@gmod/bam 7.1.10 → 7.1.12
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 +5 -7
- package/README.md +2 -18
- package/dist/bai.js +1 -1
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +4 -3
- package/dist/bamFile.js +73 -75
- package/dist/bamFile.js.map +1 -1
- package/dist/htsget.d.ts +1 -11
- package/dist/htsget.js +23 -49
- package/dist/htsget.js.map +1 -1
- package/dist/index.d.ts +5 -2
- package/dist/index.js.map +1 -1
- package/dist/record.d.ts +5 -0
- package/dist/record.js +214 -73
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +13 -0
- package/dist/util.js +25 -0
- package/dist/util.js.map +1 -1
- package/esm/bai.js +1 -1
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +4 -3
- package/esm/bamFile.js +74 -76
- package/esm/bamFile.js.map +1 -1
- package/esm/htsget.d.ts +1 -11
- package/esm/htsget.js +23 -49
- package/esm/htsget.js.map +1 -1
- package/esm/index.d.ts +5 -2
- package/esm/index.js +1 -1
- package/esm/index.js.map +1 -1
- package/esm/record.d.ts +5 -0
- package/esm/record.js +214 -73
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +13 -0
- package/esm/util.js +22 -0
- package/esm/util.js.map +1 -1
- package/package.json +1 -1
- package/src/bai.ts +1 -1
- package/src/bamFile.ts +111 -100
- package/src/htsget.ts +26 -58
- package/src/index.ts +6 -6
- package/src/record.ts +216 -81
- package/src/util.ts +41 -0
package/CHANGELOG.md
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## [7.1.
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## [7.1.12](https://github.com/GMOD/bam-js/compare/v7.1.11...v7.1.12) (2025-12-17)
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## [7.1.
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## [7.1.11](https://github.com/GMOD/bam-js/compare/v7.1.10...v7.1.11) (2025-12-16)
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## [7.1.
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## [7.1.10](https://github.com/GMOD/bam-js/compare/v7.1.9...v7.1.10) (2025-12-15)
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## [7.1.9](https://github.com/GMOD/bam-js/compare/v7.1.8...v7.1.9) (2025-12-13)
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## [7.1.8](https://github.com/GMOD/bam-js/compare/v7.1.7...v7.1.8) (2025-12-13)
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## [7.1.7](https://github.com/GMOD/bam-js/compare/v7.1.6...v7.1.7) (2025-12-13)
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## [7.1.6](https://github.com/GMOD/bam-js/compare/v7.1.5...v7.1.6) (2025-12-13)
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## [7.1.5](https://github.com/GMOD/bam-js/compare/v7.1.4...v7.1.5) (2025-12-13)
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## [7.1.4](https://github.com/GMOD/bam-js/compare/v7.1.3...v7.1.4) (2025-12-13)
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package/README.md
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@@ -93,24 +93,6 @@ Note: you must run getHeader before running getRecordsForRange
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- `opts.maxInsertSize` - control the viewAsPairs option behavior to limit
