@gmod/bam 7.1.1 → 7.1.3
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 +8 -0
- package/dist/bai.js +10 -14
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +5 -0
- package/dist/bamFile.js +17 -0
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.js +5 -4
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +6 -0
- package/dist/indexFile.js +11 -0
- package/dist/indexFile.js.map +1 -1
- package/dist/record.d.ts +1 -0
- package/dist/record.js +59 -0
- package/dist/record.js.map +1 -1
- package/dist/util.js +50 -21
- package/dist/util.js.map +1 -1
- package/esm/bai.js +10 -14
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +5 -0
- package/esm/bamFile.js +17 -0
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.js +5 -4
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +6 -0
- package/esm/indexFile.js +11 -0
- package/esm/indexFile.js.map +1 -1
- package/esm/record.d.ts +1 -0
- package/esm/record.js +59 -0
- package/esm/record.js.map +1 -1
- package/esm/util.js +50 -21
- package/esm/util.js.map +1 -1
- package/package.json +2 -2
- package/src/bai.ts +10 -15
- package/src/bamFile.ts +21 -0
- package/src/csi.ts +5 -4
- package/src/indexFile.ts +22 -1
- package/src/record.ts +62 -0
- package/src/util.ts +55 -20
package/esm/bai.js.map
CHANGED
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+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,WAAW,CAAA;AAEhC,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EAEL,aAAa,EACb,cAAc,EACd,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAiB,SAAS,EAAE,MAAM,oBAAoB,CAAA;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,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;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,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IAAI,CAAC,CAAA;gBACT,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,MAAM,CAAC,CAAA;gBACpD,WAAW,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;YACzB,CAAC;QACH,CAAC;QACD,MAAM,YAAY,GAAG,IAAI,QAAQ,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,cAAc,CAAC,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,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,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,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IAAI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|
package/esm/bamFile.d.ts
CHANGED
|
@@ -86,4 +86,9 @@ export default class BamFile {
|
|
|
86
86
|
indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai.ts").IndexCovEntry[]>;
|
|
87
87
|
blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
|
|
88
88
|
clearFeatureCache(): void;
|
|
89
|
+
estimatedBytesForRegions(regions: {
|
|
90
|
+
refName: string;
|
|
91
|
+
start: number;
|
|
92
|
+
end: number;
|
|
93
|
+
}[], opts?: BaseOpts): Promise<number>;
|
|
89
94
|
}
|
package/esm/bamFile.js
CHANGED
|
@@ -351,5 +351,22 @@ export default class BamFile {
|
|
|
351
351
|
clearFeatureCache() {
|
|
352
352
|
this.chunkFeatureCache.clear();
|
|
353
353
|
}
|
|
354
|
+
async estimatedBytesForRegions(regions, opts) {
|
|
355
|
+
if (!this.index) {
|
|
356
|
+
return 0;
|
|
357
|
+
}
|
|
358
|
+
await this.getHeader(opts);
|
|
359
|
+
if (!this.chrToIndex) {
|
|
360
|
+
throw new Error('Header not yet parsed');
|
|
361
|
+
}
|
|
362
|
+
const regionsWithIds = regions.map(r => {
|
|
363
|
+
const refId = this.chrToIndex[r.refName];
|
|
364
|
+
if (refId === undefined) {
|
|
365
|
+
throw new Error(`Unknown reference name: ${r.refName}`);
|
|
366
|
+
}
|
|
