@gmod/bbi 6.0.2 → 7.0.0

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.
Files changed (42) hide show
  1. package/CHANGELOG.md +8 -0
  2. package/dist/bbi.d.ts +2 -2
  3. package/dist/bbi.js +5 -3
  4. package/dist/bbi.js.map +1 -1
  5. package/dist/bigbed.d.ts +3 -3
  6. package/dist/bigbed.js +7 -5
  7. package/dist/bigbed.js.map +1 -1
  8. package/dist/bigint-polyfill/polyfill.js +3 -3
  9. package/dist/bigint-polyfill/polyfill.js.map +1 -1
  10. package/dist/bigwig.d.ts +3 -3
  11. package/dist/bigwig.js +4 -4
  12. package/dist/bigwig.js.map +1 -1
  13. package/dist/block-view.d.ts +1 -1
  14. package/dist/block-view.js +11 -11
  15. package/dist/block-view.js.map +1 -1
  16. package/dist/index.d.ts +4 -4
  17. package/dist/index.js +5 -5
  18. package/dist/index.js.map +1 -1
  19. package/esm/bbi.d.ts +2 -2
  20. package/esm/bbi.js +4 -2
  21. package/esm/bbi.js.map +1 -1
  22. package/esm/bigbed.d.ts +3 -3
  23. package/esm/bigbed.js +6 -4
  24. package/esm/bigbed.js.map +1 -1
  25. package/esm/bigint-polyfill/polyfill.js +1 -1
  26. package/esm/bigint-polyfill/polyfill.js.map +1 -1
  27. package/esm/bigwig.d.ts +3 -3
  28. package/esm/bigwig.js +2 -2
  29. package/esm/bigwig.js.map +1 -1
  30. package/esm/block-view.d.ts +1 -1
  31. package/esm/block-view.js +3 -3
  32. package/esm/block-view.js.map +1 -1
  33. package/esm/index.d.ts +4 -4
  34. package/esm/index.js +3 -3
  35. package/esm/index.js.map +1 -1
  36. package/package.json +14 -6
  37. package/src/bbi.ts +6 -3
  38. package/src/bigbed.ts +8 -6
  39. package/src/bigint-polyfill/polyfill.ts +1 -1
  40. package/src/bigwig.ts +3 -3
  41. package/src/block-view.ts +4 -4
  42. package/src/index.ts +4 -4
package/CHANGELOG.md CHANGED
@@ -1,3 +1,11 @@
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+ # [7.0.0](https://github.com/GMOD/bbi-js/compare/v6.0.3...v7.0.0) (2025-04-30)
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+
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+
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+
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+ ## [6.0.3](https://github.com/GMOD/bbi-js/compare/v6.0.2...v6.0.3) (2025-04-11)
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+
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+
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+
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  ## [6.0.2](https://github.com/GMOD/bbi-js/compare/v6.0.1...v6.0.2) (2025-03-18)
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package/dist/bbi.d.ts CHANGED
@@ -1,6 +1,6 @@
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  import { Observable } from 'rxjs';
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- import { BlockView } from './block-view';
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- import type { BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions } from './types';
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+ import { BlockView } from './block-view.ts';
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+ import type { BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions } from './types.ts';
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  import type { GenericFilehandle } from 'generic-filehandle2';
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  export declare abstract class BBI {
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  protected bbi: GenericFilehandle;
package/dist/bbi.js CHANGED
@@ -4,7 +4,7 @@ exports.BBI = void 0;
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  const generic_filehandle2_1 = require("generic-filehandle2");
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  const rxjs_1 = require("rxjs");
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  const operators_1 = require("rxjs/operators");
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- const block_view_1 = require("./block-view");
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+ const block_view_ts_1 = require("./block-view.js");
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  const BIG_WIG_MAGIC = -2003829722;
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  const BIG_BED_MAGIC = -2021002517;
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  class BBI {
@@ -189,6 +189,9 @@ class BBI {
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  }
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  const isLeafNode = dataView.getUint8(offset);
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  offset += 2; //skip 1
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+ if (offset >= b.length) {
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+ return;