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distance within a chromosome to fetch. default: 200kb
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### async \*streamRecordsForRange(refName, start, end, opts)
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This is a async generator function that takes the same signature as
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`getRecordsForRange` but results can be processed using
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```typescript
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for await (const chunk of file.streamRecordsForRange(
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end,
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)) {
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}
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```
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The `getRecordsForRange` simply wraps this process by concatenating chunks into
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an array
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### async getHeader(opts: {....anything to pass to generic-filehandle2 opts})
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This obtains the header from `HtsgetFile` or `BamFile`. Retrieves BAM file and
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// Auxiliary data
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record.tags // object with all aux tags e.g. {MD: "100", NM: 0}
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record.getTag('MD') // get a single tag (more efficient than record.tags when you only need one)
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record.getTagRaw('MD') // get tag as Uint8Array for string tags (avoids string conversion)
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record.NUMERIC_MD // MD tag as Uint8Array (for fast mismatch rendering)
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record.NUMERIC_CIGAR // Uint32Array of packed CIGAR operations
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record.NUMERIC_SEQ // Uint8Array of packed sequence (4-bit encoded)
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package/dist/bai.js
CHANGED
package/dist/bai.js.map
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+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;AAAA,0DAAgC;AAEhC,0DAA8B;AAC9B,kEAAsC;AACtC,uCAKkB;AAClB,yDAA6D;AAE7D,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;IAGxC,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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|
package/dist/bamFile.d.ts
CHANGED
|
@@ -14,6 +14,8 @@ export interface BamRecordLike {
|
|
|
14
14
|
fileOffset: number;
|
|
15
15
|
next_pos: number;
|
|
16
16
|
next_refid: number;
|
|
17
|
+
flags: number;
|
|
18
|
+
tags: Record<string, unknown>;
|
|
17
19
|
}
|
|
18
20
|
export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
|
|
19
21
|
bytes: Bytes;
|
|
@@ -76,12 +78,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
76
78
|
}[];
|
|
77
79
|
};
|
|
78
80
|
getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
|
|
79
|
-
streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
