@gmod/bbi 1.0.34 → 1.0.35

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 (48) hide show
  1. package/CHANGELOG.md +8 -8
  2. package/dist/bbi.js +2 -1
  3. package/dist/bbi.js.map +1 -0
  4. package/dist/bigbed.js +1 -0
  5. package/dist/bigbed.js.map +1 -0
  6. package/dist/bigwig.js +1 -0
  7. package/dist/bigwig.js.map +1 -0
  8. package/dist/blockView.js +1 -0
  9. package/dist/blockView.js.map +1 -0
  10. package/dist/index.js +1 -0
  11. package/dist/index.js.map +1 -0
  12. package/dist/range.js +2 -0
  13. package/dist/range.js.map +1 -0
  14. package/dist/unzip-pako.js +1 -0
  15. package/dist/unzip-pako.js.map +1 -0
  16. package/dist/unzip.js +1 -0
  17. package/dist/unzip.js.map +1 -0
  18. package/dist/util.js +1 -0
  19. package/dist/util.js.map +1 -0
  20. package/esm/bbi.js +23 -29
  21. package/esm/bbi.js.map +1 -0
  22. package/esm/bigbed.js +22 -29
  23. package/esm/bigbed.js.map +1 -0
  24. package/esm/bigwig.js +5 -8
  25. package/esm/bigwig.js.map +1 -0
  26. package/esm/blockView.js +32 -38
  27. package/esm/blockView.js.map +1 -0
  28. package/esm/index.js +3 -7
  29. package/esm/index.js.map +1 -0
  30. package/esm/range.js +3 -4
  31. package/esm/range.js.map +1 -0
  32. package/esm/unzip-pako.js +4 -7
  33. package/esm/unzip-pako.js.map +1 -0
  34. package/esm/unzip.js +3 -5
  35. package/esm/unzip.js.map +1 -0
  36. package/esm/util.js +5 -11
  37. package/esm/util.js.map +1 -0
  38. package/package.json +5 -4
  39. package/src/bbi.ts +380 -0
  40. package/src/bigbed.ts +239 -0
  41. package/src/bigwig.ts +46 -0
  42. package/src/blockView.ts +462 -0
  43. package/src/declare.d.ts +4 -0
  44. package/src/index.ts +3 -0
  45. package/src/range.ts +142 -0
  46. package/src/unzip-pako.ts +5 -0
  47. package/src/unzip.ts +2 -0
  48. package/src/util.ts +74 -0
package/CHANGELOG.md CHANGED
@@ -1,26 +1,26 @@
1
- ## [1.0.34](https://github.com/GMOD/bbi-js/compare/v1.0.33...v1.0.34) (2022-03-11)
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+ ## [1.0.35](https://github.com/GMOD/bbi-js/compare/v1.0.34...v1.0.35) (2022-04-22)
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- ### Reverts
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- * Revert "Use subarray instead of slice since slice is deprecated under node xref 'https://nodejs.org/api/buffer.html#bufslicestart-end'" ([44116cc](https://github.com/GMOD/bbi-js/commit/44116cce54601727d37f1c449bfcc60c1b4e602d))
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+ - Produce actual ESM module for the "module" field in package.json, was commonJS
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+ - Add sourceMap:true to tsconfig
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+ ## [1.0.34](https://github.com/GMOD/bbi-js/compare/v1.0.33...v1.0.34) (2022-03-11)
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+
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+ ### Reverts
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+ - Revert "Use subarray instead of slice since slice is deprecated under node xref 'https://nodejs.org/api/buffer.html#bufslicestart-end'" ([44116cc](https://github.com/GMOD/bbi-js/commit/44116cce54601727d37f1c449bfcc60c1b4e602d))
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- - Back to slice instead of subarray, as subarray returned a UInt8Array instead
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+ * Back to slice instead of subarray, as subarray returned a UInt8Array instead
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  of a true Buffer
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  ## [1.0.33](https://github.com/GMOD/bbi-js/compare/v1.0.32...v1.0.33) (2022-02-25)
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  - Use subarray instead of slice since slice is deprecated under node xref
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  'https://nodejs.org/api/buffer.html#bufslicestart-end'"