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+ }
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  const cnt = dataView.getUint16(offset, true);
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  offset += 2;
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  if (isLeafNode) {
@@ -210,7 +213,6 @@ class BBI {
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  }
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  }
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  else {
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- // parse index node
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  const nextNodes = [];
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  for (let n = 0; n < cnt; n++) {
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  offset += keySize;
@@ -233,7 +235,7 @@ class BBI {
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  */
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  async getUnzoomedView(opts) {
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  const { unzoomedIndexOffset, refsByName, uncompressBufSize, fileType } = await this.getHeader(opts);
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- return new block_view_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, uncompressBufSize > 0, fileType);
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+ return new block_view_ts_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, uncompressBufSize > 0, fileType);
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  }
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  /**
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  * Gets features from a BigWig file
package/dist/bbi.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/bigbed.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import AbortablePromiseCache from '@gmod/abortable-promise-cache';
2
- import { BBI } from './bbi';
3
- import type { Feature, RequestOptions } from './types';
2
+ import { BBI } from './bbi.ts';
3
+ import type { Feature, RequestOptions } from './types.ts';
4
4
  interface Index {
5
5
  type: number;
6
6
  fieldcount: number;
@@ -11,7 +11,7 @@ export declare function filterUndef<T>(ts: (T | undefined)[]): T[];
11
11
  export declare class BigBed extends BBI {
12
12
  readIndicesCache: AbortablePromiseCache<RequestOptions, Index[]>;
13
13
  readIndices(opts?: RequestOptions): Promise<Index[]>;
14
- protected getView(_scale: number, opts?: RequestOptions): Promise<import("./block-view").BlockView>;
14
+ protected getView(_scale: number, opts?: RequestOptions): Promise<import("./block-view.ts").BlockView>;
15
15
  private _readIndices;
16
16
  private searchExtraIndexBlocks;
17
17
  searchExtraIndex(name: string, opts?: RequestOptions): Promise<Feature[]>;
package/dist/bigbed.js CHANGED
@@ -9,11 +9,11 @@ const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promi
9
9
  const quick_lru_1 = __importDefault(require("quick-lru"));
10
10
  const rxjs_1 = require("rxjs");
11
11
  const operators_1 = require("rxjs/operators");
12
- const bbi_1 = require("./bbi");
12
+ const bbi_ts_1 = require("./bbi.js");
13
13
  function filterUndef(ts) {
14
14
  return ts.filter((t) => !!t);
15
15
  }
16
- class BigBed extends bbi_1.BBI {
16
+ class BigBed extends bbi_ts_1.BBI {
17
17
  constructor() {
18
18
  super(...arguments);
19
19
  this.readIndicesCache = new abortable_promise_cache_1.default({
@@ -159,14 +159,16 @@ class BigBed extends bbi_1.BBI {
159
159
  }
160
160
  for (const n of keys) {
161
161
  if (n.key === name) {
162
- return { ...n, field };
162
+ return {
163
+ ...n,
164
+ field,
165
+ };
163
166
  }
164
167
  }
165
168
  return undefined;
166
169
  }
167
170
  };
168
- const rootNodeOffset = 32;
169
- return bptReadNode(offset2 + rootNodeOffset);
171
+ return bptReadNode(offset2 + 32);
170
172
  });
171
173
  return filterUndef(await Promise.all(locs));
172
174
  }
package/dist/bigbed.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/bigint-polyfill/polyfill.js CHANGED
@@ -3,15 +3,15 @@ Object.defineProperty(exports, "__esModule", { value: true });
3
3
  // from https://github.com/yume-chan/ya-webadb/blob/main/libraries/dataview-bigint-polyfill
4
4
  // license:MIT
5
5
  // needed for browsers including safari 14
6
- const pure_1 = require("./pure");
6
+ const pure_ts_1 = require("./pure.js");
7
7
  if (!('getBigInt64' in DataView)) {
8
8
  DataView.prototype.getBigInt64 = function (byteOffset, littleEndian) {
9
- return (0, pure_1.getBigInt64)(this, byteOffset, littleEndian);
9
+ return (0, pure_ts_1.getBigInt64)(this, byteOffset, littleEndian);
10
10
  };
11
11
  }
12
12
  if (!('getBigUint64' in DataView)) {
13
13
