClass });
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this.baseUrl = args.baseUrl;
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this.trackId = args.trackId;
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}
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package/esm/htsget.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;
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+
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|
package/package.json
CHANGED
package/src/htsget.ts
CHANGED
|
@@ -2,9 +2,11 @@ import { unzip } from '@gmod/bgzf-filehandle'
|
|
|
2
2
|
|
|
3
3
|
import BamFile, { BAM_MAGIC } from './bamFile.ts'
|
|
4
4
|
import Chunk from './chunk.ts'
|
|
5
|
+
import BamRecord from './record.ts'
|
|
5
6
|
import { parseHeaderText } from './sam.ts'
|
|
6
7
|
import { concatUint8Array } from './util.ts'
|
|
7
8
|
|
|
9
|
+
import type { BamRecordClass, BamRecordLike } from './bamFile.ts'
|
|
8
10
|
import type { BamOpts, BaseOpts } from './util.ts'
|
|
9
11
|
|
|
10
12
|
interface HtsgetChunk {
|
|
@@ -47,13 +49,19 @@ async function concat(arr: HtsgetChunk[], opts?: Record<string, any>) {
|
|
|
47
49
|
return concatUint8Array(await Promise.all(res.map(elt => unzip(elt))))
|
|
48
50
|
}
|
|
49
51
|
|
|
50
|
-
export default class HtsgetFile
|
|
52
|
+
export default class HtsgetFile<
|
|
53
|
+
T extends BamRecordLike = BamRecord,
|
|
54
|
+
> extends BamFile<T> {
|
|
51
55
|
private baseUrl: string
|
|
52
56
|
|
|
53
57
|
private trackId: string
|
|
54
58
|
|
|
55
|
-
constructor(args: {
|
|
56
|
-
|
|
59
|
+
constructor(args: {
|
|
60
|
+
trackId: string
|
|
61
|
+
baseUrl: string
|
|
62
|
+
recordClass?: BamRecordClass<T>
|
|
63
|
+
}) {
|
|
64
|
+
super({ htsget: true, recordClass: args.recordClass })
|
|
57
65
|
this.baseUrl = args.baseUrl
|
|
58
66
|
this.trackId = args.trackId
|
|
59
67
|
}
|