@jbrowse/plugin-bed 2.10.3 → 2.11.0

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Files changed (15) hide show
  1. package/dist/BedAdapter/BedAdapter.js +2 -1
  2. package/dist/BigBedAdapter/BigBedAdapter.d.ts +4 -4
  3. package/dist/BigBedAdapter/BigBedAdapter.js +52 -41
  4. package/dist/BigBedAdapter/configSchema.d.ts +8 -0
  5. package/dist/BigBedAdapter/configSchema.js +8 -0
  6. package/dist/util.d.ts +46 -3
  7. package/dist/util.js +84 -73
  8. package/esm/BedAdapter/BedAdapter.js +2 -1
  9. package/esm/BigBedAdapter/BigBedAdapter.d.ts +4 -4
  10. package/esm/BigBedAdapter/BigBedAdapter.js +53 -42
  11. package/esm/BigBedAdapter/configSchema.d.ts +8 -0
  12. package/esm/BigBedAdapter/configSchema.js +8 -0
  13. package/esm/util.d.ts +46 -3
  14. package/esm/util.js +81 -72
  15. package/package.json +2 -2
package/dist/BedAdapter/BedAdapter.js CHANGED
@@ -7,9 +7,10 @@ const bed_1 = __importDefault(require("@gmod/bed"));
7
7
  const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
8
8
  const io_1 = require("@jbrowse/core/util/io");
9
9
  const rxjs_1 = require("@jbrowse/core/util/rxjs");
10
- const util_1 = require("../util");
11
10
  const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
12
11
  const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
12
+ // locals
13
+ const util_1 = require("../util");
13
14
  function isGzip(buf) {
14
15
  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
15
16
  }
package/dist/BigBedAdapter/BigBedAdapter.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import { BigBed } from '@gmod/bbi';
1
+ import { BigBed, Header } from '@gmod/bbi';
2
2
  import BED from '@gmod/bed';
3
3
  import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
4
4
  import { Region } from '@jbrowse/core/util/types';
@@ -7,18 +7,18 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
7
7
  private cached?;
8
8
  configurePre(opts?: BaseOptions): Promise<{
9
9
  bigbed: BigBed;
10
- header: import("@gmod/bbi").Header;
10
+ header: Header;
11
11
  parser: BED;
12
12
  }>;
13
13
  configure(opts?: BaseOptions): Promise<{
14
14
  bigbed: BigBed;
15
- header: any;
15
+ header: Header;
16
16
  parser: BED;
17
17
  }>;
18
18
  getRefNames(opts?: BaseOptions): Promise<string[]>;
19
19
  getHeader(opts?: BaseOptions): Promise<{
20
20
  version: any;
21
- fileType: any;
21
+ fileType: string;
22
22
  autoSql: {};
23
23
  fields: {
24
24
  [k: string]: string;
package/dist/BigBedAdapter/BigBedAdapter.js CHANGED
@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
- /* eslint-disable @typescript-eslint/no-explicit-any */
7
6
  const bbi_1 = require("@gmod/bbi");
8
7
  const bed_1 = __importDefault(require("@gmod/bed"));
9
8
  const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
@@ -11,10 +10,8 @@ const io_1 = require("@jbrowse/core/util/io");
11
10
  const rxjs_1 = require("@jbrowse/core/util/rxjs");
12
11
  const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
13
12
  const operators_1 = require("rxjs/operators");
13
+ // locals
14
14
  const util_1 = require("../util");
15
- function isUCSC(f) {
16
- return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0;
17
- }
18
15
  class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
19
16
  async configurePre(opts) {
20
17
  const pm = this.pluginManager;
@@ -40,6 +37,7 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
40
37
  }
41
38
  async getHeader(opts) {
42
39
  const { parser, header } = await this.configure(opts);
40
+ // @ts-expect-error
43
41
  const { version, fileType } = header;
44
42
  const { fields, ...rest } = parser.autoSql;
45
43
  return {
@@ -50,53 +48,66 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
50
48
  };
51
49
  }
52
50
  getFeatures(region, opts = {}) {