  DataView.prototype.getBigUint64 = function (byteOffset, littleEndian) {
14
- return (0, pure_1.getBigUint64)(this, byteOffset, littleEndian);
14
+ return (0, pure_ts_1.getBigUint64)(this, byteOffset, littleEndian);
15
15
  };
16
16
  }
17
17
  //# sourceMappingURL=polyfill.js.map
package/dist/bigint-polyfill/polyfill.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"polyfill.js","sourceRoot":"","sources":["../../src/bigint-polyfill/polyfill.ts"],"names":[],"mappings":";;AAAA,2FAA2F;AAC3F,cAAc;AACd,0CAA0C;AAC1C,iCAAkD;AAElD,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE,CAAC;IACjC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,YAAY;QACjE,OAAO,IAAA,kBAAW,EAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;AACH,CAAC;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE,CAAC;IAClC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,YAAY;QAClE,OAAO,IAAA,mBAAY,EAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;AACH,CAAC"}
1
+ {"version":3,"file":"polyfill.js","sourceRoot":"","sources":["../../src/bigint-polyfill/polyfill.ts"],"names":[],"mappings":";;AAAA,2FAA2F;AAC3F,cAAc;AACd,0CAA0C;AAC1C,uCAAqD;AAErD,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE,CAAC;IACjC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,YAAY;QACjE,OAAO,IAAA,qBAAW,EAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;AACH,CAAC;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE,CAAC;IAClC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,YAAY;QAClE,OAAO,IAAA,sBAAY,EAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;AACH,CAAC"}
package/dist/bigwig.d.ts CHANGED
@@ -1,6 +1,6 @@
1
- import { BBI } from './bbi';
2
- import { BlockView } from './block-view';
3
- import type { RequestOptions } from './types';
1
+ import { BBI } from './bbi.ts';
2
+ import { BlockView } from './block-view.ts';
3
+ import type { RequestOptions } from './types.ts';
4
4
  export declare class BigWig extends BBI {
5
5
  /**
6
6
  * Retrieves a BlockView of a specific zoomLevel
package/dist/bigwig.js CHANGED
@@ -1,9 +1,9 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.BigWig = void 0;
4
- const bbi_1 = require("./bbi");
5
- const block_view_1 = require("./block-view");
6
- class BigWig extends bbi_1.BBI {
4
+ const bbi_ts_1 = require("./bbi.js");
5
+ const block_view_ts_1 = require("./block-view.js");
6
+ class BigWig extends bbi_ts_1.BBI {
7
7
  /**
8
8
  * Retrieves a BlockView of a specific zoomLevel
9
9
  *
@@ -20,7 +20,7 @@ class BigWig extends bbi_1.BBI {
20
20
  const zh = zoomLevels[i];
21
21
  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
22
22
  if (zh && zh.reductionLevel <= 2 * basesPerPx) {
23
- return new block_view_1.BlockView(this.bbi, refsByName, zh.indexOffset, uncompressBufSize > 0, 'summary');
23
+ return new block_view_ts_1.BlockView(this.bbi, refsByName, zh.indexOffset, uncompressBufSize > 0, 'summary');
24
24
  }
25
25
  }
26
26
  return this.getUnzoomedView(opts);
package/dist/bigwig.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;AAAA,+BAA2B;AAC3B,6CAAwC;AAIxC,MAAa,MAAO,SAAQ,SAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,iBAAiB,EAAE,GACjD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,uEAAuE;YACvE,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,OAAO,IAAI,sBAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF;AA9BD,wBA8BC"}
1
+ {"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;AAAA,qCAA8B;AAC9B,mDAA2C;AAI3C,MAAa,MAAO,SAAQ,YAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,iBAAiB,EAAE,GACjD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,uEAAuE;YACvE,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,OAAO,IAAI,yBAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF;AA9BD,wBA8BC"}
package/dist/block-view.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import type { Feature } from './types';
1
+ import type { Feature } from './types.ts';
2
2
  import type { GenericFilehandle } from 'generic-filehandle2';
3
3
  import type { Observer } from 'rxjs';
4
4
  interface CoordRequest {
package/dist/block-view.js CHANGED
@@ -6,9 +6,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
6
6
  exports.BlockView = void 0;
7
7
  const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
8
8
  const quick_lru_1 = __importDefault(require("quick-lru"));
9
- const range_1 = __importDefault(require("./range"));
10
- const unzip_1 = require("./unzip");
11
- const util_1 = require("./util");
9
+ const range_ts_1 = __importDefault(require("./range.js"));
10
+ const unzip_ts_1 = require("./unzip.js");
11
+ const util_ts_1 = require("./util.js");
12
12
  const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
13
13
  function coordFilter(s1, e1, s2, e2) {
14
14
  return s1 < e2 && e1 >= s2;
