@gmod/bbi 5.0.1 → 6.0.0

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 (34) hide show
  1. package/CHANGELOG.md +8 -0
  2. package/README.md +5 -5
  3. package/dist/bbi.d.ts +15 -16
  4. package/dist/bbi.js +195 -220
  5. package/dist/bbi.js.map +1 -1
  6. package/dist/bigbed.js +138 -159
  7. package/dist/bigbed.js.map +1 -1
  8. package/dist/bigwig.js +11 -21
  9. package/dist/bigwig.js.map +1 -1
  10. package/dist/block-view.d.ts +2 -3
  11. package/dist/block-view.js +190 -205
  12. package/dist/block-view.js.map +1 -1
  13. package/dist/unzip-pako.d.ts +1 -2
  14. package/dist/unzip-pako.js.map +1 -1
  15. package/dist/util.js +3 -14
  16. package/dist/util.js.map +1 -1
  17. package/esm/bbi.d.ts +15 -16
  18. package/esm/bbi.js +66 -70
  19. package/esm/bbi.js.map +1 -1
  20. package/esm/bigbed.js +47 -40
  21. package/esm/bigbed.js.map +1 -1
  22. package/esm/bigwig.js +3 -2
  23. package/esm/bigwig.js.map +1 -1
  24. package/esm/block-view.d.ts +2 -3
  25. package/esm/block-view.js +36 -41
  26. package/esm/block-view.js.map +1 -1
  27. package/esm/unzip-pako.d.ts +1 -2
  28. package/esm/unzip-pako.js.map +1 -1
  29. package/package.json +14 -18
  30. package/src/bbi.ts +78 -99
  31. package/src/bigbed.ts +47 -62
  32. package/src/bigwig.ts +2 -2
  33. package/src/block-view.ts +46 -57
  34. package/src/unzip-pako.ts +1 -2
package/esm/bigwig.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,WAAW,EAAE,iBAAiB,EAAE,GAC9D,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,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,WAAW,EACX,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,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,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
@@ -1,5 +1,5 @@
1
1
  import { Observer } from 'rxjs';
2
- import { GenericFilehandle } from 'generic-filehandle';
2
+ import { GenericFilehandle } from 'generic-filehandle2';
3
3
  import { Feature } from './bbi';
4
4
  interface CoordRequest {
5
5
  chrId: number;
@@ -21,12 +21,11 @@ export declare class BlockView {
21
21
  private bbi;
22
22
  private refsByName;
23
23
  private cirTreeOffset;
24
- private isBigEndian;
25
24
  private isCompressed;
26
25
  private blockType;
27
26
  private cirTreePromise?;
28
27
  private featureCache;
29
- constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
28
+ constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, isCompressed: boolean, blockType: string);
30
29
  readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts?: Options): Promise<void>;
31
30
  private parseSummaryBlock;
32
31
  private parseBigBedBlock;
package/esm/block-view.js CHANGED
@@ -1,10 +1,10 @@
1
- import { Buffer } from 'buffer';
2
1
  import AbortablePromiseCache from '@gmod/abortable-promise-cache';
3
2
  import QuickLRU from 'quick-lru';
4
3
  // locals
5
4
  import Range from './range';
6
5
  import { unzip } from './unzip';
7
6
  import { groupBlocks, checkAbortSignal } from './util';
7
+ const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
8
8
  function coordFilter(s1, e1, s2, e2) {
9
9
  return s1 < e2 && e1 >= s2;
10
10
  }
@@ -16,22 +16,18 @@ function coordFilter(s1, e1, s2, e2) {
16
16
  * @constructs
17
17
  */
18
18
  export class BlockView {
19
- constructor(bbi, refsByName, cirTreeOffset, isBigEndian, isCompressed, blockType) {
19
+ constructor(bbi, refsByName, cirTreeOffset, isCompressed, blockType) {
20
20
  this.bbi = bbi;
21
21
  this.refsByName = refsByName;
22
22