367
|
+
return { refId, start: r.start, end: r.end };
|
|
368
|
+
});
|
|
369
|
+
return this.index.estimatedBytesForRegions(regionsWithIds, opts);
|
|
370
|
+
}
|
|
354
371
|
}
|
|
355
372
|
//# sourceMappingURL=bamFile.js.map
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/esm/csi.js
CHANGED
|
@@ -180,12 +180,13 @@ export default class CSI extends IndexFile {
|
|
|
180
180
|
}
|
|
181
181
|
const chunks = [];
|
|
182
182
|
// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
|
|
183
|
+
const { binIndex } = ba;
|
|
183
184
|
for (const [start, end] of overlappingBins) {
|
|
184
185
|
for (let bin = start; bin <= end; bin++) {
|
|
185
|
-
|
|
186
|
-
|
|
187
|
-
for (
|
|
188
|
-
chunks.push(
|
|
186
|
+
const binChunks = binIndex[bin];
|
|
187
|
+
if (binChunks) {
|
|
188
|
+
for (let i = 0, l = binChunks.length; i < l; i++) {
|
|
189
|
+
chunks.push(binChunks[i]);
|
|
189
190
|
}
|
|
190
191
|
}
|
|
191
192
|
}
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,QAAQ,MAAM,WAAW,CAAA;AAEhC,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,aAAa,EACb,cAAc,EACd,cAAc,EACd,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;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,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;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,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,QAAQ,MAAM,WAAW,CAAA;AAEhC,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,aAAa,EACb,cAAc,EACd,cAAc,EACd,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;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,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;IAwPtB,CAAC;IApPC,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,cAAc,CACf,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,KAAK,CAAC,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,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;oBACjD,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,YAAY,GAAG,IAAI,QAAQ,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,cAAc,CAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACjD,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACpE,IAAI,IAAI,CAAC,CAAA;oBACT,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,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,OAAO;gBACL,QAAQ;gBACR,KAAK,EAAE,cAAc;aACtB,CAAA;QACH,CAAC;QAED,OAAO;YACL,UAAU;YACV,aAAa;YACb,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;YACR,GAAG,EAAE,IAAI;YACT,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,GAAG,GAAG;SACP,CAAA;IACH,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,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAEnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAE/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,MAAM,GAAG,EAAE,CAAA;QACjB,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,OAAO,cAAc,CAAC,MAAM,EAAE,IAAI,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACxD,CAAC;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,CAAC,IAAI,EAAE,EAAE,CAAC;YAClB,GAAG,GAAG,CAAC,IAAI,EAAE,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;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"}
|
package/esm/indexFile.d.ts
CHANGED
|
@@ -1,6 +1,11 @@
|
|
|
1
1
|
import Chunk from './chunk.ts';
|
|
2
2
|
import { BaseOpts } from './util.ts';
|
|
3
3
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
4
|
+
export interface Region {
|
|
5
|
+
refId: number;
|
|
6
|
+
start: number;
|
|
7
|
+
end: number;
|
|
8
|
+
}
|
|
4
9
|