@@ -159,14 +159,14 @@ class BlockView {
159
159
  outstanding += offset.length;
160
160
  // Upper bound on size, based on a completely full leaf node.
161
161
  const maxCirBlockSpan = 4 + cirBlockSize * 32;
162
- let spans = new range_1.default([
162
+ let spans = new range_ts_1.default([
163
163
  {
164
164
  min: offset[0],
165
165
  max: offset[0] + maxCirBlockSpan,
166
166
  },
167
167
  ]);
168
168
  for (let i = 1; i < offset.length; i += 1) {
169
- const blockSpan = new range_1.default([
169
+ const blockSpan = new range_ts_1.default([
170
170
  {
171
171
  min: offset[i],
172
172
  max: offset[i] + maxCirBlockSpan,
@@ -331,19 +331,19 @@ class BlockView {
331
331
  try {
332
332
  const { blockType, isCompressed } = this;
333
333
  const { signal, request } = opts;
334
- const blockGroupsToFetch = (0, util_1.groupBlocks)(blocks);
335
- (0, util_1.checkAbortSignal)(signal);
334
+ const blockGroupsToFetch = (0, util_ts_1.groupBlocks)(blocks);
335
+ (0, util_ts_1.checkAbortSignal)(signal);
336
336
  await Promise.all(blockGroupsToFetch.map(async (blockGroup) => {
337
- (0, util_1.checkAbortSignal)(signal);
337
+ (0, util_ts_1.checkAbortSignal)(signal);
338
338
  const { length, offset } = blockGroup;
339
339
  const data = await this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
340
340
  for (const block of blockGroup.blocks) {
341
- (0, util_1.checkAbortSignal)(signal);
341
+ (0, util_ts_1.checkAbortSignal)(signal);
342
342
  let resultData = data.subarray(Number(block.offset) - Number(blockGroup.offset));
343
343
  if (isCompressed) {
344
- resultData = (0, unzip_1.unzip)(resultData);
344
+ resultData = (0, unzip_ts_1.unzip)(resultData);
345
345
  }
346
- (0, util_1.checkAbortSignal)(signal);
346
+ (0, util_ts_1.checkAbortSignal)(signal);
347
347
  switch (blockType) {
348
348
  case 'summary': {
349
349
  observer.next(this.parseSummaryBlock(resultData, 0, request));
package/dist/block-view.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/index.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import './bigint-polyfill/polyfill';
2
- export { BigWig } from './bigwig';
3
- export { BigBed } from './bigbed';
4
- export type { BigWigHeader, Feature, RequestOptions } from './types';
1
+ import './bigint-polyfill/polyfill.ts';
2
+ export { BigWig } from './bigwig.ts';
3
+ export { BigBed } from './bigbed.ts';
4
+ export type { BigWigHeader, Feature, RequestOptions } from './types.ts';
package/dist/index.js CHANGED
@@ -1,9 +1,9 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.BigBed = exports.BigWig = void 0;
4
- require("./bigint-polyfill/polyfill");
5
- var bigwig_1 = require("./bigwig");
6
- Object.defineProperty(exports, "BigWig", { enumerable: true, get: function () { return bigwig_1.BigWig; } });
7
- var bigbed_1 = require("./bigbed");
8
- Object.defineProperty(exports, "BigBed", { enumerable: true, get: function () { return bigbed_1.BigBed; } });
4
+ require("./bigint-polyfill/polyfill.js");
5
+ var bigwig_ts_1 = require("./bigwig.js");
6
+ Object.defineProperty(exports, "BigWig", { enumerable: true, get: function () { return bigwig_ts_1.BigWig; } });
7
+ var bigbed_ts_1 = require("./bigbed.js");
8
+ Object.defineProperty(exports, "BigBed", { enumerable: true, get: function () { return bigbed_ts_1.BigBed; } });
9
9
  //# sourceMappingURL=index.js.map
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,sCAAmC;AACnC,mCAAiC;AAAxB,gGAAA,MAAM,OAAA;AACf,mCAAiC;AAAxB,gGAAA,MAAM,OAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,yCAAsC;AACtC,yCAAoC;AAA3B,mGAAA,MAAM,OAAA;AACf,yCAAoC;AAA3B,mGAAA,MAAM,OAAA"}
package/esm/bbi.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import { Observable } from 'rxjs';
2
- import { BlockView } from './block-view';
3
- import type { BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions } from './types';
2
+ import { BlockView } from './block-view.ts';
3
+ import type { BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions } from './types.ts';
4
4
  import type { GenericFilehandle } from 'generic-filehandle2';
5
5
  export declare abstract class BBI {
6
6
  protected bbi: GenericFilehandle;
package/esm/bbi.js CHANGED
@@ -1,7 +1,7 @@
1
1
  import { LocalFile, RemoteFile } from 'generic-filehandle2';
2
2
  import { Observable, firstValueFrom } from 'rxjs';
3
3
  import { toArray } from 'rxjs/operators';
4
- import { BlockView } from './block-view';
4
+ import { BlockView } from "./block-view.js";
5
5
  const BIG_WIG_MAGIC = -2003829722;
6
6
  const BIG_BED_MAGIC = -2021002517;
7
7
  export class BBI {
@@ -186,6 +186,9 @@ export class BBI {
186
186
  }
187
187
  const isLeafNode = dataView.getUint8(offset);
188
188
  offset += 2; //skip 1