  this.cirTreeOffset = cirTreeOffset;
23
- this.isBigEndian = isBigEndian;
24
23
  this.isCompressed = isCompressed;
25
24
  this.blockType = blockType;
26
25
  this.featureCache = new AbortablePromiseCache({
27
26
  cache: new QuickLRU({ maxSize: 1000 }),
28
27
  fill: async (requestData, signal) => {
29
- const len = requestData.length;
30
- const off = requestData.offset;
31
- const { buffer } = await this.bbi.read(Buffer.alloc(len), 0, len, off, {
28
+ return this.bbi.read(requestData.length, requestData.offset, {
32
29
  signal,
33
30
  });
34
- return buffer;
35
31
  },
36
32
  });
37
33
  if (!(cirTreeOffset >= 0)) {
@@ -40,22 +36,20 @@ export class BlockView {
40
36
  }
41
37
  async readWigData(chrName, start, end, observer, opts) {
42
38
  try {
43
- const { refsByName, bbi, cirTreeOffset, isBigEndian } = this;
39
+ const { refsByName, bbi, cirTreeOffset } = this;
44
40
  const chrId = refsByName[chrName];
45
41
  if (chrId === undefined) {
46
42
  observer.complete();
47
43
  }
48
44
  const request = { chrId, start, end };
49
45
  if (!this.cirTreePromise) {
50
- this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, cirTreeOffset, opts);
46
+ this.cirTreePromise = bbi.read(48, cirTreeOffset, opts);
51
47
  }
52
- const { buffer } = await this.cirTreePromise;
53
- const cirBlockSize = isBigEndian
54
- ? buffer.readUInt32BE(4)
55
- : buffer.readUInt32LE(4);
48
+ const buffer = await this.cirTreePromise;
49
+ const dataView = new DataView(buffer.buffer);
50
+ const cirBlockSize = dataView.getUint32(4, true);
56
51
  let blocksToFetch = [];
57
52
  let outstanding = 0;
58
- const le = true;
59
53
  const cirFobRecur2 = (cirBlockData, offset2, level) => {
60
54
  try {
61
55
  const data = cirBlockData.subarray(offset2);
@@ -64,22 +58,22 @@ export class BlockView {
64
58
  let offset = 0;
65
59
  const isLeaf = dataView.getUint8(offset);
66
60
  offset += 2; // 1 skip
67
- const cnt = dataView.getUint16(offset, le);
61
+ const cnt = dataView.getUint16(offset, true);
68
62
  offset += 2;
69
63
  if (isLeaf === 1) {
70
64
  const blocksToFetch2 = [];
71
65
  for (let i = 0; i < cnt; i++) {
72
- const startChrom = dataView.getUint32(offset, le);
66
+ const startChrom = dataView.getUint32(offset, true);
73
67
  offset += 4;
74
- const startBase = dataView.getUint32(offset, le);
68
+ const startBase = dataView.getUint32(offset, true);
75
69
  offset += 4;
76
- const endChrom = dataView.getUint32(offset, le);
70
+ const endChrom = dataView.getUint32(offset, true);
77
71
  offset += 4;
78
- const endBase = dataView.getUint32(offset, le);
72
+ const endBase = dataView.getUint32(offset, true);
79
73
  offset += 4;
80
- const blockOffset = Number(dataView.getBigUint64(offset, le));
74
+ const blockOffset = Number(dataView.getBigUint64(offset, true));
81
75
  offset += 8;
82
- const blockSize = Number(dataView.getBigUint64(offset, le));
76
+ const blockSize = Number(dataView.getBigUint64(offset, true));
83
77
  offset += 8;
84
78
  blocksToFetch2.push({
85
79
  startChrom,
@@ -101,15 +95,15 @@ export class BlockView {
101
95
  else if (isLeaf === 0) {
102
96
  const recurOffsets = [];
103
97
  for (let i = 0; i < cnt; i++) {
104
- const startChrom = dataView.getUint32(offset, le);
98
+ const startChrom = dataView.getUint32(offset, true);
105
99
  offset += 4;
106
- const startBase = dataView.getUint32(offset, le);
100
+ const startBase = dataView.getUint32(offset, true);
107
101
  offset += 4;
108
- const endChrom = dataView.getUint32(offset, le);
102