|
|
80
81
|
private chunkCacheKey;
|
|
81
82
|
private blocksOverlap;
|
|
82
83
|
private evictOverlappingChunks;
|
|
83
|
-
|
|
84
|
-
fetchPairs(chrId: number,
|
|
84
|
+
private _fetchChunkFeaturesDirect;
|
|
85
|
+
fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
|
|
85
86
|
_readChunk({ chunk, opts }: {
|
|
86
87
|
chunk: Chunk;
|
|
87
88
|
opts: BaseOpts;
|
package/dist/bamFile.js
CHANGED
|
@@ -130,26 +130,26 @@ class BamFile {
|
|
|
130
130
|
const refName = this.renameRefSeq(decoder.decode(uncba.subarray(p + 4, p + 4 + lName - 1)));
|
|
131
131
|
const lRef = dataView.getInt32(p + lName + 4, true);
|
|
132
132
|
chrToIndex[refName] = i;
|
|
133
|
-
indexToChr.push({
|
|
133
|
+
indexToChr.push({
|
|
134
|
+
refName,
|
|
135
|
+
length: lRef,
|
|
136
|
+
});
|
|
134
137
|
p = p + 8 + lName;
|
|
135
138
|
}
|
|
136
139
|
return { chrToIndex, indexToChr };
|
|
137
140
|
}
|
|
138
141
|
async getRecordsForRange(chr, min, max, opts) {
|
|
139
|
-
return (0, util_ts_1.gen2array)(this.streamRecordsForRange(chr, min, max, opts));
|
|
140
|
-
}
|
|
141
|
-
async *streamRecordsForRange(chr, min, max, opts) {
|
|
142
142
|
await this.getHeader(opts);
|
|
143
143
|
const chrId = this.chrToIndex?.[chr];
|
|
144
144
|
if (chrId === undefined || !this.index) {
|
|
145
|
-
return;
|
|
145
|
+
return [];
|
|
146
146
|
}
|
|
147
147
|
const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
|
|
148
|
-
|
|
148
|
+
return this._fetchChunkFeaturesDirect(chunks, chrId, min, max, opts);
|
|
149
149
|
}
|
|
150
|
-
chunkCacheKey(chunk) {
|
|
150
|
+
chunkCacheKey(chunk, filterBy) {
|
|
151
151
|
const { minv, maxv } = chunk;
|
|
152
|
-
return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
|
|
152
|
+
return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}${(0, util_ts_1.filterCacheKey)(filterBy)}`;
|
|
153
153
|
}
|
|
154
154
|
blocksOverlap(minBlock1, maxBlock1, minBlock2, maxBlock2) {
|
|
155
155
|
return minBlock1 <= maxBlock2 && maxBlock1 >= minBlock2;
|
|
@@ -158,28 +158,23 @@ class BamFile {
|
|
|
158
158
|
evictOverlappingChunks(minBlock, maxBlock) {
|
|
159
159
|
for (const [key, entry] of this.chunkFeatureCache) {
|
|
160
160
|
if (this.blocksOverlap(minBlock, maxBlock, entry.minBlock, entry.maxBlock)) {
|
|
161
|
-
// console.log(
|
|
162
|
-
// `[BAM Cache] Evicting overlapping chunk: ${key} (${entry.features.length} features, blocks ${entry.minBlock}-${entry.maxBlock})`,
|
|
163
|
-
// )
|
|
164
161
|
this.chunkFeatureCache.delete(key);
|
|
165
162
|
}
|
|
166
163
|
}
|
|
167
164
|
}
|
|
168
|
-
async
|
|
169
|
-
const { viewAsPairs } = opts;
|
|
170
|
-
const
|
|
171
|
-
|
|
172
|
-
|
|
173
|
-
|
|
174
|
-
|
|
175
|
-
const cacheKey = this.chunkCacheKey(chunk);
|
|
165
|
+
async _fetchChunkFeaturesDirect(chunks, chrId, min, max, opts = {}) {
|
|
166
|
+
const { viewAsPairs, filterBy } = opts;
|
|
167
|
+
const { flagInclude = 0, flagExclude = 0, tagFilter } = filterBy || {};
|
|
168
|
+
const result = [];
|
|
169
|
+
for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
|
|
170
|
+
const chunk = chunks[ci];
|
|
171
|
+
const cacheKey = this.chunkCacheKey(chunk, filterBy);
