@gmod/bam 2.0.4 → 3.0.0
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 +7 -6
- package/README.md +10 -42
- package/dist/bai.js +6 -1
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.js +14 -12
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.d.ts +1 -1
- package/dist/csi.js +4 -2
- package/dist/csi.js.map +1 -1
- package/dist/htsget.js +1 -1
- package/dist/record.d.ts +43 -54
- package/dist/record.js +121 -206
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +0 -2
- package/dist/util.js +3 -10
- package/dist/util.js.map +1 -1
- package/esm/bai.js +6 -1
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.js +13 -11
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.d.ts +1 -1
- package/esm/csi.js +4 -2
- package/esm/csi.js.map +1 -1
- package/esm/record.d.ts +43 -54
- package/esm/record.js +121 -206
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +0 -2
- package/esm/util.js +3 -9
- package/esm/util.js.map +1 -1
- package/package.json +14 -15
- package/src/bai.ts +7 -2
- package/src/bamFile.ts +13 -11
- package/src/csi.ts +5 -3
- package/src/record.ts +138 -241
- package/src/util.ts +4 -15
package/CHANGELOG.md
CHANGED
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# [3.0.0](https://github.com/GMOD/bam-js/compare/v2.0.4...v3.0.0) (2024-11-07)
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## [2.0.
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## [2.0.4](https://github.com/GMOD/bam-js/compare/v2.0.3...v2.0.4) (2024-08-09)
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## [2.0.3](https://github.com/GMOD/bam-js/compare/v2.0.2...v2.0.3) (2024-07-23)
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### Reverts
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- Revert "Migrate to eslint9"
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([65adcbb](https://github.com/GMOD/bam-js/commit/65adcbb2793243659682d30694f8604d241a5337))
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- Revert "Run format"
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([2a02535](https://github.com/GMOD/bam-js/commit/2a02535db4df80f245232522cdba771cbf5ea214))
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## [2.0.2](https://github.com/GMOD/bam-js/compare/v2.0.1...v2.0.2) (2024-02-21)
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package/README.md
CHANGED
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@@ -142,53 +142,21 @@ Returns whether we have this refName in the sample
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### Returned features
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The returned features from BAM are lazy features meaning that it delays
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processing of all the feature tags until necessary.
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You can access data feature.get('field') to get the value of a feature attribute
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Example
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```typescript
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feature.
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feature.
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feature.
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feature.
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feature.
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feature.get('qual') // qualities
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feature.get('cigar') // cigar string
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feature.get('MD') // MD string
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feature.get('SA') // supplementary alignments
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feature.get('template_length') // TLEN
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feature.get('length_on_ref') // derived from CIGAR using standard algorithm
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```
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#### Flags
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```typescript
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feature.get('flags') // see https://broadinstitute.github.io/picard/explain-flags.html
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feature.ref_id // numerical sequence id corresponding to position in the sam header
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feature.start // 0-based half open start coordinate
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feature.end // 0-based half open end coordinate
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feature.name // QNAME
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feature.seq // feature sequence
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feature.qual // qualities
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feature.CIGAR // CIGAR string
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feature.tags // tags
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feature.flags // flags
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feature.template_length // TLEN
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```
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#### Tags
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BAM tags such as MD can be obtained via
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```typescript
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feature.get('MD')
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```
