@gmod/bam 1.1.10 → 1.1.11

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.
Files changed (11) hide show
  1. package/CHANGELOG.md +7 -0
  2. package/dist/bamFile.js.map +1 -1
  3. package/dist/indexFile.d.ts +1 -0
  4. package/dist/indexFile.js +8 -1
  5. package/dist/indexFile.js.map +1 -1
  6. package/esm/bamFile.js +1 -1
  7. package/esm/bamFile.js.map +1 -1
  8. package/esm/indexFile.d.ts +1 -0
  9. package/esm/indexFile.js +7 -1
  10. package/esm/indexFile.js.map +1 -1
  11. package/package.json +1 -1
package/CHANGELOG.md CHANGED
@@ -1,3 +1,10 @@
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+ <a name="1.1.11"></a>
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+ ## [1.1.11](https://github.com/GMOD/bam-js/compare/v1.1.10...v1.1.11) (2022-01-26)
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+
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+ - Cache setup of index file parsing
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+
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  <a name="1.1.10"></a>
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  ## [1.1.10](https://github.com/GMOD/bam-js/compare/v1.1.9...v1.1.10) (2022-01-18)
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package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/indexFile.d.ts CHANGED
@@ -5,6 +5,7 @@ import { BaseOpts } from './util';
5
5
  export default abstract class IndexFile {
6
6
  filehandle: GenericFilehandle;
7
7
  renameRefSeq: (s: string) => string;
8
+ setupP?: Promise<any>;
8
9
  /**
9
10
  * @param {filehandle} filehandle
10
11
  * @param {function} [renameRefSeqs]
package/dist/indexFile.js CHANGED
@@ -59,8 +59,15 @@ var IndexFile = /** @class */ (function () {
59
59
  IndexFile.prototype.parse = function (opts) {
60
60
  if (opts === void 0) { opts = {}; }
61
61
  return __awaiter(this, void 0, void 0, function () {
62
+ var _this = this;
62
63
  return __generator(this, function (_a) {
63
- return [2 /*return*/, this._parse(opts)];
64
+ if (!this.setupP) {
65
+ this.setupP = this._parse(opts).catch(function (e) {
66
+ _this.setupP = undefined;
67
+ throw e;
68
+ });
69
+ }
70
+ return [2 /*return*/, this.setupP];
64
71
  });
65
72
  });
66
73
  };
package/dist/indexFile.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAKA;IAKE;;;OAGG;IACH,mBAAY,EAMX;YALC,UAAU,gBAAA,EACV,oBAA+B,EAA/B,YAAY,mBAAG,UAAC,CAAS,IAAK,OAAA,CAAC,EAAD,CAAC,KAAA;QAK/B,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAgBD,kCAAc,GAAd,UAAe,IAAS,EAAE,aAA4B;QACpD,IAAM,UAAU,GAAG,IAAI,CAAC,aAAa,CAAA;QACrC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,aAAa;gBAChB,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,UAAU,CAAA;SACvE;aAAM;YACL,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;SACnC;IACH,CAAC;IAEK,yBAAK,GAAX,UAAY,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;gBAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;oBAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,UAAA,CAAC;wBACrC,KAAI,CAAC,MAAM,GAAG,SAAS,CAAA;wBACvB,MAAM,CAAC,CAAA;oBACT,CAAC,CAAC,CAAA;iBACH;gBACD,sBAAO,IAAI,CAAC,MAAM,EAAA;;;KACnB;IAEK,6BAAS,GAAf,UAAgB,KAAa,EAAE,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;4BACrC,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;4BAAjC,sBAAO,CAAC,CAAC,CAAC,CAAC,SAAsB,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,EAAA;;;;KAClE;IACH,gBAAC;AAAD,CAAC,AAzDD,IAyDC"}
package/esm/bamFile.js CHANGED
@@ -171,7 +171,7 @@ export default class BamFile {
171
171
  }
172
172
  }
173
173
  const totalSize = chunks
174
- .map((s) => s.fetchedSize())
174
+ .map(s => s.fetchedSize())
175
175
  .reduce((a, b) => a + b, 0);
176
176
  if (totalSize > this.fetchSizeLimit) {
177
177
  throw new Error(`data size of ${totalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
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package/esm/indexFile.d.ts CHANGED
@@ -5,6 +5,7 @@ import { BaseOpts } from './util';
5
5
  export default abstract class IndexFile {
6
6
  filehandle: GenericFilehandle;
7
7
  renameRefSeq: (s: string) => string;
8
+ setupP?: Promise<any>;
8
9
  /**
9
10
  * @param {filehandle} filehandle
10
11
  * @param {function} [renameRefSeqs]
package/esm/indexFile.js CHANGED
@@ -18,7 +18,13 @@ export default class IndexFile {
18
18
  }
19
19
  }
20
20
  async parse(opts = {}) {
21
- return this._parse(opts);
21
+ if (!this.setupP) {
22
+ this.setupP = this._parse(opts).catch(e => {
23
+ this.setupP = undefined;
24
+ throw e;
25
+ });
26
+ }
27
+ return this.setupP;
22
28
  }
23
29
  async hasRefSeq(seqId, opts = {}) {
24
30
  return !!((await this.parse(opts)).indices[seqId] || {}).binIndex;
package/esm/indexFile.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAKA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAIrC;;;OAGG;IACH,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,cAAc,CAAC,IAAS,EAAE,aAA4B;QACpD,MAAM,UAAU,GAAG,IAAI,CAAC,aAAa,CAAA;QACrC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,aAAa;gBAChB,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,UAAU,CAAA;SACvE;aAAM;YACL,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;SACnC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAiB,EAAE;QAC7B,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;QAChD,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAA;IACnE,CAAC;CACF"}
1
+ {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAKA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC;;;OAGG;IACH,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;IAgBD,cAAc,CAAC,IAAS,EAAE,aAA4B;QACpD,MAAM,UAAU,GAAG,IAAI,CAAC,aAAa,CAAA;QACrC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,aAAa;gBAChB,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,UAAU,CAAA;SACvE;aAAM;YACL,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;SACnC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAiB,EAAE;QAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;QAChD,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAA;IACnE,CAAC;CACF"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "1.1.10",
3
+ "version": "1.1.11",
4
4
  "description": "Parser for BAM and BAM index (bai) files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bam-js",