189
+ if (offset >= b.length) {
190
+ return;
191
+ }
189
192
  const cnt = dataView.getUint16(offset, true);
190
193
  offset += 2;
191
194
  if (isLeafNode) {
@@ -207,7 +210,6 @@ export class BBI {
207
210
  }
208
211
  }
209
212
  else {
210
- // parse index node
211
213
  const nextNodes = [];
212
214
  for (let n = 0; n < cnt; n++) {
213
215
  offset += keySize;
package/esm/bbi.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/bigbed.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import AbortablePromiseCache from '@gmod/abortable-promise-cache';
2
- import { BBI } from './bbi';
3
- import type { Feature, RequestOptions } from './types';
2
+ import { BBI } from './bbi.ts';
3
+ import type { Feature, RequestOptions } from './types.ts';
4
4
  interface Index {
5
5
  type: number;
6
6
  fieldcount: number;
@@ -11,7 +11,7 @@ export declare function filterUndef<T>(ts: (T | undefined)[]): T[];
11
11
  export declare class BigBed extends BBI {
12
12
  readIndicesCache: AbortablePromiseCache<RequestOptions, Index[]>;
13
13
  readIndices(opts?: RequestOptions): Promise<Index[]>;
14
- protected getView(_scale: number, opts?: RequestOptions): Promise<import("./block-view").BlockView>;
14
+ protected getView(_scale: number, opts?: RequestOptions): Promise<import("./block-view.ts").BlockView>;
15
15
  private _readIndices;
16
16
  private searchExtraIndexBlocks;
17
17
  searchExtraIndex(name: string, opts?: RequestOptions): Promise<Feature[]>;
package/esm/bigbed.js CHANGED
@@ -2,7 +2,7 @@ import AbortablePromiseCache from '@gmod/abortable-promise-cache';
2
2
  import QuickLRU from 'quick-lru';
3
3
  import { Observable, firstValueFrom, merge } from 'rxjs';
4
4
  import { map, reduce } from 'rxjs/operators';
5
- import { BBI } from './bbi';
5
+ import { BBI } from "./bbi.js";
6
6
  export function filterUndef(ts) {
7
7
  return ts.filter((t) => !!t);
8
8
  }
@@ -152,14 +152,16 @@ export class BigBed extends BBI {
152
152
  }
153
153
  for (const n of keys) {
154
154
  if (n.key === name) {
155
- return { ...n, field };
155
+ return {
156
+ ...n,
157
+ field,
158
+ };
156
159
  }
157
160
  }
158
161
  return undefined;
159
162
  }
160
163
  };
161
- const rootNodeOffset = 32;
162
- return bptReadNode(offset2 + rootNodeOffset);
164
+ return bptReadNode(offset2 + 32);
163
165
  });
164
166
  return filterUndef(await Promise.all(locs));
165
167
  }
package/esm/bigbed.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/bigint-polyfill/polyfill.js CHANGED
@@ -1,7 +1,7 @@
1
1
  // from https://github.com/yume-chan/ya-webadb/blob/main/libraries/dataview-bigint-polyfill
2
2
  // license:MIT
3
3
  // needed for browsers including safari 14
4
- import { getBigInt64, getBigUint64 } from './pure';
4
+ import { getBigInt64, getBigUint64 } from "./pure.js";
5
5
  if (!('getBigInt64' in DataView)) {
6
6
  DataView.prototype.getBigInt64 = function (byteOffset, littleEndian) {
7
7
  return getBigInt64(this, byteOffset, littleEndian);
package/esm/bigint-polyfill/polyfill.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"polyfill.js","sourceRoot":"","sources":["../../src/bigint-polyfill/polyfill.ts"],"names":[],"mappings":"AAAA,2FAA2F;AAC3F,cAAc;AACd,0CAA0C;AAC1C,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAElD,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE,CAAC;IACjC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,YAAY;QACjE,OAAO,WAAW,CAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;AACH,CAAC;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE,CAAC;IAClC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,YAAY;QAClE,OAAO,YAAY,CAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;AACH,CAAC"}
1
+ {"version":3,"file":"polyfill.js","sourceRoot":"","sources":["../../src/bigint-polyfill/polyfill.ts"],"names":[],"mappings":"AAAA,2FAA2F;AAC3F,cAAc;AACd,0CAA0C;AAC1C,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,MAAM,WAAW,CAAA;AAErD,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE,CAAC;IACjC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,YAAY;QACjE,OAAO,WAAW,CAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;AACH,CAAC;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE,CAAC;IAClC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,YAAY;QAClE,OAAO,YAAY,CAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;AACH,CAAC"}
package/esm/bigwig.d.ts CHANGED
@@ -1,6 +1,6 @@
1
- import { BBI } from './bbi';
2
- import { BlockView } from './block-view';
3
- import type { RequestOptions } from './types';
1
+ import { BBI } from './bbi.ts';
2
+ import { BlockView } from './block-view.ts';
3
+ import type { RequestOptions } from './types.ts';
4
4
  export declare class BigWig extends BBI {
5
5