export default abstract class IndexFile {
|
|
5
10
|
filehandle: GenericFilehandle;
|
|
6
11
|
renameRefSeq: (s: string) => string;
|
|
@@ -15,4 +20,5 @@ export default abstract class IndexFile {
|
|
|
15
20
|
score: number;
|
|
16
21
|
}[]>;
|
|
17
22
|
abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
|
|
23
|
+
estimatedBytesForRegions(regions: Region[], opts?: BaseOpts): Promise<number>;
|
|
18
24
|
}
|
package/esm/indexFile.js
CHANGED
|
@@ -1,7 +1,18 @@
|
|
|
1
|
+
import { optimizeChunks } from "./util.js";
|
|
1
2
|
export default class IndexFile {
|
|
2
3
|
constructor({ filehandle, renameRefSeq = (n) => n, }) {
|
|
3
4
|
this.filehandle = filehandle;
|
|
4
5
|
this.renameRefSeq = renameRefSeq;
|
|
5
6
|
}
|
|
7
|
+
async estimatedBytesForRegions(regions, opts) {
|
|
8
|
+
const blockResults = await Promise.all(regions.map(r => this.blocksForRange(r.refId, r.start, r.end, opts)));
|
|
9
|
+
// Deduplicate and merge overlapping blocks across all regions
|
|
10
|
+
const mergedBlocks = optimizeChunks(blockResults.flat());
|
|
11
|
+
let total = 0;
|
|
12
|
+
for (const block of mergedBlocks) {
|
|
13
|
+
total += block.fetchedSize();
|
|
14
|
+
}
|
|
15
|
+
return total;
|
|
16
|
+
}
|
|
6
17
|
}
|
|
7
18
|
//# sourceMappingURL=indexFile.js.map
|
package/esm/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":"AACA,OAAO,EAAY,cAAc,EAAE,MAAM,WAAW,CAAA;AAUpD,MAAM,CAAC,OAAO,OAAgB,SAAS;IAIrC,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,cAAc,CAAC,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"}
|
package/esm/record.d.ts
CHANGED
|
@@ -23,6 +23,7 @@ export default class BamRecord {
|
|
|
23
23
|
get strand(): 1 | -1;
|
|
24
24
|
get b0(): number;
|
|
25
25
|
get name(): string;
|
|
26
|
+
get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
|
|
26
27
|
get tags(): Record<string, unknown>;
|
|
27
28
|
/**
|
|
28
29
|
* @returns {boolean} true if the read is paired, regardless of whether both
|
package/esm/record.js
CHANGED
|
@@ -66,6 +66,65 @@ export default class BamRecord {
|
|
|
66
66
|
}
|
|
67
67
|
return str;
|
|
68
68
|
}
|
|
69
|
+
get NUMERIC_MD() {
|
|
70
|
+
let p = this.b0 +
|
|
71
|
+
this.read_name_length +
|
|
72
|
+
this.num_cigar_bytes +
|
|
73
|
+
this.num_seq_bytes +
|
|
74
|
+
this.seq_length;
|
|
75
|
+
const blockEnd = this.bytes.end;
|
|
76
|
+
while (p < blockEnd) {
|
|
77
|
+
const tag = String.fromCharCode(this.byteArray[p]) +
|
|
78
|
+
String.fromCharCode(this.byteArray[p + 1]);
|
|
79
|
+
const type = String.fromCharCode(this.byteArray[p + 2]);
|
|
80
|
+
p += 3;
|
|
81
|
+
if (tag === 'MD' && type === 'Z') {
|
|
82
|
+
const start = p;
|
|
83
|
+
while (p < blockEnd && this.byteArray[p] !== 0) {
|
|
84
|
+
p++;
|
|
85
|
+
}
|
|
86
|
+
return this.byteArray.subarray(start, p);
|
|
87
|
+
}
|
|
88
|
+
switch (type) {
|
|
89
|
+
case 'A':
|
|
90
|
+
p += 1;
|
|
91
|
+
break;
|
|
92
|
+
case 'i':
|
|
93
|
+
case 'I':
|
|
94
|
+
case 'f':
|
|
95
|
+
p += 4;
|
|
96
|
+
break;
|
|
97
|
+
case 'c':
|
|
98
|
+
case 'C':
|
|
99
|
+
p += 1;
|
|
100
|
+
break;
|
|
101
|
+
case 's':
|
|
102
|
+
case 'S':
|
|
103
|
+
p += 2;
|
|
104
|
+
break;
|
|
105
|
+
case 'Z':
|
|
106
|
+
case 'H':
|
|
107
|
+
while (p <= blockEnd && this.byteArray[p++] !== 0) { }
|
|
108
|
+
break;
|
|
109
|
+
case 'B': {
|
|
110
|
+
const Btype = String.fromCharCode(this.byteArray[p++]);
|
|
111
|
+
const limit = this._dataView.getInt32(p, true);
|
|
112
|
+
p += 4;
|
|
113
|
+
if (Btype === 'i' || Btype === 'I' || Btype === 'f') {