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A full list of tags that can be obtained can be obtained via
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feature._tags()
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The feature format may change in future versions to be more raw data records,
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but this will be a major version bump
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#### Note
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The reason that we hide the data behind this ".get" function is that we lazily
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package/dist/bai.js
CHANGED
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@@ -118,6 +118,7 @@ class BAI extends indexFile_1.default {
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const range = start !== undefined;
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const indexData = yield this.parse(opts);
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const seqIdx = indexData.indices[seqId];
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// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
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if (!seqIdx) {
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return [];
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}
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min = 0;
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}
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const indexData = yield this.parse(opts);
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// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
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if (!indexData) {
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return [];
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}
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const ba = indexData.indices[refId];
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// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
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if (!ba) {
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return [];
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}
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// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
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for (const [start, end] of overlappingBins) {
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for (let bin = start; bin <= end; bin++) {
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// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
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if (ba.binIndex[bin]) {
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const binChunks = ba.binIndex[bin];
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for (const binChunk of binChunks) {
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const maxLin = Math.min(max >> 14, nintv - 1);
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for (let i = minLin; i <= maxLin; ++i) {
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const vp = ba.linearIndex[i];
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// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
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if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
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lowest = vp;
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}
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parse() {
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return __awaiter(this, arguments, void 0, function* (opts = {}) {
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if (!this.setupP) {
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this.setupP = this._parse(opts).catch(e => {
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this.setupP = this._parse(opts).catch((e) => {
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this.setupP = undefined;
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throw e;
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});
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package/dist/bai.js.map
CHANGED
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@@ -1 +1 @@
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+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,mDAA0D;AAC1D,oDAA2B;AAE3B,iCAAgF;AAChF,4DAAmC;AAEnC,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;AAED,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,mBAAS;IAGlC,SAAS,CAAC,KAAa,EAAE,IAAe;;;YAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,OAAO,CAAA,MAAA,MAAA,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,KAAK,0CAAE,SAAS,KAAI,CAAC,CAAA;QACxD,CAAC;KAAA;IAED,4BAA4B;IACtB,MAAM,CAAC,IAAe;;YAC1B,MAAM,KAAK,GAAG,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAA;YAE9D,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE,CAAC;gBACxC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;YAED,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACrC,MAAM,KAAK,GAAG,CAAC,CAAA;YACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YAEnD,+CAA+C;YAC/C,IAAI,IAAI,GAAG,CAAC,CAAA;YACZ,IAAI,aAAwC,CAAA;YAI5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAItB,QAAQ,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACxC,IAAI,KAAK,CAAA;gBAET,IAAI,IAAI,CAAC,CAAA;gBACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;gBAE5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;oBACrC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