53
- const { refName, start, end } = region;
54
51
  const { signal } = opts;
52
+ const scoreColumn = this.getConf('scoreColumn');
55
53
  return (0, rxjs_1.ObservableCreate)(async (observer) => {
56
54
  try {
57
55
  const { parser, bigbed } = await this.configure(opts);
58
- const ob = await bigbed.getFeatureStream(refName, start, end, {
56
+ const ob = await bigbed.getFeatureStream(region.refName, region.start, region.end, {
59
57
  signal,
60
- basesPerSpan: end - start,
58
+ basesPerSpan: region.end - region.start,
61
59
  });
62
- ob.pipe((0, operators_1.mergeAll)(), (0, operators_1.map)(r => {
63
- const data = parser.parseLine(`${refName}\t${r.start}\t${r.end}\t${r.rest}`, {
64
- uniqueId: r.uniqueId,
60
+ ob.pipe((0, operators_1.mergeAll)(), (0, operators_1.map)(feat => {
61
+ const data = parser.parseLine(`${region.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`, {
62
+ uniqueId: feat.uniqueId,
65
63
  });
66
- const { blockCount, blockSizes, blockStarts, chromStarts } = data;
67
- if (blockCount) {
68
- const starts = chromStarts || blockStarts || [];
69
- const sizes = blockSizes;
70
- const blocksOffset = r.start;
71
- data.subfeatures = [];
72
- for (let b = 0; b < blockCount; b += 1) {
73
- const bmin = (starts[b] || 0) + blocksOffset;
74
- const bmax = bmin + (sizes[b] || 0);
75
- data.subfeatures.push({
76
- uniqueId: `${r.uniqueId}-${b}`,
77
- start: bmin,
78
- end: bmax,
79
- type: 'block',
80
- });
81
- }
82
- }
83
- if (r.uniqueId === undefined) {
64
+ if (feat.uniqueId === undefined) {
84
65
  throw new Error('invalid bbi feature');
85
66
  }
86
- const { chromStart, chromEnd, chrom, ...rest } = data;
87
- const f = new simpleFeature_1.default({
88
- id: `${this.id}-${r.uniqueId}`,
89
- data: {
90
- ...rest,
91
- start: r.start,
92
- end: r.end,
93
- refName,
94
- },
67
+ const { uniqueId, type, chromStart, chromStarts, blockStarts, blockCount, blockSizes, chromEnd, thickStart, thickEnd, chrom, score, ...rest } = data;
68
+ const subfeatures = blockCount
69
+ ? (0, util_1.makeBlocks)({
70
+ chromStarts,
71
+ blockStarts,
72
+ blockCount,
73
+ blockSizes,
74
+ uniqueId,
75
+ refName: region.refName,
76
+ start: feat.start,
77
+ })
78
+ : [];
79
+ // collection of heuristics for suggesting that this feature should
80
+ // be converted to a gene, CNV bigbed has many gene like features
81
+ // including thickStart and blockCount but no strand
82
+ return new simpleFeature_1.default({
83
+ id: `${this.id}-${uniqueId}`,
84
+ data: (0, util_1.isUCSC)(data)
85
+ ? (0, util_1.ucscProcessedTranscript)({
86
+ ...rest,
87
+ uniqueId,
88
+ type,
89
+ start: feat.start,
90
+ end: feat.end,
91
+ refName: region.refName,
92
+ score: scoreColumn ? +data[scoreColumn] : score,
93
+ chromStarts,
94
+ blockCount,
95
+ blockSizes,
96
+ thickStart,
97
+ thickEnd,
98
+ subfeatures,
99
+ })
100
+ : {
101
+ ...rest,
102
+ uniqueId,
103
+ type,
104
+ start: feat.start,
105
+ score: scoreColumn ? +data[scoreColumn] : score,
106
+ end: feat.end,
107
+ refName: region.refName,
108
+ subfeatures,
109
+ },
95
110
  });
96
- // collection of heuristics for suggesting that this feature
97
- // should be converted to a gene, CNV bigbed has many gene like
98
- // features including thickStart and blockCount but no strand
99
- return isUCSC(f) ? (0, util_1.ucscProcessedTranscript)(f) : f;
100
111
  })).subscribe(observer);
101
112
  }
102
113
  catch (e) {
package/dist/BigBedAdapter/configSchema.d.ts CHANGED
@@ -9,5 +9,13 @@ declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSc
9
9
  locationType: string;
10
10
  };
11
11
  };
12
+ /**
13
+ * #slot
14
+ */
15
+ scoreColumn: {
16
+ type: string;
17
+ description: string;
18
+ defaultValue: string;
19
+ };
12
20
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