|
|
114
|
+
p += limit << 2;
|
|
115
|
+
}
|
|
116
|
+
else if (Btype === 's' || Btype === 'S') {
|
|
117
|
+
p += limit << 1;
|
|
118
|
+
}
|
|
119
|
+
else if (Btype === 'c' || Btype === 'C') {
|
|
120
|
+
p += limit;
|
|
121
|
+
}
|
|
122
|
+
break;
|
|
123
|
+
}
|
|
124
|
+
}
|
|
125
|
+
}
|
|
126
|
+
return undefined;
|
|
127
|
+
}
|
|
69
128
|
get tags() {
|
|
70
129
|
let p = this.b0 +
|
|
71
130
|
this.read_name_length +
|
package/esm/record.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/esm/util.js
CHANGED
|
@@ -7,33 +7,62 @@ export function makeOpts(obj = {}) {
|
|
|
7
7
|
return 'aborted' in obj ? { signal: obj } : obj;
|
|
8
8
|
}
|
|
9
9
|
export function optimizeChunks(chunks, lowest) {
|
|
10
|
-
const
|
|
11
|
-
|
|
12
|
-
if (chunks.length === 0) {
|
|
10
|
+
const n = chunks.length;
|
|
11
|
+
if (n === 0) {
|
|
13
12
|
return chunks;
|
|
14
13
|
}
|
|
15
|
-
chunks
|
|
14
|
+
// Pre-filter chunks below lowest threshold before sorting
|
|
15
|
+
let filtered;
|
|
16
|
+
if (lowest) {
|
|
17
|
+
const lowestBlock = lowest.blockPosition;
|
|
18
|
+
const lowestData = lowest.dataPosition;
|
|
19
|
+
filtered = [];
|
|
20
|
+
for (let i = 0; i < n; i++) {
|
|
21
|
+
const chunk = chunks[i];
|
|
22
|
+
const maxv = chunk.maxv;
|
|
23
|
+
const cmp = maxv.blockPosition - lowestBlock || maxv.dataPosition - lowestData;
|
|
24
|
+
if (cmp > 0) {
|
|
25
|
+
filtered.push(chunk);
|
|
26
|
+
}
|
|
27
|
+
}
|
|
28
|
+
if (filtered.length === 0) {
|
|
29
|
+
return filtered;
|
|
30
|
+
}
|
|
31
|
+
}
|
|
32
|
+
else {
|
|
33
|
+
filtered = chunks;
|
|
34
|
+
}
|
|
35
|
+
filtered.sort((c0, c1) => {
|
|
16
36
|
const dif = c0.minv.blockPosition - c1.minv.blockPosition;
|
|
17
|
-
return dif
|
|
37
|
+
return dif !== 0 ? dif : c0.minv.dataPosition - c1.minv.dataPosition;
|
|
18
38
|
});
|
|
19
|
-
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
39
|
+
const mergedChunks = [];
|
|
40
|
+
let lastChunk = filtered[0];
|
|
41
|
+
mergedChunks.push(lastChunk);
|
|
42
|
+
let lastMinBlock = lastChunk.minv.blockPosition;
|
|
43
|
+
let lastMaxBlock = lastChunk.maxv.blockPosition;
|
|
44
|
+
for (let i = 1; i < filtered.length; i++) {
|
|
45
|
+
const chunk = filtered[i];
|
|
46
|
+
const chunkMinBlock = chunk.minv.blockPosition;
|
|
47
|
+
const chunkMaxBlock = chunk.maxv.blockPosition;
|
|
48
|
+
// Inlined canMergeBlocks: check if chunks are close enough to merge
|
|
49
|
+
if (chunkMinBlock - lastMaxBlock < 65000 &&
|
|
50
|
+
chunkMaxBlock - lastMinBlock < 5000000) {
|
|
51
|
+
const chunkMaxv = chunk.maxv;
|
|
52
|
+
const lastMaxv = lastChunk.maxv;
|
|
53
|
+
const cmp = chunkMaxBlock - lastMaxBlock ||
|
|
54
|
+
chunkMaxv.dataPosition - lastMaxv.dataPosition;
|
|
55
|
+
if (cmp > 0) {
|
|
56
|
+
lastChunk.maxv = chunkMaxv;
|
|
57
|
+
lastMaxBlock = chunkMaxBlock;
|
|
35
58
|
}
|
|
36
59
|
}
|
|
60
|
+
else {
|
|
61
|
+
mergedChunks.push(chunk);
|
|
62
|
+
lastChunk = chunk;
|
|
63
|
+
lastMinBlock = chunkMinBlock;
|
|
64
|
+
lastMaxBlock = chunkMaxBlock;
|
|
65
|
+
}
|
|
37
66
|
}
|
|
38
67
|
return mergedChunks;
|
|
39
68
|
}