  /**
6
6
  * Retrieves a BlockView of a specific zoomLevel
package/esm/bigwig.js CHANGED
@@ -1,5 +1,5 @@
1
- import { BBI } from './bbi';
2
- import { BlockView } from './block-view';
1
+ import { BBI } from "./bbi.js";
2
+ import { BlockView } from "./block-view.js";
3
3
  export class BigWig extends BBI {
4
4
  /**
5
5
  * Retrieves a BlockView of a specific zoomLevel
package/esm/bigwig.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,OAAO,CAAA;AAC3B,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AAIxC,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,iBAAiB,EAAE,GACjD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,uEAAuE;YACvE,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}
1
+ {"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAC9B,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAI3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,iBAAiB,EAAE,GACjD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,uEAAuE;YACvE,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}
package/esm/block-view.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import type { Feature } from './types';
1
+ import type { Feature } from './types.ts';
2
2
  import type { GenericFilehandle } from 'generic-filehandle2';
3
3
  import type { Observer } from 'rxjs';
4
4
  interface CoordRequest {
package/esm/block-view.js CHANGED
@@ -1,8 +1,8 @@
1
1
  import AbortablePromiseCache from '@gmod/abortable-promise-cache';
2
2
  import QuickLRU from 'quick-lru';
3
- import Range from './range';
4
- import { unzip } from './unzip';
5
- import { checkAbortSignal, groupBlocks } from './util';
3
+ import Range from "./range.js";
4
+ import { unzip } from "./unzip.js";
5
+ import { checkAbortSignal, groupBlocks } from "./util.js";
6
6
  const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
7
7
  function coordFilter(s1, e1, s2, e2) {
8
8
  return s1 < e2 && e1 >= s2;
package/esm/block-view.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/index.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import './bigint-polyfill/polyfill';
2
- export { BigWig } from './bigwig';
3
- export { BigBed } from './bigbed';
4
- export type { BigWigHeader, Feature, RequestOptions } from './types';
1
+ import './bigint-polyfill/polyfill.ts';
2
+ export { BigWig } from './bigwig.ts';
3
+ export { BigBed } from './bigbed.ts';
4
+ export type { BigWigHeader, Feature, RequestOptions } from './types.ts';
package/esm/index.js CHANGED
@@ -1,4 +1,4 @@
1
- import './bigint-polyfill/polyfill';
2
- export { BigWig } from './bigwig';
3
- export { BigBed } from './bigbed';
1
+ import "./bigint-polyfill/polyfill.js";
2
+ export { BigWig } from "./bigwig.js";
3
+ export { BigBed } from "./bigbed.js";
4
4
  //# sourceMappingURL=index.js.map
package/esm/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,4BAA4B,CAAA;AACnC,OAAO,EAAE,MAAM,EAAE,MAAM,UAAU,CAAA;AACjC,OAAO,EAAE,MAAM,EAAE,MAAM,UAAU,CAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,+BAA+B,CAAA;AACtC,OAAO,EAAE,MAAM,EAAE,MAAM,aAAa,CAAA;AACpC,OAAO,EAAE,MAAM,EAAE,MAAM,aAAa,CAAA"}
package/package.json CHANGED
@@ -1,11 +1,19 @@
1
1
  {
2
2
  "name": "@gmod/bbi",
3
- "version": "6.0.2",
3
+ "version": "7.0.0",
4
4
  "description": "Parser for BigWig/BigBed files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bbi-js",
7
- "main": "dist/index.js",
8
- "module": "esm/index.js",
7
+ "type": "module",
8
+ "types": "./dist/index.d.ts",
9
+ "exports": {
10
+ "import": {
11
+ "import": "./esm/index.js"
12
+ },
13
+ "require": {
14
+ "require": "./dist/index.js"
15
+ }
16
+ },
9
17
  "author": {
10
18
  "name": "Colin Diesh",
11
19
  "email": "colin.diesh@gmail.com",
@@ -42,21 +50,21 @@
42
50
  ],
43
51
  "dependencies": {
44
52
  "@gmod/abortable-promise-cache": "^2.0.0",
45
- "generic-filehandle2": "^1.0.0",
53
+ "generic-filehandle2": "^2.0.1",
46
54
  "pako": "^2.0.0",
47
55
  "quick-lru": "^4.0.0",
48
56
  "rxjs": "^7.8.0"
49
57
  },
50
58
  "devDependencies": {
51
59
  "@gmod/bed": "^2.1.2",
52
- "@types/node": "^20.11.16",
60
+ "@types/node": "^22.15.3",
53
61
  "@types/pako": "^2.0.0",
54
62
  "@typescript-eslint/eslint-plugin": "^8.4.0",
55
63
  "@typescript-eslint/parser": "^8.4.0",
56
64
  "@vitest/coverage-v8": "^3.0.1",
57
65
  "eslint": "^9.9.1",
58
66
  "eslint-plugin-import": "^2.31.0",
59
- "eslint-plugin-unicorn": "^57.0.0",
67
+ "eslint-plugin-unicorn": "^59.0.0",
60
68
  "prettier": "^3.2.5",
61
69
  "rimraf": "^6.0.1",
62
70
  "standard-changelog": "^6.0.0",
package/src/bbi.ts CHANGED
@@ -2,7 +2,7 @@ import { LocalFile, RemoteFile } from 'generic-filehandle2'
2
2
  import { Observable, firstValueFrom } from 'rxjs'
3
3
  import { toArray } from 'rxjs/operators'
4
4
 