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  ## [1.0.32](https://github.com/GMOD/bbi-js/compare/v1.0.31...v1.0.32) (2022-02-16)
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-
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  - Use pako to decode on command line instead of using zlib to avoid need to
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  manually polyfill zlib
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package/dist/bbi.js CHANGED
@@ -123,8 +123,8 @@ var BBI = /** @class */ (function () {
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  * @param renameRefSeqs - an optional method to rename the internal reference sequences using a mapping function
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  */
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  function BBI(options) {
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- var _this = this;
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  if (options === void 0) { options = {}; }
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+ var _this = this;
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  this.headerCache = new abortable_promise_cache_1.default({
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  cache: new quick_lru_1.default({ maxSize: 1 }),
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  fill: function (params, signal) { return __awaiter(_this, void 0, void 0, function () {
@@ -389,3 +389,4 @@ var BBI = /** @class */ (function () {
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  return BBI;
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  }());
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  exports.BBI = BBI;
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+ //# sourceMappingURL=bbi.js.map
package/dist/bbi.js.map ADDED
@@ -0,0 +1 @@
1
+ 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package/dist/bigbed.js CHANGED
@@ -311,3 +311,4 @@ var BigBed = /** @class */ (function (_super) {
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  }(bbi_1.BBI));
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  exports.BigBed = BigBed;
314
+ //# sourceMappingURL=bigbed.js.map
package/dist/bigbed.js.map ADDED
@@ -0,0 +1 @@
1
+ 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package/dist/bigwig.js CHANGED
@@ -98,3 +98,4 @@ var BigWig = /** @class */ (function (_super) {
98
98
  return BigWig;
99
99
  }(bbi_1.BBI));
100
100
  exports.BigWig = BigWig;
101
+ //# sourceMappingURL=bigwig.js.map
package/dist/bigwig.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,yCAAuC;AACvC,6BAA2C;AAE3C;IAA4B,0BAAG;IAA/B;;IA0CA,CAAC;IAzCC;;;;;;;OAOG;IACa,wBAAO,GAAvB,UACE,KAAa,EACb,IAAoB;;;;;4BAGlB,qBAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAA;;wBADtB,KACJ,SAA0B,EADpB,UAAU,gBAAA,EAAE,UAAU,gBAAA,EAAE,QAAQ,cAAA,EAAE,WAAW,iBAAA,EAAE,iBAAiB,uBAAA;wBAElE,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;wBACxB,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;wBAChC,IAAI,CAAC,QAAQ,EAAE;4BACb,4EAA4E;4BAC5E,QAAQ,IAAI,CAAC,CAAA;yBACd;wBAED,KAAS,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;4BAC/B,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;4BACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE;gCACvC,WAAW,GACf,CAAC,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC;oCACvB,CAAC,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,GAAG,EAAE,CAAC,WAAW;oCAC/C,CAAC,CAAC,QAAQ,GAAG,CAAC,GAAG,EAAE,CAAC,WAAW,CAAA;gCACnC,sBAAO,IAAI,qBAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,EAAA;6BACF;yBACF;wBACD,sBAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,EAAA;;;;KAClC;IACH,aAAC;AAAD,CAAC,AA1CD,CAA4B,SAAG,GA0C9B;AA1CY,wBAAM"}
package/dist/blockView.js CHANGED
@@ -423,3 +423,4 @@ var BlockView = /** @class */ (function () {
423
423
  return BlockView;
424
424
  }());
425
425
  exports.BlockView = BlockView;
426
+ //# sourceMappingURL=blockView.js.map
package/dist/blockView.js.map ADDED
@@ -0,0 +1 @@
1