13
21
  export default BigBedAdapter;
package/dist/BigBedAdapter/configSchema.js CHANGED
@@ -13,5 +13,13 @@ const BigBedAdapter = (0, configuration_1.ConfigurationSchema)('BigBedAdapter',
13
13
  type: 'fileLocation',
14
14
  defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
15
15
  },
16
+ /**
17
+ * #slot
18
+ */
19
+ scoreColumn: {
20
+ type: 'string',
21
+ description: 'The column to use as a "score" attribute',
22
+ defaultValue: '',
23
+ },
16
24
  }, { explicitlyTyped: true });
17
25
  exports.default = BigBedAdapter;
package/dist/util.d.ts CHANGED
@@ -1,4 +1,47 @@
1
- import { SimpleFeature, Feature } from '@jbrowse/core/util';
2
1
  import BED from '@gmod/bed';
3
- export declare function ucscProcessedTranscript(feature: Feature): Feature | SimpleFeature;
4
- export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): Feature | SimpleFeature;
2
+ import { SimpleFeature } from '@jbrowse/core/util';
3
+ interface MinimalFeature {
4
+ type: string;
5
+ start: number;
6
+ end: number;
7
+ refName: string;
8
+ }
9
+ interface TranscriptFeat {
10
+ thickStart: number;
11
+ thickEnd: number;
12
+ blockCount: number;
13
+ blockSizes: number[];
14
+ chromStarts: number[];
15
+ refName: string;
16
+ strand?: number;
17
+ subfeatures: MinimalFeature[];
18
+ [key: string]: unknown;
19
+ }
20
+ export declare function ucscProcessedTranscript(feature: TranscriptFeat): TranscriptFeat | {
21
+ strand: number;
22
+ type: string;
23
+ refName: string;
24
+ subfeatures: MinimalFeature[];
25
+ };
26
+ export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
27
+ blockCount: number;
28
+ start: number;
29
+ uniqueId: string;
30
+ refName: string;
31
+ chromStarts: number[];
32
+ blockSizes: number[];
33
+ blockStarts: number[];
34
+ }): {
35
+ uniqueId: string;
36
+ start: number;
37
+ end: number;
38
+ refName: string;
39
+ type: string;
40
+ }[];
41
+ export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): SimpleFeature;
42
+ export declare function isUCSC(f: {
43
+ thickStart?: number;
44
+ blockCount?: number;
45
+ strand?: number;
46
+ }): boolean | 0 | undefined;
47
+ export {};
package/dist/util.js CHANGED
@@ -1,29 +1,23 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.featureData = exports.ucscProcessedTranscript = void 0;
3
+ exports.isUCSC = exports.featureData = exports.makeBlocks = exports.ucscProcessedTranscript = void 0;
4
4
  const util_1 = require("@jbrowse/core/util");
5
5
  function ucscProcessedTranscript(feature) {
6
- const children = feature.children();
7
- // split the blocks into UTR, CDS, and exons
8
- const thickStart = feature.get('thickStart');
9
- const thickEnd = feature.get('thickEnd');
10
- const refName = feature.get('refName');
11
- if (!thickStart && !thickEnd) {
6
+ var _a;
7
+ const { subfeatures: oldSubfeatures, thickStart, thickEnd, blockCount, blockSizes, chromStarts, refName, strand = 0, ...rest } = feature;
8
+ if (!thickStart || !thickEnd || !strand) {
12
9
  return feature;
13
10
  }
14
- const blocks = children
15
- ? children
16
- .filter(child => child.get('type') === 'block')
17
- .sort((a, b) => a.get('start') - b.get('start'))
18
- : [];
19
- const newChildren = [];
20
- blocks.forEach(block => {
21
- const start = block.get('start');
22
- const end = block.get('end');
11
+ const subfeatures = [];
12
+ (_a = oldSubfeatures
13
+ .filter(child => child.type === 'block')
14
+ .sort((a, b) => a.start - b.start)) === null || _a === void 0 ? void 0 : _a.forEach(block => {
15
+ const start = block.start;
16
+ const end = block.end;
23
17
  if (thickStart >= end) {
24
18
  // left-side UTR
25
- const prime = feature.get('strand') > 0 ? 'five' : 'three';
26
- newChildren.push({
19
+ const prime = strand > 0 ? 'five' : 'three';