|
|
176
172
|
const minBlock = chunk.minv.blockPosition;
|
|
177
173
|
const maxBlock = chunk.maxv.blockPosition;
|
|
178
174
|
let records;
|
|
179
175
|
const cached = this.chunkFeatureCache.get(cacheKey);
|
|
180
176
|
if (cached) {
|
|
181
177
|
records = cached.features;
|
|
182
|
-
// cacheHits++
|
|
183
178
|
}
|
|
184
179
|
else {
|
|
185
180
|
this.evictOverlappingChunks(minBlock, maxBlock);
|
|
@@ -187,86 +182,87 @@ class BamFile {
|
|
|
187
182
|
chunk,
|
|
188
183
|
opts,
|
|
189
184
|
});
|
|
190
|
-
|
|
185
|
+
const allRecords = await this.readBamFeatures(data, cpositions, dpositions, chunk);
|
|
186
|
+
if (filterBy) {
|
|
187
|
+
records = [];
|
|
188
|
+
for (let i = 0, l = allRecords.length; i < l; i++) {
|
|
189
|
+
const record = allRecords[i];
|
|
190
|
+
if ((0, util_ts_1.filterReadFlag)(record.flags, flagInclude, flagExclude)) {
|
|
191
|
+
continue;
|
|
192
|
+
}
|
|
193
|
+
if (tagFilter &&
|
|
194
|
+
(0, util_ts_1.filterTagValue)(record.tags[tagFilter.tag], tagFilter.value)) {
|
|
195
|
+
continue;
|
|
196
|
+
}
|
|
197
|
+
records.push(record);
|
|
198
|
+
}
|
|
199
|
+
}
|
|
200
|
+
else {
|
|
201
|
+
records = allRecords;
|
|
202
|
+
}
|
|
191
203
|
this.chunkFeatureCache.set(cacheKey, {
|
|
192
204
|
minBlock,
|
|
193
205
|
maxBlock,
|
|
194
206
|
features: records,
|
|
195
207
|
});
|
|
196
|
-
// cacheMisses++
|
|
197
208
|
}
|
|
198
|
-
|
|
199
|
-
for (
|
|
209
|
+
let done = false;
|
|
210
|
+
for (let i = 0, l = records.length; i < l; i++) {
|
|
211
|
+
const feature = records[i];
|
|
200
212
|
if (feature.ref_id === chrId) {
|
|
201
213
|
if (feature.start >= max) {
|
|
202
214
|
done = true;
|
|
203
215
|
break;
|
|
204
216
|
}
|
|
205
217
|
else if (feature.end >= min) {
|
|
206
|
-
|
|
218
|
+
result.push(feature);
|
|
207
219
|
}
|
|
208
220
|
}
|
|
209
221
|
}
|
|
210
|
-
feats.push(recs);
|
|
211
|
-
yield recs;
|
|
212
222
|
if (done) {
|
|
213
223
|
break;
|
|
214
224
|
}
|
|
215
225
|
}
|
|
216
|
-
// const total = cacheHits + cacheMisses
|
|
217
|
-
// if (total > 0) {
|
|
218
|
-
// const hitRate = (cacheHits / total) * 100
|
|
219
|
-
// console.log(
|
|
220
|
-
// `[BAM Cache] chunks: ${total}, hits: ${cacheHits}, misses: ${cacheMisses}, rate: ${hitRate.toFixed(1)}%, cacheSize: ${this.chunkFeatureCache.size}`,
|
|
221
|
-
// )
|
|
222
|
-
// }
|
|
223
226
|
if (viewAsPairs) {
|
|
224
|
-
|
|
227
|
+
const pairs = await this.fetchPairs(chrId, result, opts);
|
|
228
|
+
for (let i = 0, l = pairs.length; i < l; i++) {
|
|
229
|
+
result.push(pairs[i]);
|
|
230
|
+
}
|
|
225
231
|
}
|
|
232
|
+
return result;
|
|
226
233
|
}
|
|
227
|
-
async fetchPairs(chrId,
|
|
234
|
+
async fetchPairs(chrId, records, opts) {
|
|
228
235
|
const { pairAcrossChr, maxInsertSize = 200000 } = opts;
|
|
229
|
-
const
|
|
236
|
+
const readNameCounts = {};
|
|
230
237
|
const readIds = {};
|
|
231
|
-
for (
|
|
232
|
-
const
|
|
233
|
-
|
|
234
|
-
|
|
235
|
-
|
|
236
|
-
if (!readNames[name]) {
|
|
237
|
-
readNames[name] = 0;
|
|
238
|
-
}
|
|
239
|
-
readNames[name]++;
|
|
240
|
-
readIds[id] = 1;
|
|
241
|
-
}
|
|
242
|
-
for (const [k, v] of Object.entries(readNames)) {