,CAAA;oBACpC,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;wBACzB,IAAI,IAAI,CAAC,CAAA;wBACT,KAAK,GAAG,IAAA,qBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;wBACxC,IAAI,IAAI,EAAE,CAAA;oBACZ,CAAC;yBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;wBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;oBACrE,CAAC;yBAAM,CAAC;wBACN,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;wBAC1C,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;wBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;4BACpC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;4BAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;wBAClC,CAAC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;oBACxB,CAAC;gBACH,CAAC;gBAED,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBAC3C,IAAI,IAAI,CAAC,CAAA;gBACT,mEAAmE;gBACnE,qEAAqE;gBACrE,OAAO;gBACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;gBACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;oBACrC,MAAM,MAAM,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;oBACrC,IAAI,IAAI,CAAC,CAAA;oBACT,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;oBACpD,WAAW,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;gBACzB,CAAC;gBAED,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;YAC/C,CAAC;YAED,OAAO;gBACL,GAAG,EAAE,IAAI;gBACT,aAAa;gBACb,YAAY,EAAE,CAAC,IAAI,EAAE;gBACrB,OAAO;gBACP,QAAQ;aACT,CAAA;QACH,CAAC;KAAA;IAEK,QAAQ;6DACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,OAAiB,EAAE;YAEnB,MAAM,CAAC,GAAG,KAAK,CAAA;YACf,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;YACjC,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACvC,uEAAuE;YACvE,IAAI,CAAC,MAAM,EAAE,CAAC;gBACZ,OAAO,EAAE,CAAA;YACX,CAAC;YACD,MAAM,EAAE,WAAW,GAAG,EAAE,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;YAC1C,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC7B,OAAO,EAAE,CAAA;YACX,CAAC;YACD,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;YAC5E,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;YACvD,MAAM,MAAM,GAAG,KAAK;gBAClB,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;gBACxB,CAAC,CAAC,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;YACrC,MAAM,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;YACnE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBACrC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;YAC3D,CAAC;YACD,IAAI,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;YACjD,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAA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|
package/dist/bamFile.js
CHANGED
|
@@ -24,7 +24,7 @@ var __asyncDelegator = (this && this.__asyncDelegator) || function (o) {
|
|
|
24
24
|
var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _arguments, generator) {
|
|
25
25
|
if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
|
|
26
26
|
var g = generator.apply(thisArg, _arguments || []), i, q = [];
|
|
27
|
-
return i =
|
|
27
|
+
return i = Object.create((typeof AsyncIterator === "function" ? AsyncIterator : Object).prototype), verb("next"), verb("throw"), verb("return", awaitReturn), i[Symbol.asyncIterator] = function () { return this; }, i;
|
|
28
28
|
function awaitReturn(f) { return function (v) { return Promise.resolve(v).then(f, reject); }; }
|
|
29
29
|
function verb(n, f) { if (g[n]) { i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; if (f) i[n] = f(i[n]); } }
|
|
30
30
|
function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }
|
|
@@ -190,7 +190,7 @@ class BamFile {
|
|
|
190
190
|
}
|
|
191
191
|
getHeader(opts) {
|
|
192
192
|
if (!this.headerP) {
|
|
193
|
-
this.headerP = this.getHeaderPre(opts).catch(e => {
|
|
193
|
+
this.headerP = this.getHeaderPre(opts).catch((e) => {
|
|
194
194
|
this.headerP = undefined;
|
|
195
195
|
throw e;
|
|
196
196
|
});
|
|
@@ -263,13 +263,13 @@ class BamFile {
|
|
|
263
263
|
const records = yield __await(this.featureCache.get(chunk.toString(), { chunk, opts }, opts.signal));
|
|
264
264
|
const recs = [];
|
|
265
265
|
for (const feature of records) {
|
|
266
|
-
if (feature.
|
|
267
|
-
if (feature.
|
|
266
|
+
if (feature.ref_id === chrId) {
|
|
267
|
+
if (feature.start >= max) {
|
|
268
268
|
// past end of range, can stop iterating
|
|
269
269
|
done = true;
|
|
270
270
|
break;
|
|
271
271
|
}
|
|
272
|
-
else if (feature.
|
|
272
|
+
else if (feature.end >= min) {
|
|
273
273
|
// must be in range
|
|
274
274
|
recs.push(feature);
|
|
275
275
|
}
|
|
@@ -295,8 +295,8 @@ class BamFile {
|
|
|
295
295
|
feats.map(ret => {
|
|
296
296
|
const readNames = {};
|
|
297
297
|
for (const element of ret) {
|
|
298
|
-
const name = element.name
|
|
299
|
-
const id = element.id
|
|
298
|
+
const name = element.name;
|
|
299
|
+
const id = element.id;
|
|
300
300
|
if (!readNames[name]) {
|
|
301
301
|
readNames[name] = 0;
|
|
302
302
|
}
|
|
@@ -312,10 +312,10 @@ class BamFile {
|
|
|
312
312
|
const matePromises = [];
|
|
313
313
|
feats.map(ret => {
|
|
314
314
|
for (const f of ret) {
|
|
315
|
-
const name = f.name
|
|
316
|
-
const start = f.
|
|
317
|
-
const pnext = f.
|
|
318
|
-
const rnext = f.
|
|
315
|
+
const name = f.name;
|
|
316
|
+
const start = f.start;
|
|
317
|
+
const pnext = f.next_pos;
|
|
318
|
+
const rnext = f.next_refid;
|
|
319
319
|
if (this.index &&
|
|
320
320
|
unmatedPairs[name] &&
|
|
321
321
|
(pairAcrossChr ||
|
|
@@ -340,7 +340,7 @@ class BamFile {
|
|
|
340
340
|
});
|
|
341
341
|
const mateRecs = [];
|
|
342
342
|
for (const feature of yield this.readBamFeatures(data, cpositions, dpositions, chunk)) {
|
|
343
|
-
if (unmatedPairs[feature.