5
- import { BlockView } from './block-view'
5
+ import { BlockView } from './block-view.ts'
6
6
 
7
7
  import type {
8
8
  BigWigHeader,
@@ -13,7 +13,7 @@ import type {
13
13
  RequestOptions,
14
14
  Statistics,
15
15
  ZoomLevel,
16
- } from './types'
16
+ } from './types.ts'
17
17
  import type { GenericFilehandle } from 'generic-filehandle2'
18
18
 
19
19
  const BIG_WIG_MAGIC = -2003829722
@@ -227,6 +227,10 @@ export abstract class BBI {
227
227
  }
228
228
  const isLeafNode = dataView.getUint8(offset)
229
229
  offset += 2 //skip 1
230
+
231
+ if (offset >= b.length) {
232
+ return
233
+ }
230
234
  const cnt = dataView.getUint16(offset, true)
231
235
  offset += 2
232
236
  if (isLeafNode) {
@@ -248,7 +252,6 @@ export abstract class BBI {
248
252
  }
249
253
  }
250
254
  } else {
251
- // parse index node
252
255
  const nextNodes = []
253
256
  for (let n = 0; n < cnt; n++) {
254
257
  offset += keySize
package/src/bigbed.ts CHANGED
@@ -3,9 +3,9 @@ import QuickLRU from 'quick-lru'
3
3
  import { Observable, firstValueFrom, merge } from 'rxjs'
4
4
  import { map, reduce } from 'rxjs/operators'
5
5
 