|
|
243
|
-
if (v === 1) {
|
|
244
|
-
unmatedPairs[k] = true;
|
|
245
|
-
}
|
|
246
|
-
}
|
|
238
|
+
for (let i = 0, l = records.length; i < l; i++) {
|
|
239
|
+
const r = records[i];
|
|
240
|
+
const name = r.name;
|
|
241
|
+
readNameCounts[name] = (readNameCounts[name] || 0) + 1;
|
|
242
|
+
readIds[r.fileOffset] = 1;
|
|
247
243
|
}
|
|
248
244
|
const matePromises = [];
|
|
249
|
-
for (
|
|
250
|
-
|
|
251
|
-
|
|
252
|
-
|
|
253
|
-
|
|
254
|
-
|
|
255
|
-
|
|
256
|
-
|
|
257
|
-
|
|
258
|
-
(rnext === chrId && Math.abs(start - pnext) < maxInsertSize))) {
|
|
259
|
-
matePromises.push(this.index.blocksForRange(rnext, pnext, pnext + 1, opts));
|
|
260
|
-
}
|
|
245
|
+
for (let i = 0, l = records.length; i < l; i++) {
|
|
246
|
+
const f = records[i];
|
|
247
|
+
const name = f.name;
|
|
248
|
+
if (this.index &&
|
|
249
|
+
readNameCounts[name] === 1 &&
|
|
250
|
+
(pairAcrossChr ||
|
|
251
|
+
(f.next_refid === chrId &&
|
|
252
|
+
Math.abs(f.start - f.next_pos) < maxInsertSize))) {
|
|
253
|
+
matePromises.push(this.index.blocksForRange(f.next_refid, f.next_pos, f.next_pos + 1, opts));
|
|
261
254
|
}
|
|
262
255
|
}
|
|
263
|
-
// filter out duplicate chunks (the blocks are lists of chunks, blocks are
|
|
264
|
-
// concatenated, then filter dup chunks)
|
|
265
256
|
const map = new Map();
|
|
266
257
|
const res = await Promise.all(matePromises);
|
|
267
|
-
for (
|
|
268
|
-
|
|
269
|
-
|
|
258
|
+
for (let i = 0, l = res.length; i < l; i++) {
|
|
259
|
+
const chunks = res[i];
|
|
260
|
+
for (let j = 0, jl = chunks.length; j < jl; j++) {
|
|
261
|
+
const m = chunks[j];
|
|
262
|
+
const key = m.toString();
|
|
263
|
+
if (!map.has(key)) {
|
|
264
|
+
map.set(key, m);
|
|
265
|
+
}
|
|
270
266
|
}
|
|
271
267
|
}
|
|
272
268
|
const mateFeatPromises = await Promise.all([...map.values()].map(async (c) => {
|
|
@@ -275,8 +271,11 @@ class BamFile {
|
|
|
275
271
|
opts,
|
|
276
272
|
});
|
|
277
273
|
const mateRecs = [];
|
|
278
|
-
|
|
279
|
-
|
|
274
|
+
const features = await this.readBamFeatures(data, cpositions, dpositions, chunk);
|
|
275
|
+
for (let i = 0, l = features.length; i < l; i++) {
|
|
276
|
+
const feature = features[i];
|
|
277
|
+
if (readNameCounts[feature.name] === 1 &&
|
|
278
|
+
!readIds[feature.fileOffset]) {
|
|
280
279
|
mateRecs.push(feature);
|
|
281
280
|
}
|
|
282
281
|
}
|
|
@@ -360,7 +359,7 @@ class BamFile {
|
|
|
360
359
|
if (!this.chrToIndex) {
|
|
361
360
|
throw new Error('Header not yet parsed');
|
|
362
361
|
}
|
|
363
|
-
|
|
362
|
+
return this.index.estimatedBytesForRegions(regions.map(r => {
|
|
364
363
|
const refId = this.chrToIndex[r.refName];
|
|
365
364
|
if (refId === undefined) {
|
|
366
365
|
throw new Error(`Unknown reference name: ${r.refName}`);
|
|
@@ -370,8 +369,7 @@ class BamFile {
|
|
|
370
369
|
start: r.start,
|
|
371
370
|
end: r.end,
|
|
372
371
|
};
|
|
373
|
-
});
|
|
374
|
-
return this.index.estimatedBytesForRegions(regionsWithIds, opts);
|
|
372
|
+
}), opts);
|
|
375
373
|
}
|
|
376
374
|
}
|
|
377
375
|
exports.default = BamFile;
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/htsget.d.ts
CHANGED
|