|
|
343
|
+
if (unmatedPairs[feature.name] && !readIds[feature.id]) {
|
|
344
344
|
mateRecs.push(feature);
|
|
345
345
|
}
|
|
346
346
|
}
|
|
@@ -372,6 +372,7 @@ class BamFile {
|
|
|
372
372
|
const blockSize = ba.readInt32LE(blockStart);
|
|
373
373
|
const blockEnd = blockStart + 4 + blockSize - 1;
|
|
374
374
|
// increment position to the current decompressed status
|
|
375
|
+
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
|
|
375
376
|
if (dpositions) {
|
|
376
377
|
while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]) { }
|
|
377
378
|
pos--;
|
|
@@ -410,6 +411,7 @@ class BamFile {
|
|
|
410
411
|
chunk.minv.dataPosition +
|
|
411
412
|
1
|
|
412
413
|
: // must be slice, not subarray for buffer polyfill on web
|
|
414
|
+
// eslint-disable-next-line @typescript-eslint/no-deprecated
|
|
413
415
|
crc32_1.default.signed(ba.slice(blockStart, blockEnd)),
|
|
414
416
|
});
|
|
415
417
|
sink.push(feature);
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/csi.d.ts
CHANGED
|
@@ -57,7 +57,7 @@ export default class CSI extends IndexFile {
|
|
|
57
57
|
* calculate the list of bins that may overlap with region [beg,end)
|
|
58
58
|
* (zero-based half-open)
|
|
59
59
|
*/
|
|
60
|
-
reg2bins(beg: number, end: number): number
|
|
60
|
+
reg2bins(beg: number, end: number): (readonly [number, number])[];
|
|
61
61
|
parse(opts?: BaseOpts): Promise<{
|
|
62
62
|
refNameToId?: Record<string, number> | undefined;
|
|
63
63
|
refIdToName?: string[] | undefined;
|
package/dist/csi.js
CHANGED
|
@@ -162,7 +162,8 @@ class CSI extends indexFile_1.default {
|
|
|
162
162
|
min = 0;
|
|
163
163
|
}
|
|
164
164
|
const indexData = yield this.parse(opts);
|
|
165
|
-
const ba = indexData
|
|
165
|
+
const ba = indexData.indices[refId];
|
|
166
|
+
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
|
|
166
167
|
if (!ba) {
|
|
167
168
|
return [];
|
|
168
169
|
}
|
|
@@ -174,6 +175,7 @@ class CSI extends indexFile_1.default {
|
|
|
174
175
|
// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
|
|
175
176
|
for (const [start, end] of overlappingBins) {
|
|
176
177
|
for (let bin = start; bin <= end; bin++) {
|
|
178
|
+
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
|
|
177
179
|
if (ba.binIndex[bin]) {
|
|
178
180
|
const binChunks = ba.binIndex[bin];
|
|
179
181
|
for (const c of binChunks) {
|
|
@@ -215,7 +217,7 @@ class CSI extends indexFile_1.default {
|
|
|
215
217
|
parse() {
|
|
216
218
|
return __awaiter(this, arguments, void 0, function* (opts = {}) {
|
|
217
219
|
if (!this.setupP) {
|
|
218
|
-
this.setupP = this._parse(opts).catch(e => {
|
|
220
|
+
this.setupP = this._parse(opts).catch((e) => {
|
|
219
221
|
this.setupP = undefined;
|
|
220
222
|
throw e;
|
|
221
223
|
});
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAC7C,iEAA0D;AAC1D,oDAA2B;AAC3B,iCAMe;AAEf,4DAAmC;AAEnC,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,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,mBAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAC7C,iEAA0D;AAC1D,oDAA2B;AAC3B,iCAMe;AAEf,4DAAmC;AAEnC,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,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,mBAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;IA+MtB,CAAC;IA3MO,SAAS,CAAC,KAAa,EAAE,IAAe;;;YAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,OAAO,CAAA,MAAA,MAAA,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,KAAK,0CAAE,SAAS,KAAI,CAAC,CAAA;QACxD,CAAC;KAAA;IAEK,QAAQ;;YACZ,OAAO,EAAE,CAAA;QACX,CAAC;KAAA;IAED,YAAY,CAAC,KAAa,EAAE,MAAc;QACxC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC7C,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,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,uBACE,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW,IACR,IAAA,qBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB,EACF;IACH,CAAC;IAED,4BAA4B;IACtB,MAAM,CAAC,IAA8B;;YACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;YAEjC,IAAI,UAAU,CAAA;YACd,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC;gBACzC,UAAU,GAAG,CAAC,CAAA;YAChB,CAAC;iBAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC;gBAChD,UAAU,GAAG,CAAC,CAAA;YAChB,CAAC;iBAAM,CAAC;gBACN,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;YACtD,CAAC;YAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACjC,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;YAC3D,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACvC,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;YACtE,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;YAIlD,+CAA+C;YAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;YAC7B,IAAI,aAAwC,CAAA;YAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAGtB,QAAQ,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACxC,IAAI,IAAI,CAAC,CAAA;gBACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;gBAC5C,IAAI,KAAK,CAAA,CAAC,iDAAiD;gBAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;oBAClC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,CAAA;oBACpC,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;wBAC5B,KAAK,GAAG,IAAA,qBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;wBACxC,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;oBACjB,CAAC;yBAAM,CAAC;wBACN,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;wBACpE,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;wBAC1C,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;wBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;4BACvC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;4BAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;wBAClC,CAAC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;oBACxB,CAAC;gBACH,CAAC;gBAED,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;YAClC,CAAC;YAED,uBACE,UAAU;gBACV,aAAa;gBACb,OAAO;gBACP,QAAQ,EACR,GAAG,EAAE,IAAI,EACT,YAAY,EAAE,CAAC,IAAI,EAAE,IAClB,GAAG,EACP;QACH,CAAC;KAAA;IAEK,cAAc;6DAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;YAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,GAAG,GAAG,CAAC,CAAA;YACT,CAAC;YAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACnC,uEAAuE;YACvE,IAAI,CAAC,EAAE,EAAE,CAAC;gBACR,OAAO,EAAE,CAAA;YACX,CAAC;YACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;YAE/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACjC,OAAO,EAAE,CAAA;YACX,CAAC;YAED,MAAM,MAAM,GAAG,EAAE,CAAA;YACjB,sEAAsE;YACtE,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;gBAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;oBACxC,uEAAuE;oBACvE,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;wBACrB,MAAM,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;wBAClC,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;4BAC1B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;wBAChB,CAAC;oBACH,CAAC;gBACH,CAAC;YACH,CAAC;YAED,OAAO,IAAA,qBAAc,EAAC,MAAM,EAAE,IAAI,uBAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QACxD,CAAC;KAAA;IAED;;;OAGG;IACH,QAAQ,CAAC,GAAW,EAAE,GAAW;QAC/B,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;QACvC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QACD,IAAI,GAAG,GAAG,SAAA,CAAC,EAAI,EAAE,CAAA,EAAE,CAAC;YAClB,GAAG,GAAG,SAAA,CAAC,EAAI,EAAE,CAAA,CAAA;QACf,CAAC,CAAC,wCAAwC;QAC1C,GAAG,IAAI,CAAC,CAAA;QACR,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,OAAO,CAAC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9D,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;gBAC5C,MAAM,IAAI,KAAK,CACb,SAAS,GAAG,IAAI,GAAG,mDAAmD,IAAI,CAAC,QAAQ,WAAW,IAAI,CAAC,KAAK,0DAA0D,CACnK,CAAA;YACH,CAAC;YACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAU,CAAC,CAAA;QAC5B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAEK,KAAK;6DAAC,OAAiB,EAAE;YAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;gBACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;oBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;oBACvB,MAAM,CAAC,CAAA;gBACT,CAAC,CAAC,CAAA;YACJ,CAAC;YACD,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;KAAA;IAEK,SAAS;6DAAC,KAAa,EAAE,OAAiB,EAAE;;YAChD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACrC,OAAO,CAAC,CAAC,CAAA,MAAA,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAA,CAAA;QAC1C,CAAC;KAAA;CACF;AAlND,sBAkNC"}