+ 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package/dist/index.js CHANGED
@@ -5,3 +5,4 @@ var bigwig_1 = require("./bigwig");
5
5
  Object.defineProperty(exports, "BigWig", { enumerable: true, get: function () { return bigwig_1.BigWig; } });
6
6
  var bigbed_1 = require("./bigbed");
7
7
  Object.defineProperty(exports, "BigBed", { enumerable: true, get: function () { return bigbed_1.BigBed; } });
8
+ //# sourceMappingURL=index.js.map
package/dist/index.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,mCAAiC;AAAxB,gGAAA,MAAM,OAAA;AACf,mCAAiC;AAAxB,gGAAA,MAAM,OAAA"}
package/dist/range.js CHANGED
@@ -106,6 +106,7 @@ var Range = /** @class */ (function () {
106
106
  var b = tmpb;
107
107
  if (arguments.length < 2) {
108
108
  b = a;
109
+ // eslint-disable-next-line @typescript-eslint/no-this-alias
109
110
  a = this;
110
111
  }
111
112
  if (a.min() < b.min()) {
@@ -125,3 +126,4 @@ var Range = /** @class */ (function () {
125
126
  return Range;
126
127
  }());
127
128
  exports.default = Range;
129
+ //# sourceMappingURL=range.js.map
package/dist/range.js.map ADDED
@@ -0,0 +1 @@
1
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package/dist/unzip-pako.js CHANGED
@@ -6,3 +6,4 @@ function unzip(input) {
6
6
  return Buffer.from((0, pako_1.inflate)(input));
7
7
  }
8
8
  exports.unzip = unzip;
9
+ //# sourceMappingURL=unzip-pako.js.map
package/dist/unzip-pako.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;;AAAA,6BAA8B;AAE9B,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,MAAM,CAAC,IAAI,CAAC,IAAA,cAAO,EAAC,KAAK,CAAC,CAAC,CAAA;AACpC,CAAC;AAFD,sBAEC"}
package/dist/unzip.js CHANGED
@@ -3,3 +3,4 @@ Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.unzip = void 0;
4
4
  var zlib_1 = require("zlib");
5
5
  Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.inflateSync; } });
6
+ //# sourceMappingURL=unzip.js.map
package/dist/unzip.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,6BAAkC;AACV,sFADf,kBAAW,OACS"}
package/dist/util.js CHANGED
@@ -135,3 +135,4 @@ function abortBreakPoint(signal) {
135
135
  });
136
136
  }
137
137
  exports.abortBreakPoint = abortBreakPoint;
138
+ //# sourceMappingURL=util.js.map
package/dist/util.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,sDAAsD;AACtD;IAAgC,8BAAK;IAGnC,oBAAmB,OAAe;QAAlC,YACE,kBAAM,OAAO,CAAC,SAEf;QADC,KAAI,CAAC,IAAI,GAAG,aAAa,CAAA;;IAC3B,CAAC;IACH,iBAAC;AAAD,CAAC,AAPD,CAAgC,KAAK,GAOpC;AAPY,gCAAU;AAQvB,iCAAiC;AACjC,gDAAgD;AAChD,SAAgB,WAAW,CAAC,MAAa;IACvC,MAAM,CAAC,IAAI,CAAC,UAAC,EAAE,EAAE,EAAE,IAAK,OAAA,CAAC,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,EAAjC,CAAiC,CAAC,CAAA;IAE1D,IAAM,WAAW,GAAG,EAAE,CAAA;IACtB,IAAI,SAAS,CAAA;IACb,IAAI,YAAY,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QACzC,IAAI,SAAS,IAAI,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,YAAY,IAAI,IAAI,EAAE;YACxD,SAAS,CAAC,MAAM,IAAI,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,YAAY,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;YACtE,SAAS,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;SACjC;aAAM;YACL,WAAW,CAAC,IAAI,CACd,CAAC,SAAS,GAAG;gBACX,MAAM,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;gBACnB,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM;gBACxB,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM;aACzB,CAAC,CACH,CAAA;SACF;QACD,YAAY,GAAG,SAAS,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;KACnD;IAED,OAAO,WAAW,CAAA;AACpB,CAAC;AAvBD,kCAuBC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE;QACX,OAAM;KACP;IAED,IAAI,MAAM,CAAC,OAAO,EAAE;QAClB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE;YACvC,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;SAChD;aAAM;YACL,IAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;SACR;KACF;AACH,CAAC;AAfD,4CAeC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;;;wBACxD,qBAAM,OAAO,CAAC,OAAO,EAAE,EAAA;;oBAAvB,SAAuB,CAAA;oBACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;;;;;CACzB;AAHD,0CAGC"}
package/esm/bbi.js CHANGED