@@ -1,5 +1,4 @@
|
|
|
1
1
|
import BamFile from './bamFile.ts';
|
|
2
|
-
import Chunk from './chunk.ts';
|
|
3
2
|
import BamRecord from './record.ts';
|
|
4
3
|
import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
|
|
5
4
|
import type { BamOpts, BaseOpts } from './util.ts';
|
|
@@ -11,16 +10,7 @@ export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends Bam
|
|
|
11
10
|
baseUrl: string;
|
|
12
11
|
recordClass?: BamRecordClass<T>;
|
|
13
12
|
});
|
|
14
|
-
|
|
15
|
-
_readChunk({ chunk }: {
|
|
16
|
-
chunk: Chunk;
|
|
17
|
-
opts: BaseOpts;
|
|
18
|
-
}): Promise<{
|
|
19
|
-
data: Uint8Array<ArrayBuffer>;
|
|
20
|
-
cpositions: never[];
|
|
21
|
-
dpositions: never[];
|
|
22
|
-
chunk: Chunk;
|
|
23
|
-
}>;
|
|
13
|
+
getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
|
|
24
14
|
getHeader(opts?: BaseOpts): Promise<{
|
|
25
15
|
tag: string;
|
|
26
16
|
data: {
|
package/dist/htsget.js
CHANGED
|
@@ -72,62 +72,36 @@ class HtsgetFile extends bamFile_ts_1.default {
|
|
|
72
72
|
this.baseUrl = args.baseUrl;
|
|
73
73
|
this.trackId = args.trackId;
|
|
74
74
|
}
|
|
75
|
-
async
|
|
75
|
+
async getRecordsForRange(chr, min, max, opts) {
|
|
76
76
|
const base = `${this.baseUrl}/${this.trackId}`;
|
|
77
77
|
const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
|
|
78
78
|
const chrId = this.chrToIndex?.[chr];
|
|
79
79
|
if (chrId === undefined) {
|
|
80
|
-
|
|
80
|
+
return [];
|
|
81
81
|
}
|
|
82
|
-
|
|
83
|
-
|
|
84
|
-
|
|
85
|
-
throw new Error(`HTTP ${result.status} fetching ${url}: ${await result.text()}`);
|
|
86
|
-
}
|
|
87
|
-
const data = await result.json();
|
|
88
|
-
const uncba = await concat(data.htsget.urls.slice(1), opts);
|
|
89
|
-
yield* this._fetchChunkFeatures([
|
|
90
|
-
// fake stuff to pretend to be a Chunk
|
|
91
|
-
{
|
|
92
|
-
buffer: uncba,
|
|
93
|
-
_fetchedSize: undefined,
|
|
94
|
-
bin: 0,
|
|
95
|
-
compareTo() {
|
|
96
|
-
return 0;
|
|
97
|
-
},
|
|
98
|
-
toUniqueString() {
|
|
99
|
-
return `${chr}_${min}_${max}`;
|
|
100
|
-
},
|
|
101
|
-
fetchedSize() {
|
|
102
|
-
return 0;
|
|
103
|
-
},
|
|
104
|
-
minv: {
|
|
105
|
-
dataPosition: 0,
|
|
106
|
-
blockPosition: 0,
|
|
107
|
-
compareTo: () => 0,
|
|
108
|
-
},
|
|
109
|
-
maxv: {
|
|
110
|
-
dataPosition: Number.MAX_SAFE_INTEGER,
|
|
111
|
-
blockPosition: 0,
|
|
112
|
-
compareTo: () => 0,
|
|
113
|
-
},
|
|
114
|
-
toString() {
|
|
115
|
-
return `${chr}_${min}_${max}`;
|
|
116
|
-
},
|
|
117
|
-
},
|
|
118
|
-
], chrId, min, max, opts);
|
|
82
|
+
const result = await fetch(url, { ...opts });
|
|
83
|
+
if (!result.ok) {
|
|
84
|
+
throw new Error(`HTTP ${result.status} fetching ${url}: ${await result.text()}`);
|
|
119
85
|
}
|
|
120
|
-
|
|
121
|
-
|
|
122
|
-
|
|
123
|
-
|
|
86
|
+
const data = await result.json();
|
|
87
|
+
const uncba = await concat(data.htsget.urls.slice(1), opts);
|
|
88
|
+
const allRecords = await this.readBamFeatures(uncba, [], [], {
|
|
89
|
+
minv: { dataPosition: 0, blockPosition: 0 },
|
|
90
|
+
maxv: { dataPosition: 0, blockPosition: 0 },
|
|
91
|
+
});
|
|
92
|
+
const records = [];
|
|
93
|
+
for (let i = 0, l = allRecords.length; i < l; i++) {