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AAGnD,MAAM,UAAU,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AAaD,MAAM,UAAU,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAC,GAAG,CAAA;AAC/D,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,MAAe,EAAE,MAAe;IAC7D,MAAM,YAAY,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AAGnD,MAAM,UAAU,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AAaD,MAAM,UAAU,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAC,GAAG,CAAA;AAC/D,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,MAAe,EAAE,MAAe;IAC7D,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAA;IACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO,MAAM,CAAA;IACf,CAAC;IAED,0DAA0D;IAC1D,IAAI,QAAiB,CAAA;IACrB,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,WAAW,GAAG,MAAM,CAAC,aAAa,CAAA;QACxC,MAAM,UAAU,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,QAAQ,GAAG,EAAE,CAAA;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;YACxB,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;YACvB,MAAM,GAAG,GACP,IAAI,CAAC,aAAa,GAAG,WAAW,IAAI,IAAI,CAAC,YAAY,GAAG,UAAU,CAAA;YACpE,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACtB,CAAC;QACH,CAAC;QACD,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,OAAO,QAAQ,CAAA;QACjB,CAAC;IACH,CAAC;SAAM,CAAC;QACN,QAAQ,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,QAAQ,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACvB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAAS,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;IAC5B,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;IAE5B,IAAI,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,aAAa,CAAA;IAC/C,IAAI,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,aAAa,CAAA;IAE/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,oEAAoE;QACpE,IACE,aAAa,GAAG,YAAY,GAAG,KAAK;YACpC,aAAa,GAAG,YAAY,GAAG,OAAO,EACtC,CAAC;YACD,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAA;YAC5B,MAAM,QAAQ,GAAG,SAAS,CAAC,IAAI,CAAA;YAC/B,MAAM,GAAG,GACP,aAAa,GAAG,YAAY;gBAC5B,SAAS,CAAC,YAAY,GAAG,QAAQ,CAAC,YAAY,CAAA;YAChD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,SAAS,CAAC,IAAI,GAAG,SAAS,CAAA;gBAC1B,YAAY,GAAG,aAAa,CAAA;YAC9B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACxB,SAAS,GAAG,KAAK,CAAA;YACjB,YAAY,GAAG,aAAa,CAAA;YAC5B,YAAY,GAAG,aAAa,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO;QACL,SAAS,EAAE,uBAAuB,CAAC,KAAK,EAAE,MAAM,CAAC;KAClD,CAAA;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,aAAwC,EACxC,aAA4B;IAE5B,OAAO,aAAa;QAClB,CAAC,CAAC,aAAa,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;YAC1C,CAAC,CAAC,aAAa;YACf,CAAC,CAAC,aAAa;QACjB,CAAC,CAAC,aAAa,CAAA;AACnB,CAAC;AAED,MAAM,UAAU,cAAc,CAC5B,UAAsB,EACtB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,MAAM,WAAW,GAA2B,EAAE,CAAA;IAC9C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,KAAK,IAAI,CAAC,GAAG,aAAa,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;oBACvC,OAAO,IAAI,MAAM,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC,CAAE,CAAC,CAAA;gBAChD,CAAC;gBACD,OAAO,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;gBAC/B,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;gBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;YAClC,CAAC;YACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;YACrB,SAAS,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAkB;IACjD,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,IAAI,KAAK,CAAC,MAAM,CAAA;IAC7B,CAAC;IACD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;IAC/C,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC9B,MAAM,IAAI,KAAK,CAAC,MAAM,CAAA;IACxB,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAI,GAAuB;IACxD,MAAM,GAAG,GAAQ,EAAE,CAAA;IACnB,IAAI,KAAK,EAAE,MAAM,CAAC,IAAI,GAAG,EAAE,CAAC;QAC1B,KAAK,MAAM,IAAI,IAAI,CAAC,EAAE,CAAC;YACrB,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/bam",
|
|
3
|
-
"version": "7.1.