@@ -1,16 +1,10 @@
1
- "use strict";
2
- var __importDefault = (this && this.__importDefault) || function (mod) {
3
- return (mod && mod.__esModule) ? mod : { "default": mod };
4
- };
5
- Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.BBI = void 0;
7
- const binary_parser_1 = require("@gmod/binary-parser");
8
- const generic_filehandle_1 = require("generic-filehandle");
9
- const rxjs_1 = require("rxjs");
10
- const operators_1 = require("rxjs/operators");
11
- const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
12
- const quick_lru_1 = __importDefault(require("quick-lru"));
13
- const blockView_1 = require("./blockView");
1
+ import { Parser } from '@gmod/binary-parser';
2
+ import { LocalFile, RemoteFile } from 'generic-filehandle';
3
+ import { Observable } from 'rxjs';
4
+ import { reduce } from 'rxjs/operators';
5
+ import AbortablePromiseCache from 'abortable-promise-cache';
6
+ import QuickLRU from 'quick-lru';
7
+ import { BlockView } from './blockView';
14
8
  const BIG_WIG_MAGIC = -2003829722;
15
9
  const BIG_BED_MAGIC = -2021002517;
16
10
  /* get the compiled parsers for different sections of the bigwig file
@@ -20,7 +14,7 @@ const BIG_BED_MAGIC = -2021002517;
20
14
  */
21
15
  function getParsers(isBE) {
22
16
  const le = isBE ? 'big' : 'little';
23
- const headerParser = new binary_parser_1.Parser()
17
+ const headerParser = new Parser()
24
18
  .endianess(le)
25
19
  .int32('magic')
26
20
  .uint16('version')
@@ -36,27 +30,27 @@ function getParsers(isBE) {
36
30
  .uint64('extHeaderOffset') // name index offset, used in bigbed
37
31
  .array('zoomLevels', {
38
32
  length: 'numZoomLevels',
39
- type: new binary_parser_1.Parser()
33
+ type: new Parser()
40
34
  .uint32('reductionLevel')
41
35
  .uint32('reserved')
42
36
  .uint64('dataOffset')
43
37
  .uint64('indexOffset'),
44
38
  });
45
- const totalSummaryParser = new binary_parser_1.Parser()
39
+ const totalSummaryParser = new Parser()
46
40
  .endianess(le)
47
41
  .uint64('basesCovered')
48
42
  .double('scoreMin')
49
43
  .double('scoreMax')
50
44
  .double('scoreSum')
51
45
  .double('scoreSumSquares');
52
- const chromTreeParser = new binary_parser_1.Parser()
46
+ const chromTreeParser = new Parser()
53
47
  .endianess(le)
54
48
  .uint32('magic')
55
49
  .uint32('blockSize')
56
50
  .uint32('keySize')
57
51
  .uint32('valSize')
58
52
  .uint64('itemCount');
59
- const isLeafNode = new binary_parser_1.Parser()
53
+ const isLeafNode = new Parser()
60
54
  .endianess(le)
61
55
  .uint8('isLeafNode')
62
56
  .skip(1)
@@ -68,7 +62,7 @@ function getParsers(isBE) {
68
62
  isLeafNode,
69
63
  };
70
64
  }
71
- class BBI {
65
+ export class BBI {
72
66
  /*
73
67
  * @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
74
68
  * @param path - a Local file path as a string
@@ -76,8 +70,8 @@ class BBI {
76
70
  * @param renameRefSeqs - an optional method to rename the internal reference sequences using a mapping function
77
71
  */
78
72
  constructor(options = {}) {
79
- this.headerCache = new abortable_promise_cache_1.default({
80
- cache: new quick_lru_1.default({ maxSize: 1 }),
73
+ this.headerCache = new AbortablePromiseCache({
74
+ cache: new QuickLRU({ maxSize: 1 }),
81
75
  fill: async (params, signal) => {
82
76
  return this._getHeader({ ...params, signal });
83
77
  },
@@ -88,10 +82,10 @@ class BBI {
88
82
  this.bbi = filehandle;
89
83
  }
90
84
  else if (url) {
91
- this.bbi = new generic_filehandle_1.RemoteFile(url);
85
+ this.bbi = new RemoteFile(url);
92
86
  }
93
87
  else if (path) {
94
- this.bbi = new generic_filehandle_1.LocalFile(path);
88
+ this.bbi = new LocalFile(path);
95
89
  }
96
90
  else {
97
91
  throw new Error('no file given');
@@ -159,12 +153,12 @@ class BBI {
159
153
  const { buffer: data } = await this.bbi.read(Buffer.alloc(unzoomedDataOffset - chromTreeOffset), 0, unzoomedDataOffset - chromTreeOffset, chromTreeOffset, opts);
160
154
  const p = getParsers(isBE);