20
+ subfeatures.push({
27
21
  type: `${prime}_prime_UTR`,
28
22
  start,
29
23
  end,
@@ -32,8 +26,8 @@ function ucscProcessedTranscript(feature) {
32
26
  }
33
27
  else if (thickStart > start && thickStart < end && thickEnd >= end) {
34
28
  // UTR | CDS
35
- const prime = feature.get('strand') > 0 ? 'five' : 'three';
36
- newChildren.push({
29
+ const prime = strand > 0 ? 'five' : 'three';
30
+ subfeatures.push({
37
31
  type: `${prime}_prime_UTR`,
38
32
  start,
39
33
  end: thickStart,
@@ -47,7 +41,7 @@ function ucscProcessedTranscript(feature) {
47
41
  }
48
42
  else if (thickStart <= start && thickEnd >= end) {
49
43
  // CDS
50
- newChildren.push({
44
+ subfeatures.push({
51
45
  type: 'CDS',
52
46
  start,
53
47
  end,
@@ -56,9 +50,9 @@ function ucscProcessedTranscript(feature) {
56
50
  }
57
51
  else if (thickStart > start && thickStart < end && thickEnd < end) {
58
52
  // UTR | CDS | UTR
59
- const leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
60
- const rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
61
- newChildren.push({
53
+ const leftPrime = strand > 0 ? 'five' : 'three';
54
+ const rightPrime = strand > 0 ? 'three' : 'five';
55
+ subfeatures.push({
62
56
  type: `${leftPrime}_prime_UTR`,
63
57
  start,
64
58
  end: thickStart,
@@ -77,8 +71,8 @@ function ucscProcessedTranscript(feature) {
77
71
  }
78
72
  else if (thickStart <= start && thickEnd > start && thickEnd < end) {
79
73
  // CDS | UTR
80
- const prime = feature.get('strand') > 0 ? 'three' : 'five';
81
- newChildren.push({
74
+ const prime = strand > 0 ? 'three' : 'five';
75
+ subfeatures.push({
82
76
  type: `CDS`,
83
77
  start,
84
78
  end: thickEnd,
@@ -92,8 +86,8 @@ function ucscProcessedTranscript(feature) {
92
86
  }
93
87
  else if (thickEnd <= start) {
94
88
  // right-side UTR
95
- const prime = feature.get('strand') > 0 ? 'three' : 'five';
96
- newChildren.push({
89
+ const prime = strand > 0 ? 'three' : 'five';
90
+ subfeatures.push({
97
91
  type: `${prime}_prime_UTR`,
98
92
  start,
99
93
  end,
@@ -101,28 +95,38 @@ function ucscProcessedTranscript(feature) {
101
95
  });
102
96
  }
103
97
  });
104
- const newData = Object.fromEntries(feature.tags().map(tag => [tag, feature.get(tag)]));
105
- newData.subfeatures = newChildren;
106
- newData.type = 'mRNA';
107
- newData.uniqueId = feature.id();
108
- delete newData.chromStarts;
109
- delete newData.chromStart;
110
- delete newData.chromEnd;
111
- delete newData.chrom;
112
- delete newData.blockStarts;
113
- delete newData.blockSizes;
114
- delete newData.blockCount;
115
- delete newData.thickStart;
116
- delete newData.thickEnd;
117
- return new util_1.SimpleFeature({
118
- data: newData,
119
- id: feature.id(),
120
- });
98
+ return { ...rest, strand, type: 'mRNA', refName, subfeatures };
121
99
  }
122
100
  exports.ucscProcessedTranscript = ucscProcessedTranscript;
123
101
  function defaultParser(fields, line) {
124
- return Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
102
+ const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
103
+ return {
104
+ ...rest,
105
+ blockStarts: blockStarts === null || blockStarts === void 0 ? void 0 : blockStarts.split(',').map(r => +r),
106
+ chromStarts: chromStarts === null || chromStarts === void 0 ? void 0 : chromStarts.split(',').map(r => +r),
107
+ blockSizes: blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes.split(',').map(r => +r),
108
+ thickStart: +thickStart,
109
+ thickEnd: +thickEnd,
110
+ blockCount: +blockCount,
111
+ };
125
112
  }
113
+ function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }) {
114
+ const subfeatures = [];
115
+ const starts = chromStarts || blockStarts || [];
116
+ for (let b = 0; b < blockCount; b++) {
117