|
|
3
|
+
"version": "7.1.3",
|
|
4
4
|
"description": "Parser for BAM and BAM index (bai) files",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/bam-js",
|
|
@@ -50,7 +50,7 @@
|
|
|
50
50
|
"genomics"
|
|
51
51
|
],
|
|
52
52
|
"dependencies": {
|
|
53
|
-
"@gmod/bgzf-filehandle": "^6.0.
|
|
53
|
+
"@gmod/bgzf-filehandle": "^6.0.6",
|
|
54
54
|
"crc": "^4.3.2",
|
|
55
55
|
"generic-filehandle2": "^2.0.16",
|
|
56
56
|
"quick-lru": "^4.0.0"
|
package/src/bai.ts
CHANGED
|
@@ -246,30 +246,25 @@ export default class BAI extends IndexFile {
|
|
|
246
246
|
const chunks: Chunk[] = []
|
|
247
247
|
|
|
248
248
|
// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
|
|
249
|
+
const { binIndex } = ba
|
|
249
250
|
for (const [start, end] of overlappingBins) {
|
|
250
251
|
for (let bin = start; bin <= end; bin++) {
|
|
251
|
-
|
|
252
|
-
|
|
253
|
-
for (
|
|
254
|
-
chunks.push(
|
|
252
|
+
const binChunks = binIndex[bin]
|
|
253
|
+
if (binChunks) {
|
|
254
|
+
for (let i = 0, l = binChunks.length; i < l; i++) {
|
|
255
|
+
chunks.push(binChunks[i]!)
|
|
255
256
|
}
|
|
256
257
|
}
|
|
257
258
|
}
|
|
258
259
|
}
|
|
259
260
|
|
|
260
261
|
// Use the linear index to find minimum file position of chunks that could
|
|
261
|
-
// contain alignments in the region
|
|
262
|
-
|
|
263
|
-
|
|
262
|
+
// contain alignments in the region. Linear index entries are monotonically
|
|
263
|
+
// non-decreasing, so the first entry at minLin is the minimum.
|
|
264
|
+
const { linearIndex } = ba
|
|
265
|
+
const nintv = linearIndex.length
|
|
264
266
|
const minLin = Math.min(min >> 14, nintv - 1)
|
|
265
|
-
const
|
|
266
|
-
for (let i = minLin; i <= maxLin; ++i) {
|
|
267
|
-
const vp = ba.linearIndex[i]
|
|
268
|
-
|
|
269
|
-
if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
|
|
270
|
-
lowest = vp
|
|
271
|
-
}
|
|
272
|
-
}
|
|
267
|
+
const lowest = linearIndex[minLin]
|
|
273
268
|
|
|
274
269
|
return optimizeChunks(chunks, lowest)
|
|
275
270
|
}
|
package/src/bamFile.ts
CHANGED
|
@@ -503,4 +503,25 @@ export default class BamFile {
|
|
|
503
503
|
clearFeatureCache() {
|
|
504
504
|
this.chunkFeatureCache.clear()
|
|
505
505
|
}
|
|
506
|
+
|
|
507
|
+
async estimatedBytesForRegions(
|
|
508
|
+
regions: { refName: string; start: number; end: number }[],
|
|
509
|
+
opts?: BaseOpts,
|
|
510
|
+
) {
|
|
511
|
+
if (!this.index) {
|
|
512
|
+
return 0
|
|
513
|
+
}
|
|
514
|
+
await this.getHeader(opts)
|
|
515
|
+
if (!this.chrToIndex) {
|
|
516
|
+
throw new Error('Header not yet parsed')
|
|
517
|
+
}
|
|
518
|
+
const regionsWithIds = regions.map(r => {
|
|
519
|
+
const refId = this.chrToIndex![r.refName]
|
|
520
|
+
if (refId === undefined) {
|
|
521
|
+
throw new Error(`Unknown reference name: ${r.refName}`)
|
|
522
|
+
}
|
|
523
|
+
return { refId, start: r.start, end: r.end }
|
|
524
|
+
})
|
|
525
|
+
return this.index.estimatedBytesForRegions(regionsWithIds, opts)
|
|
526
|
+
}
|
|
506
527
|
}
|