161
155
  const { keySize } = p.chromTreeParser.parse(data).result;
162
- const leafNodeParser = new binary_parser_1.Parser()
156
+ const leafNodeParser = new Parser()
163
157
  .endianess(le)
164
158
  .string('key', { stripNull: true, length: keySize })
165
159
  .uint32('refId')
166
160
  .uint32('refSize');
167
- const nonleafNodeParser = new binary_parser_1.Parser()
161
+ const nonleafNodeParser = new Parser()
168
162
  .endianess(le)
169
163
  .skip(keySize)
170
164
  .uint64('childOffset');
@@ -214,7 +208,7 @@ class BBI {
214
208
  const { unzoomedIndexOffset, zoomLevels, refsByName, uncompressBufSize, isBigEndian, fileType, } = await this.getHeader(opts);
215
209
  const nzl = zoomLevels[0];
216
210
  const cirLen = nzl ? nzl.dataOffset - unzoomedIndexOffset : 4000;
217
- return new blockView_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, cirLen, isBigEndian, uncompressBufSize > 0, fileType);
211
+ return new BlockView(this.bbi, refsByName, unzoomedIndexOffset, cirLen, isBigEndian, uncompressBufSize > 0, fileType);
218
212
  }
219
213
  /**
220
214
  * Gets features from a BigWig file
@@ -242,7 +236,7 @@ class BBI {
242
236
  if (!view) {
243
237
  throw new Error('unable to get block view for data');
244
238
  }
245
- return new rxjs_1.Observable((observer) => {
239
+ return new Observable((observer) => {
246
240
  view.readWigData(chrName, start, end, observer, opts);
247
241
  });
248
242
  }
@@ -251,9 +245,9 @@ class BBI {
251
245
  }) {
252
246
  const ob = await this.getFeatureStream(refName, start, end, opts);
253
247
  const ret = await ob
254
- .pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)))
248
+ .pipe(reduce((acc, curr) => acc.concat(curr)))
255
249
  .toPromise();
256
250
  return ret || [];
257
251
  }
258
252
  }
259
- exports.BBI = BBI;
253
+ //# sourceMappingURL=bbi.js.map
package/esm/bbi.js.map ADDED
@@ -0,0 +1 @@
1
+ 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package/esm/bigbed.js CHANGED
@@ -1,24 +1,17 @@
1
- "use strict";
2
- var __importDefault = (this && this.__importDefault) || function (mod) {
3
- return (mod && mod.__esModule) ? mod : { "default": mod };
4
- };
5
- Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.BigBed = exports.filterUndef = void 0;
7
- const binary_parser_1 = require("@gmod/binary-parser");
8
- const rxjs_1 = require("rxjs");
9
- const operators_1 = require("rxjs/operators");
10
- const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
11
- const quick_lru_1 = __importDefault(require("quick-lru"));
12
- const bbi_1 = require("./bbi");
13
- function filterUndef(ts) {
1
+ import { Parser } from '@gmod/binary-parser';
2
+ import { Observable, merge } from 'rxjs';
3
+ import { map, reduce } from 'rxjs/operators';
4
+ import AbortablePromiseCache from 'abortable-promise-cache';
5
+ import QuickLRU from 'quick-lru';
6
+ import { BBI } from './bbi';
7
+ export function filterUndef(ts) {
14
8
  return ts.filter((t) => !!t);
15
9
  }
16
- exports.filterUndef = filterUndef;
17
- class BigBed extends bbi_1.BBI {
10
+ export class BigBed extends BBI {
18
11
  constructor(opts) {
19
12
  super(opts);
20
- this.readIndicesCache = new abortable_promise_cache_1.default({
21
- cache: new quick_lru_1.default({ maxSize: 1 }),
13
+ this.readIndicesCache = new AbortablePromiseCache({
14
+ cache: new QuickLRU({ maxSize: 1 }),
22
15
  fill: async (args, signal) => {
23
16
  return this._readIndices({ ...args, signal });
24
17
  },
@@ -46,7 +39,7 @@ class BigBed extends bbi_1.BBI {
46
39
  const { extHeaderOffset, isBigEndian } = await this.getHeader(opts);
47
40
  const { buffer: data } = await this.bbi.read(Buffer.alloc(64), 0, 64, extHeaderOffset);
48
41
  const le = isBigEndian ? 'big' : 'little';
49
- const ret = new binary_parser_1.Parser()
42
+ const ret = new Parser()
50
43
  .endianess(le)
51
44
  .uint16('size')
52
45
  .uint16('count')
@@ -60,7 +53,7 @@ class BigBed extends bbi_1.BBI {
60
53
  const blocklen = 20;