+ const bmin = (starts[b] || 0) + start;
118
+ const bmax = bmin + ((blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes[b]) || 0);
119
+ subfeatures.push({
120
+ uniqueId: `${uniqueId}-${b}`,
121
+ start: bmin,
122
+ end: bmax,
123
+ refName,
124
+ type: 'block',
125
+ });
126
+ }
127
+ return subfeatures;
128
+ }
129
+ exports.makeBlocks = makeBlocks;
126
130
  function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names) {
127
131
  const l = line.split('\t');
128
132
  const refName = l[colRef];
@@ -132,37 +136,44 @@ function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, unique
132
136
  const data = names
133
137
  ? defaultParser(names, line)
134
138
  : parser.parseLine(line, { uniqueId });
135
- const { blockCount, blockSizes, blockStarts, chromStarts } = data;
136
- if (blockCount) {
137
- const starts = chromStarts || blockStarts || [];
138
- const sizes = blockSizes;
139
- const blocksOffset = start;
140
- data.subfeatures = [];
141
- for (let b = 0; b < blockCount; b += 1) {
142
- const bmin = (starts[b] || 0) + blocksOffset;
143
- const bmax = bmin + (sizes[b] || 0);
144
- data.subfeatures.push({
145
- uniqueId: `${uniqueId}-${b}`,
146
- start: bmin,
147
- end: bmax,
148
- refName,
149
- type: 'block',
150
- });
151
- }
152
- }
153
- if (scoreColumn) {
154
- data.score = +data[scoreColumn];
155
- }
156
- delete data.chrom;
157
- delete data.chromStart;
158
- delete data.chromEnd;
159
- const f = new util_1.SimpleFeature({
160
- ...data,
139
+ const { blockCount, blockSizes, blockStarts, chromStarts, thickStart, thickEnd, type, score, chrom: _1, chromStart: _2, chromEnd: _3, ...rest } = data;
140
+ const subfeatures = blockCount
141
+ ? makeBlocks({
142
+ start,
143
+ uniqueId,
144
+ refName,
145
+ chromStarts,
146
+ blockCount,
147
+ blockSizes,
148
+ blockStarts,
149
+ })
150
+ : [];
151
+ const f = {
152
+ ...rest,
153
+ type,
154
+ score: scoreColumn ? +data[scoreColumn] : score,
161
155
  start,
162
156
  end,
163
157
  refName,
164
158
  uniqueId,
159
+ subfeatures,
160
+ };
161
+ return new util_1.SimpleFeature({
162
+ id: uniqueId,
163
+ data: isUCSC(data)
164
+ ? ucscProcessedTranscript({
165
+ thickStart,
166
+ thickEnd,
167
+ blockCount,
168
+ blockSizes,
169
+ chromStarts,
170
+ ...f,
171
+ })
172
+ : f,
165
173
  });
166
- return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
167
174
  }
168
175
  exports.featureData = featureData;
176
+ function isUCSC(f) {
177
+ return f.thickStart && f.blockCount && f.strand !== 0;
178
+ }
179
+ exports.isUCSC = isUCSC;
package/esm/BedAdapter/BedAdapter.js CHANGED
@@ -2,9 +2,10 @@ import BED from '@gmod/bed';
2
2
  import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
3
3
  import { openLocation } from '@jbrowse/core/util/io';
4
4
  import { ObservableCreate } from '@jbrowse/core/util/rxjs';
5
- import { featureData } from '../util';
6
5
  import IntervalTree from '@flatten-js/interval-tree';
7
6
  import { unzip } from '@gmod/bgzf-filehandle';
7
+ // locals
8
+ import { featureData } from '../util';
8
9
  function isGzip(buf) {
9
10
  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
10
11
  }
package/esm/BigBedAdapter/BigBedAdapter.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import { BigBed } from '@gmod/bbi';
1
+ import { BigBed, Header } from '@gmod/bbi';
2
2
  import BED from '@gmod/bed';
3
3
  import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
4
4
  import { Region } from '@jbrowse/core/util/types';
@@ -7,18 +7,18 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
7
7
  private cached?;
8
8
  configurePre(opts?: BaseOptions): Promise<{
9
9
  bigbed: BigBed;
10
- header: import("@gmod/bbi").Header;
10
+ header: Header;
11
11
  parser: BED;
12
12
  }>;
13
13
  configure(opts?: BaseOptions): Promise<{