6
- import { BBI } from './bbi'
6
+ import { BBI } from './bbi.ts'
7
7
 
8
- import type { Feature, RequestOptions } from './types'
8
+ import type { Feature, RequestOptions } from './types.ts'
9
9
 
10
10
  interface Loc {
11
11
  key: string
@@ -110,7 +110,7 @@ export class BigBed extends BBI {
110
110
  return []
111
111
  }
112
112
  const decoder = new TextDecoder('utf8')
113
- const locs = indices.map(async (index): Promise<Loc | undefined> => {
113
+ const locs = indices.map(async index => {
114
114
  const { offset: offset2, field } = index
115
115
  const b = await this.bbi.read(32, offset2, opts)
116
116
 
@@ -184,15 +184,17 @@ export class BigBed extends BBI {
184
184
 
185
185
  for (const n of keys) {
186
186
  if (n.key === name) {
187
- return { ...n, field }
187
+ return {
188
+ ...n,
189
+ field,
190
+ }
188
191
  }
189
192
  }
190
193
 
191
194
  return undefined
192
195
  }
193
196
  }
194
- const rootNodeOffset = 32
195
- return bptReadNode(offset2 + rootNodeOffset)
197
+ return bptReadNode(offset2 + 32)
196
198
  })
197
199
  return filterUndef(await Promise.all(locs))
198
200
  }
package/src/bigint-polyfill/polyfill.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  // from https://github.com/yume-chan/ya-webadb/blob/main/libraries/dataview-bigint-polyfill
2
2
  // license:MIT
3
3
  // needed for browsers including safari 14
4
- import { getBigInt64, getBigUint64 } from './pure'
4
+ import { getBigInt64, getBigUint64 } from './pure.ts'
5
5
 
6
6
  if (!('getBigInt64' in DataView)) {
7
7
  DataView.prototype.getBigInt64 = function (byteOffset, littleEndian) {
package/src/bigwig.ts CHANGED
@@ -1,7 +1,7 @@
1
- import { BBI } from './bbi'
2
- import { BlockView } from './block-view'
1
+ import { BBI } from './bbi.ts'
2
+ import { BlockView } from './block-view.ts'
3
3
 
4
- import type { RequestOptions } from './types'
4
+ import type { RequestOptions } from './types.ts'
5
5
 
6
6
  export class BigWig extends BBI {
7
7
  /**
package/src/block-view.ts CHANGED
@@ -1,11 +1,11 @@
1
1
  import AbortablePromiseCache from '@gmod/abortable-promise-cache'
2
2
  import QuickLRU from 'quick-lru'
3
3
 
4
- import Range from './range'
5
- import { unzip } from './unzip'
6
- import { checkAbortSignal, groupBlocks } from './util'
4
+ import Range from './range.ts'
5
+ import { unzip } from './unzip.ts'
6
+ import { checkAbortSignal, groupBlocks } from './util.ts'
7
7
 
8
- import type { Feature } from './types'
8
+ import type { Feature } from './types.ts'
9
9
  import type { GenericFilehandle } from 'generic-filehandle2'
10
10
  import type { Observer } from 'rxjs'
11
11
 
package/src/index.ts CHANGED
@@ -1,4 +1,4 @@
1
- import './bigint-polyfill/polyfill'
2
- export { BigWig } from './bigwig'
3
- export { BigBed } from './bigbed'
4
- export type { BigWigHeader, Feature, RequestOptions } from './types'
1
+ import './bigint-polyfill/polyfill.ts'
2
+ export { BigWig } from './bigwig.ts'
3
+ export { BigBed } from './bigbed.ts'
4
+ export type { BigWigHeader, Feature, RequestOptions } from './types.ts'