61
54
  const len = blocklen * count;
62
55
  const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, offset);
63
- const extParser = new binary_parser_1.Parser()
56
+ const extParser = new Parser()
64
57
  .endianess(le)
65
58
  .int16('type')
66
59
  .int16('fieldcount')
@@ -90,7 +83,7 @@ class BigBed extends bbi_1.BBI {
90
83
  const locs = indices.map(async (index) => {
91
84
  const { offset, field } = index;
92
85
  const { buffer: data } = await this.bbi.read(Buffer.alloc(32), 0, 32, offset, opts);
93
- const p = new binary_parser_1.Parser()
86
+ const p = new Parser()
94
87
  .endianess(isBigEndian ? 'big' : 'little')
95
88
  .int32('magic')
96
89
  .int32('blockSize')
@@ -98,7 +91,7 @@ class BigBed extends bbi_1.BBI {
98
91
  .int32('valSize')
99
92
  .uint64('itemCount');
100
93
  const { blockSize, keySize, valSize } = p.parse(data).result;
101
- const bpt = new binary_parser_1.Parser()
94
+ const bpt = new Parser()
102
95
  .endianess(isBigEndian ? 'big' : 'little')
103
96
  .int8('nodeType')
104
97
  .skip(1)
@@ -106,15 +99,15 @@ class BigBed extends bbi_1.BBI {
106
99
  .choice({
107
100
  tag: 'nodeType',
108
101
  choices: {
109
- 0: new binary_parser_1.Parser().array('leafkeys', {
102
+ 0: new Parser().array('leafkeys', {
110
103
  length: 'cnt',
111
- type: new binary_parser_1.Parser()
104
+ type: new Parser()
112
105
  .string('key', { length: keySize, stripNull: true })
113
106
  .uint64('offset'),
114
107
  }),
115
- 1: new binary_parser_1.Parser().array('keys', {
108
+ 1: new Parser().array('keys', {
116
109
  length: 'cnt',
117
- type: new binary_parser_1.Parser()
110
+ type: new Parser()
118
111
  .string('key', { length: keySize, stripNull: true })
119
112
  .uint64('offset')
120
113
  .uint32('length')
@@ -164,19 +157,19 @@ class BigBed extends bbi_1.BBI {
164
157
  }
165
158
  const view = await this.getUnzoomedView(opts);
166
159
  const res = blocks.map(block => {
167
- return new rxjs_1.Observable((observer) => {
160
+ return new Observable((observer) => {
168
161
  view.readFeatures(observer, [block], opts);
169
- }).pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)), (0, operators_1.map)(x => {
162
+ }).pipe(reduce((acc, curr) => acc.concat(curr)), map(x => {
170
163
  for (let i = 0; i < x.length; i += 1) {
171
164
  x[i].field = block.field;
172
165
  }
173
166
  return x;
174
167
  }));
175
168
  });
176
- const ret = await (0, rxjs_1.merge)(...res).toPromise();
169
+ const ret = await merge(...res).toPromise();
177
170
  return ret.filter((f) => {
178
171
  return f.rest.split('\t')[f.field - 3] === name;
179
172
  });
180
173
  }
181
174
  }
182
- exports.BigBed = BigBed;
175
+ //# sourceMappingURL=bigbed.js.map
package/esm/bigbed.js.map ADDED
@@ -0,0 +1 @@
1
+ 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package/esm/bigwig.js CHANGED
@@ -1,9 +1,6 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.BigWig = void 0;
4
- const blockView_1 = require("./blockView");
5
- const bbi_1 = require("./bbi");
6
- class BigWig extends bbi_1.BBI {
1
+ import { BlockView } from './blockView';
2
+ import { BBI } from './bbi';
3
+ export class BigWig extends BBI {
7
4
  /**
8
5
  * Retrieves a BlockView of a specific zoomLevel
9
6
  *
@@ -26,10 +23,10 @@ class BigWig extends bbi_1.BBI {
26
23
  const indexLength = i < zoomLevels.length - 1
27
24
  ? zoomLevels[i + 1].dataOffset - zh.indexOffset
28
25
  : fileSize - 4 - zh.indexOffset;
29
- return new blockView_1.BlockView(this.bbi, refsByName, zh.indexOffset, indexLength, isBigEndian, uncompressBufSize > 0, 'summary');
26
+ return new BlockView(this.bbi, refsByName, zh.indexOffset, indexLength, isBigEndian, uncompressBufSize > 0, 'summary');
30
27
  }
31
28
  }
32
29
  return this.getUnzoomedView(opts);
33
30
  }
34
31
  }
35
- exports.BigWig = BigWig;
32
+ //# sourceMappingURL=bigwig.js.map
package/esm/bigwig.js.map ADDED
@@ -0,0 +1 @@
1
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