14
14
  bigbed: BigBed;
15
- header: any;
15
+ header: Header;
16
16
  parser: BED;
17
17
  }>;
18
18
  getRefNames(opts?: BaseOptions): Promise<string[]>;
19
19
  getHeader(opts?: BaseOptions): Promise<{
20
20
  version: any;
21
- fileType: any;
21
+ fileType: string;
22
22
  autoSql: {};
23
23
  fields: {
24
24
  [k: string]: string;
package/esm/BigBedAdapter/BigBedAdapter.js CHANGED
@@ -1,4 +1,3 @@
1
- /* eslint-disable @typescript-eslint/no-explicit-any */
2
1
  import { BigBed } from '@gmod/bbi';
3
2
  import BED from '@gmod/bed';
4
3
  import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
@@ -6,10 +5,8 @@ import { openLocation } from '@jbrowse/core/util/io';
6
5
  import { ObservableCreate } from '@jbrowse/core/util/rxjs';
7
6
  import SimpleFeature from '@jbrowse/core/util/simpleFeature';
8
7
  import { map, mergeAll } from 'rxjs/operators';
9
- import { ucscProcessedTranscript } from '../util';
10
- function isUCSC(f) {
11
- return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0;
12
- }
8
+ // locals
9
+ import { isUCSC, makeBlocks, ucscProcessedTranscript } from '../util';
13
10
  export default class BigBedAdapter extends BaseFeatureDataAdapter {
14
11
  async configurePre(opts) {
15
12
  const pm = this.pluginManager;
@@ -35,6 +32,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
35
32
  }
36
33
  async getHeader(opts) {
37
34
  const { parser, header } = await this.configure(opts);
35
+ // @ts-expect-error
38
36
  const { version, fileType } = header;
39
37
  const { fields, ...rest } = parser.autoSql;
40
38
  return {
@@ -45,53 +43,66 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
45
43
  };
46
44
  }
47
45
  getFeatures(region, opts = {}) {
48
- const { refName, start, end } = region;
49
46
  const { signal } = opts;
47
+ const scoreColumn = this.getConf('scoreColumn');
50
48
  return ObservableCreate(async (observer) => {
51
49
  try {
52
50
  const { parser, bigbed } = await this.configure(opts);
53
- const ob = await bigbed.getFeatureStream(refName, start, end, {
51
+ const ob = await bigbed.getFeatureStream(region.refName, region.start, region.end, {
54
52
  signal,
55
- basesPerSpan: end - start,
53
+ basesPerSpan: region.end - region.start,
56
54
  });
57
- ob.pipe(mergeAll(), map(r => {
58
- const data = parser.parseLine(`${refName}\t${r.start}\t${r.end}\t${r.rest}`, {
59
- uniqueId: r.uniqueId,
55
+ ob.pipe(mergeAll(), map(feat => {
56
+ const data = parser.parseLine(`${region.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`, {
57
+ uniqueId: feat.uniqueId,
60
58
  });
61
- const { blockCount, blockSizes, blockStarts, chromStarts } = data;
62
- if (blockCount) {
63
- const starts = chromStarts || blockStarts || [];
64
- const sizes = blockSizes;
65
- const blocksOffset = r.start;
66
- data.subfeatures = [];
67
- for (let b = 0; b < blockCount; b += 1) {
68
- const bmin = (starts[b] || 0) + blocksOffset;
69
- const bmax = bmin + (sizes[b] || 0);
70
- data.subfeatures.push({
71
- uniqueId: `${r.uniqueId}-${b}`,
72
- start: bmin,
73
- end: bmax,
74
- type: 'block',
75
- });
76
- }
77
- }
78
- if (r.uniqueId === undefined) {
59
+ if (feat.uniqueId === undefined) {
79
60
  throw new Error('invalid bbi feature');
80
61
  }
81
- const { chromStart, chromEnd, chrom, ...rest } = data;
82
- const f = new SimpleFeature({
83
- id: `${this.id}-${r.uniqueId}`,
84
- data: {
85
- ...rest,
86
- start: r.start,
87
- end: r.end,
88
- refName,
89
- },
62
+ const { uniqueId, type, chromStart, chromStarts, blockStarts, blockCount, blockSizes, chromEnd, thickStart, thickEnd, chrom, score, ...rest } = data;
63
+ const subfeatures = blockCount
64
+ ? makeBlocks({
65
+ chromStarts,
66
+ blockStarts,
67
+ blockCount,
68
+ blockSizes,
69
+ uniqueId,
70