|
|
94
|
+
const feature = allRecords[i];
|
|
95
|
+
if (feature.ref_id === chrId) {
|
|
96
|
+
if (feature.start >= max) {
|
|
97
|
+
break;
|
|
98
|
+
}
|
|
99
|
+
else if (feature.end >= min) {
|
|
100
|
+
records.push(feature);
|
|
101
|
+
}
|
|
102
|
+
}
|
|
124
103
|
}
|
|
125
|
-
return
|
|
126
|
-
data: chunk.buffer,
|
|
127
|
-
cpositions: [],
|
|
128
|
-
dpositions: [],
|
|
129
|
-
chunk,
|
|
130
|
-
};
|
|
104
|
+
return records;
|
|
131
105
|
}
|
|
132
106
|
async getHeader(opts = {}) {
|
|
133
107
|
const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
|
package/dist/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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,
|
|
1
|
+
{"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,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,IAAI,CAAC,CAAA;QAE3D,MAAM,UAAU,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,KAAK,EAAE,EAAE,EAAE,EAAE,EAAE;YAC3D,IAAI,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,aAAa,EAAE,CAAC,EAAE;YAC3C,IAAI,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,aAAa,EAAE,CAAC,EAAE;SACnC,CAAC,CAAA;QAEX,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,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;AApGD,6BAoGC"}
|
package/dist/index.d.ts
CHANGED
|
@@ -1,5 +1,8 @@
|
|
|
1
1
|
export { default as BAI } from './bai.ts';
|
|
2
|
-
export {
|
|
2
|
+
export { default as BamFile } from './bamFile.ts';
|
|
3
3
|
export { default as CSI } from './csi.ts';
|
|
4
|
-
export {
|
|
4
|
+
export { default as BamRecord } from './record.ts';
|
|
5
5
|
export { default as HtsgetFile } from './htsget.ts';
|
|
6
|
+
export type { Bytes } from './record.ts';
|
|
7
|
+
export type { FilterBy, TagFilter } from './util.ts';
|
|
8
|
+
export type { BamRecordClass, BamRecordLike } from './bamFile.ts';
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAAiD;AAAxC,sHAAA,OAAO,OAAW;AAC3B,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc"}
|
package/dist/record.d.ts
CHANGED
|
@@ -18,6 +18,7 @@ export default class BamRecord {
|
|
|
18
18
|
private _cachedTags?;
|
|
19
19
|
private _cachedCigarAndLength?;
|
|
20
20
|
private _cachedNUMERIC_MD?;
|
|
21
|
+
private _cachedTagsStart?;
|
|
21
22
|
constructor(args: {
|
|
22
23
|
bytes: Bytes;
|
|
23
24
|
fileOffset: number;
|
|
@@ -32,9 +33,13 @@ export default class BamRecord {
|
|
|
32
33
|
get qual(): Uint8Array<ArrayBufferLike> | null;
|
|
33
34
|
get strand(): 1 | -1;
|
|
34
35
|
get b0(): number;
|
|
36
|
+
get tagsStart(): number;
|
|
35
37
|
get name(): string;
|
|
36
38
|
get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
|
|
37
39
|
get tags(): Record<string, unknown>;
|
|
40
|
+
getTag(tagName: string): unknown;
|
|
41
|
+
getTagRaw(tagName: string): string | number | number[] | Int8Array<ArrayBufferLike> | Uint8Array<ArrayBufferLike> | Int16Array<ArrayBufferLike> | Uint16Array<ArrayBufferLike> | Int32Array<ArrayBufferLike> | Uint32Array<ArrayBufferLike> | Float32Array<ArrayBufferLike> | undefined;
|
|
42
|
+
private _findTag;
|
|
38
43
|
private _computeTags;
|
|
39
44
|
isPaired(): boolean;
|
|
40
45
|
isProperlyPaired(): boolean;
|