+ const endChrom = dataView.getUint32(offset, true);
109
103
  offset += 4;
110
- const endBase = dataView.getUint32(offset, le);
104
+ const endBase = dataView.getUint32(offset, true);
111
105
  offset += 4;
112
- const blockOffset = Number(dataView.getBigUint64(offset, le));
106
+ const blockOffset = Number(dataView.getBigUint64(offset, true));
113
107
  offset += 8;
114
108
  recurOffsets.push({
115
109
  startChrom,
@@ -141,7 +135,7 @@ export class BlockView {
141
135
  try {
142
136
  const length = fr.max - fr.min;
143
137
  const offset = fr.min;
144
- const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, opts === null || opts === void 0 ? void 0 : opts.signal);
138
+ const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, opts?.signal);
145
139
  for (const element of off) {
146
140
  if (fr.contains(element)) {
147
141
  cirFobRecur2(resultBuffer, element - offset, level);
@@ -150,7 +144,9 @@ export class BlockView {
150
144
  this.readFeatures(observer, blocksToFetch, {
151
145
  ...opts,
152
146
  request,
153
- }).catch(e => observer.error(e));
147
+ }).catch((e) => {
148
+ observer.error(e);
149
+ });
154
150
  }
155
151
  }
156
152
  }
@@ -186,7 +182,8 @@ export class BlockView {
186
182
  observer.error(e);
187
183
  }
188
184
  };
189
- return cirFobRecur([Number(cirTreeOffset) + 48], 1);
185
+ cirFobRecur([Number(cirTreeOffset) + 48], 1);
186
+ return;
190
187
  }
191
188
  catch (e) {
192
189
  observer.error(e);
@@ -235,16 +232,15 @@ export class BlockView {
235
232
  parseBigBedBlock(data, startOffset, offset, request) {
236
233
  const items = [];
237
234
  let currOffset = startOffset;
238
- const le = true;
239
235
  const b = data;
240
236
  const dataView = new DataView(b.buffer, b.byteOffset, b.length);
241
237
  while (currOffset < data.byteLength) {
242
238
  const c2 = currOffset;
243
- const chromId = dataView.getUint32(currOffset, le);
239
+ const chromId = dataView.getUint32(currOffset, true);
244
240
  currOffset += 4;
245
- const start = dataView.getInt32(currOffset, le);
241
+ const start = dataView.getInt32(currOffset, true);
246
242
  currOffset += 4;
247
- const end = dataView.getInt32(currOffset, le);
243
+ const end = dataView.getInt32(currOffset, true);
248
244
  currOffset += 4;
249
245
  let i = currOffset;
250
246
  for (; i < data.length; i++) {
@@ -252,7 +248,8 @@ export class BlockView {
252
248
  break;
253
249
  }
254
250
  }
255
- const rest = data.subarray(currOffset, i).toString();
251
+ const b = data.subarray(currOffset, i);
252
+ const rest = decoder?.decode(b) ?? b.toString();
256
253
  currOffset = i + 1;
257
254
  items.push({
258
255
  chromId,
@@ -343,24 +340,22 @@ export class BlockView {
343
340
  const data = await this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
344
341
  for (const block of blockGroup.blocks) {
345
342
  checkAbortSignal(signal);
346
- let blockOffset = Number(block.offset) - Number(blockGroup.offset);
347
- let resultData = data;
343
+ let resultData = data.subarray(Number(block.offset) - Number(blockGroup.offset));
348
344
  if (isCompressed) {
349
- resultData = unzip(data.subarray(blockOffset));
350
- blockOffset = 0;
345
+ resultData = unzip(resultData);
351
346
  }
352
347
  checkAbortSignal(signal);
353
348
  switch (blockType) {
354
349
  case 'summary': {
355
- observer.next(this.parseSummaryBlock(resultData, blockOffset, request));
350
+ observer.next(this.parseSummaryBlock(resultData, 0, request));
356
351
  break;
357
352
  }
358
353
