@gmod/bbi 8.0.0 → 8.0.1

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 (25) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/dist/bbi.js +4 -1
  3. package/dist/bbi.js.map +1 -1
  4. package/dist/bigbed.js +2 -1
  5. package/dist/bigbed.js.map +1 -1
  6. package/dist/block-view.js.map +1 -1
  7. package/dist/unzip.js.map +1 -1
  8. package/dist/wasm/inflate-wasm-inlined.d.ts +6 -7
  9. package/dist/wasm/inflate-wasm-inlined.js +452 -114
  10. package/dist/wasm/inflate-wasm-inlined.js.map +1 -1
  11. package/esm/bbi.js +4 -1
  12. package/esm/bbi.js.map +1 -1
  13. package/esm/bigbed.js +2 -1
  14. package/esm/bigbed.js.map +1 -1
  15. package/esm/block-view.js.map +1 -1
  16. package/esm/unzip.js.map +1 -1
  17. package/esm/wasm/inflate-wasm-inlined.d.ts +6 -7
  18. package/esm/wasm/inflate-wasm-inlined.js +448 -110
  19. package/esm/wasm/inflate-wasm-inlined.js.map +1 -1
  20. package/package.json +7 -7
  21. package/src/bbi.ts +5 -3
  22. package/src/bigbed.ts +3 -3
  23. package/src/block-view.ts +9 -6
  24. package/src/unzip.ts +1 -3
  25. package/src/wasm/inflate-wasm-inlined.js +547 -1
package/esm/wasm/inflate-wasm-inlined.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bbi",
3
- "version": "8.0.0",
3
+ "version": "8.0.1",
4
4
  "description": "Parser for BigWig/BigBed files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bbi-js",
@@ -50,7 +50,7 @@
50
50
  ],
51
51
  "dependencies": {
52
52
  "@gmod/abortable-promise-cache": "^3.0.1",
53
- "generic-filehandle2": "^2.0.10",
53
+ "generic-filehandle2": "^2.0.16",
54
54
  "pako-esm2": "^2.0.2",
55
55
  "quick-lru": "^4.0.0",
56
56
  "rxjs": "^7.8.0"
@@ -58,19 +58,19 @@
58
58
  "devDependencies": {
59
59
  "@gmod/bed": "^2.1.2",
60
60
  "@types/node": "^24.10.0",
61
- "@typescript-eslint/eslint-plugin": "^8.49.0",
62
- "@typescript-eslint/parser": "^8.49.0",
61
+ "@typescript-eslint/eslint-plugin": "^8.50.0",
62
+ "@typescript-eslint/parser": "^8.50.0",
63
63
  "@vitest/coverage-v8": "^4.0.15",
64
- "eslint": "^9.9.1",
64
+ "eslint": "^9.39.2",
65
65
  "eslint-plugin-import": "^2.31.0",
66
66
  "eslint-plugin-unicorn": "^62.0.0",
67
67
  "prettier": "^3.7.4",
68
68
  "rimraf": "^6.1.2",
69
69
  "standard-changelog": "^7.0.1",
70
70
  "typescript": "^5.1.6",
71
- "typescript-eslint": "^8.49.0",
71
+ "typescript-eslint": "^8.50.0",
72
72
  "vitest": "^4.0.15",
73
- "webpack": "^5.103.0",
73
+ "webpack": "^5.104.0",
74
74
  "webpack-cli": "^6.0.1"
75
75
  },
76
76
  "publishConfig": {
package/src/bbi.ts CHANGED
@@ -244,9 +244,11 @@ export abstract class BBI {
244
244
 
245
245
  for (let n = 0; n < count; n++) {
246
246
  const keyEnd = b.indexOf(0, offset)
247
- const key = decoder.decode(
248
- b.subarray(offset, keyEnd !== -1 ? keyEnd : offset + keySize),
249
- )
247
+ const effectiveKeyEnd =
248
+ keyEnd !== -1 && keyEnd < offset + keySize
249
+ ? keyEnd
250
+ : offset + keySize
251
+ const key = decoder.decode(b.subarray(offset, effectiveKeyEnd))
250
252
  offset += keySize
251
253
  const refId = dataView.getUint32(offset, true)
252
254
  offset += 4
package/src/bigbed.ts CHANGED
@@ -47,9 +47,9 @@ function getTabField(str: string, fieldIndex: number) {
47
47
  // Parses a null-terminated string key from a B+ tree node
48
48
  function parseKey(buffer: Uint8Array, offset: number, keySize: number) {
49
49
  const keyEnd = buffer.indexOf(0, offset)
50
- return decoder.decode(
51
- buffer.subarray(offset, keyEnd !== -1 ? keyEnd : offset + keySize),
52
- )
50
+ const effectiveKeyEnd =
51
+ keyEnd !== -1 && keyEnd < offset + keySize ? keyEnd : offset + keySize
52
+ return decoder.decode(buffer.subarray(offset, effectiveKeyEnd))
53
53
  }
54
54
 
55
55
  // Recursively traverses a B+ tree to search for a specific name in the BigBed extraIndex
package/src/block-view.ts CHANGED
@@ -10,10 +10,7 @@ import {
10
10
  import { groupBlocks } from './util.ts'
11
11
 
12
12
  import type { Feature } from './types.ts'
13
- import type {
14
- BigWigFeatureArrays,
15
- SummaryFeatureArrays,
16
- } from './unzip.ts'
13
+ import type { BigWigFeatureArrays, SummaryFeatureArrays } from './unzip.ts'
17
14
  import type { GenericFilehandle } from 'generic-filehandle2'
18
15
  import type { Observer } from 'rxjs'
19
16
 
@@ -563,7 +560,10 @@ export class BlockView {
563
560
  }
564
561
  } else {
565
562
  for (const block of localBlocks) {
566
- const blockData = data.subarray(block.offset, block.offset + block.length)
563
+ const blockData = data.subarray(
564
+ block.offset,
565
+ block.offset + block.length,
566
+ )
567
567
  const features = this.parseBigWigBlock(blockData, 0, request)
568
568
  if (features.length > 0) {
569
569
  const starts = new Int32Array(features.length)
@@ -663,7 +663,10 @@ export class BlockView {
663
663
  }
664
664
  } else {
665
665
  for (const block of localBlocks) {
666
- const blockData = data.subarray(block.offset, block.offset + block.length)
666
+ const blockData = data.subarray(
667
+ block.offset,
668
+ block.offset + block.length,
669
+ )
667
670
  const features = this.parseSummaryBlock(blockData, 0, request)
668
671
  if (features.length > 0) {
669
672
  const starts = new Int32Array(features.length)
package/src/unzip.ts CHANGED
@@ -9,8 +9,6 @@ import type {
9
9
  SummaryFeatureArrays,
10
10
  } from './wasm/inflate-wasm-inlined.js'
11
11
 
12
-
13
-
14
12
  export interface UnzipBatchResult {
15
13
  data: Uint8Array
16
14
  offsets: number[]
@@ -87,4 +85,4 @@ export async function decompressAndParseSummaryBlocks(
87
85
  )
88
86
  }
89
87
 
90
- export type { BigWigFeatureArrays, SummaryFeatureArrays } from './types.ts'
88
+ export type { BigWigFeatureArrays, SummaryFeatureArrays } from './types.ts'