|
package/dist/htsget.js
CHANGED
|
@@ -58,7 +58,7 @@ var __asyncDelegator = (this && this.__asyncDelegator) || function (o) {
|
|
|
58
58
|
var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _arguments, generator) {
|
|
59
59
|
if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
|
|
60
60
|
var g = generator.apply(thisArg, _arguments || []), i, q = [];
|
|
61
|
-
return i =
|
|
61
|
+
return i = Object.create((typeof AsyncIterator === "function" ? AsyncIterator : Object).prototype), verb("next"), verb("throw"), verb("return", awaitReturn), i[Symbol.asyncIterator] = function () { return this; }, i;
|
|
62
62
|
function awaitReturn(f) { return function (v) { return Promise.resolve(v).then(f, reject); }; }
|
|
63
63
|
function verb(n, f) { if (g[n]) { i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; if (f) i[n] = f(i[n]); } }
|
|
64
64
|
function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }
|
package/dist/record.d.ts
CHANGED
|
@@ -1,42 +1,30 @@
|
|
|
1
|
-
|
|
2
|
-
|
|
3
|
-
|
|
1
|
+
import type { Buffer } from 'buffer';
|
|
2
|
+
interface Bytes {
|
|
3
|
+
start: number;
|
|
4
|
+
end: number;
|
|
5
|
+
byteArray: Buffer;
|
|
6
|
+
}
|
|
4
7
|
export default class BamRecord {
|
|
5
|
-
|
|
8
|
+
fileOffset: number;
|
|
6
9
|
private bytes;
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
get(
|
|
15
|
-
end():
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
mq(): number | undefined;
|
|
26
|
-
score(): any;
|
|
27
|
-
qual(): string | undefined;
|
|
28
|
-
qualRaw(): Buffer | undefined;
|
|
29
|
-
strand(): 1 | -1;
|
|
30
|
-
multi_segment_next_segment_strand(): 1 | -1 | undefined;
|
|
31
|
-
name(): any;
|
|
32
|
-
_read_name(): string;
|
|
33
|
-
/**
|
|
34
|
-
* Get the value of a tag, parsing the tags as far as necessary.
|
|
35
|
-
* Only called if we have not already parsed that field.
|
|
36
|
-
*/
|
|
37
|
-
_parseTag(tagName?: string): string | number | undefined;
|
|
38
|
-
_parseAllTags(): void;
|
|
39
|
-
_parseCigar(cigar: string): (string | number)[][];
|
|
10
|
+
constructor(args: {
|
|
11
|
+
bytes: Bytes;
|
|
12
|
+
fileOffset: number;
|
|
13
|
+
});
|
|
14
|
+
get byteArray(): Buffer;
|
|
15
|
+
get flags(): number;
|
|
16
|
+
get ref_id(): number;
|
|
17
|
+
get start(): number;
|
|
18
|
+
get end(): number;
|
|
19
|
+
get id(): number;
|
|
20
|
+
get mq(): number | undefined;
|
|
21
|
+
get score(): number | undefined;
|
|
22
|
+
get qual(): string | undefined;
|
|
23
|
+
get qualRaw(): Buffer | undefined;
|
|
24
|
+
get strand(): 1 | -1;
|
|
25
|
+
get b0(): number;
|
|
26
|
+
get name(): string;
|
|
27
|
+
get tags(): Record<string, unknown>;
|
|
40
28
|
/**
|
|
41
29
|
* @returns {boolean} true if the read is paired, regardless of whether both
|
|
42
30
|
* segments are mapped
|
|
@@ -64,22 +52,23 @@ export default class BamRecord {
|
|
|
64
52
|
isDuplicate(): boolean;
|
|
65
53
|
/** @returns {boolean} true if this is a supplementary alignment */
|
|
66
54
|
isSupplementary(): boolean;
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
|
|
75
|
-
|
|
76
|
-
seq(): string;
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
|
|
80
|
-
seq_length(): number;
|
|
81
|
-
|
|
82
|
-
|
|
83
|
-
template_length(): number;
|
|
55
|
+
get cigarAndLength(): {
|
|
56
|
+
length_on_ref: number;
|
|
57
|
+
CIGAR: string;
|
|
58
|
+
};
|
|
59
|
+
get length_on_ref(): number;
|
|
60
|
+
get CIGAR(): string;
|
|
61
|
+
get num_cigar_ops(): number;
|
|
62
|
+
get read_name_length(): number;
|
|
63
|
+
get num_seq_bytes(): number;
|
|
64
|
+
get seq(): string;
|
|
65
|
+
get pair_orientation(): string;
|
|
66
|
+
get bin_mq_nl(): number;
|
|
67
|
+
get flag_nc(): number;
|
|
68
|
+
get seq_length(): number;
|
|
69
|
+
get next_refid(): number;
|
|
70
|
+
get next_pos(): number;
|
|
71
|
+
get template_length(): number;
|
|
84
72
|
toJSON(): Record<string, any>;
|
|
85
73
|
}
|
|
74
|
+
export {};
|