  case 'bigwig': {
359
- observer.next(this.parseBigWigBlock(resultData, blockOffset, request));
354
+ observer.next(this.parseBigWigBlock(resultData, 0, request));
360
355
  break;
361
356
  }
362
357
  case 'bigbed': {
363
- observer.next(this.parseBigBedBlock(resultData, blockOffset, Number(block.offset) * (1 << 8), request));
358
+ observer.next(this.parseBigBedBlock(resultData, 0, Number(block.offset) * (1 << 8), request));
364
359
  break;
365
360
  }
366
361
  default: {
package/esm/block-view.js.map CHANGED
@@ -1 +1 @@
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- 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package/esm/unzip-pako.d.ts CHANGED
@@ -1,2 +1 @@
1
- import { Buffer } from 'buffer';
2
- export declare function unzip(input: Buffer): Uint8Array;
1
+ export declare function unzip(input: Uint8Array): Uint8Array;
package/esm/unzip-pako.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AAEjC,MAAM,UAAU,KAAK,CAAC,KAAa;IACjC,OAAO,UAAU,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC"}
1
+ {"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AAEjC,MAAM,UAAU,KAAK,CAAC,KAAiB;IACrC,OAAO,UAAU,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bbi",
3
- "version": "5.0.1",
3
+ "version": "6.0.0",
4
4
  "description": "Parser for BigWig/BigBed files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bbi-js",
@@ -20,16 +20,15 @@
20
20
  "src"
21
21
  ],
22
22
  "scripts": {
23
- "test": "jest",
24
- "coverage": "npm test -- --coverage",
23
+ "test": "vitest",
25
24
  "lint": "eslint --report-unused-disable-directives --max-warnings 0 src",
26
25
  "format": "prettier",
27
26
  "clean": "rimraf dist esm",
28
27
  "prebuild": "npm run clean",
29
- "build:esm": "tsc --target es2018 --outDir esm --module es2020",
30
- "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
28
+ "build:esm": "tsc --outDir esm",
29
+ "build:es5": "tsc --module commonjs --outDir dist",
31
30
  "build": "npm run build:esm && npm run build:es5",
32
- "preversion": "npm run lint && npm test && npm run build",
31
+ "preversion": "npm run lint && npm test run && npm run build",
33
32
  "version": "standard-changelog && git add CHANGELOG.md",
34
33
  "postversion": "git push origin master --follow-tags"
35
34
  },
@@ -43,29 +42,26 @@
43
42
  ],
44
43
  "dependencies": {
45
44
  "@gmod/abortable-promise-cache": "^2.0.0",
46
- "generic-filehandle": "^3.0.0",
45
+ "generic-filehandle2": "^0.0.1",
47
46
  "pako": "^2.0.0",
48
47
  "quick-lru": "^4.0.0",
49
48
  "rxjs": "^7.8.0"
50
49
  },
51
50
  "devDependencies": {
52
51
  "@gmod/bed": "^2.1.2",
53
- "@types/jest": "^29.5.12",
54
52
  "@types/node": "^20.11.16",
55
53
  "@types/pako": "^2.0.0",
56
- "@typescript-eslint/eslint-plugin": "^8.0.1",
57
- "@typescript-eslint/parser": "^8.0.1",
58
- "eslint": "^9.0.0",
59
- "eslint-config-prettier": "^9.1.0",
60
- "eslint-plugin-prettier": "^5.1.3",
61
- "eslint-plugin-unicorn": "^55.0.0",
62
- "jest": "^29.6.2",
63
- "jest-environment-jsdom": "^29.6.2",
54
+ "@typescript-eslint/eslint-plugin": "^8.4.0",
55
+ "@typescript-eslint/parser": "^8.4.0",
56
+ "@vitest/coverage-v8": "^2.0.5",
57
+ "eslint": "^9.9.1",
58
+ "eslint-plugin-unicorn": "^56.0.0",
64
59
  "prettier": "^3.2.5",
65
60
  "rimraf": "^6.0.1",
66
61
  "standard-changelog": "^6.0.0",
67
- "ts-jest": "^29.1.2",
68
- "typescript": "^5.1.6"
62
+ "typescript": "^5.1.6",
63
+ "typescript-eslint": "^8.4.0",
64
+ "vitest": "^2.0.5"
69
65
  },
70
66
  "publishConfig": {
71
67
  "access": "public"