+ refName: region.refName,
71
+ start: feat.start,
72
+ })
73
+ : [];
74
+ // collection of heuristics for suggesting that this feature should
75
+ // be converted to a gene, CNV bigbed has many gene like features
76
+ // including thickStart and blockCount but no strand
77
+ return new SimpleFeature({
78
+ id: `${this.id}-${uniqueId}`,
79
+ data: isUCSC(data)
80
+ ? ucscProcessedTranscript({
81
+ ...rest,
82
+ uniqueId,
83
+ type,
84
+ start: feat.start,
85
+ end: feat.end,
86
+ refName: region.refName,
87
+ score: scoreColumn ? +data[scoreColumn] : score,
88
+ chromStarts,
89
+ blockCount,
90
+ blockSizes,
91
+ thickStart,
92
+ thickEnd,
93
+ subfeatures,
94
+ })
95
+ : {
96
+ ...rest,
97
+ uniqueId,
98
+ type,
99
+ start: feat.start,
100
+ score: scoreColumn ? +data[scoreColumn] : score,
101
+ end: feat.end,
102
+ refName: region.refName,
103
+ subfeatures,
104
+ },
90
105
  });
91
- // collection of heuristics for suggesting that this feature
92
- // should be converted to a gene, CNV bigbed has many gene like
93
- // features including thickStart and blockCount but no strand
94
- return isUCSC(f) ? ucscProcessedTranscript(f) : f;
95
106
  })).subscribe(observer);
96
107
  }
97
108
  catch (e) {
package/esm/BigBedAdapter/configSchema.d.ts CHANGED
@@ -9,5 +9,13 @@ declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSc
9
9
  locationType: string;
10
10
  };
11
11
  };
12
+ /**
13
+ * #slot
14
+ */
15
+ scoreColumn: {
16
+ type: string;
17
+ description: string;
18
+ defaultValue: string;
19
+ };
12
20
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
13
21
  export default BigBedAdapter;
package/esm/BigBedAdapter/configSchema.js CHANGED
@@ -11,5 +11,13 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
11
11
  type: 'fileLocation',
12
12
  defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
13
13
  },
14
+ /**
15
+ * #slot
16
+ */
17
+ scoreColumn: {
18
+ type: 'string',
19
+ description: 'The column to use as a "score" attribute',
20
+ defaultValue: '',
21
+ },
14
22
  }, { explicitlyTyped: true });
15
23
  export default BigBedAdapter;
package/esm/util.d.ts CHANGED
@@ -1,4 +1,47 @@
1
- import { SimpleFeature, Feature } from '@jbrowse/core/util';
2
1
  import BED from '@gmod/bed';
3
- export declare function ucscProcessedTranscript(feature: Feature): Feature | SimpleFeature;
4
- export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): Feature | SimpleFeature;
2
+ import { SimpleFeature } from '@jbrowse/core/util';
3
+ interface MinimalFeature {
4
+ type: string;
5
+ start: number;
6
+ end: number;
7
+ refName: string;
8
+ }
9
+ interface TranscriptFeat {
10
+ thickStart: number;
11
+ thickEnd: number;
12
+ blockCount: number;
13
+ blockSizes: number[];
14
+ chromStarts: number[];
15
+ refName: string;
16
+ strand?: number;
17
+ subfeatures: MinimalFeature[];
18
+ [key: string]: unknown;
19
+ }
20
+ export declare function ucscProcessedTranscript(feature: TranscriptFeat): TranscriptFeat | {
21
+ strand: number;
22
+ type: string;
23
+ refName: string;
24
+ subfeatures: MinimalFeature[];
25
+ };
26
+ export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
27
+ blockCount: number;
28
+ start: number;
29
+ uniqueId: string;
30
+ refName: string;
31
+ chromStarts: number[];
32
+ blockSizes: number[];
33
+ blockStarts: number[];
34
+ }): {
35
+ uniqueId: string;
36
+ start: number;
37
+ end: number;
38
+ refName: string;
39
+ type: string;
40
+ }[];
41
+ export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): SimpleFeature;
42
+ export declare function isUCSC(f: {
43
+ thickStart?: number;
44
+ blockCount?: number;
45
+ strand?: number;
46
+ }): boolean | 0 | undefined;
47
+ export {};
package/esm/util.js CHANGED
@@ -1,26 +1,20 @@
1
1
  import { SimpleFeature } from '@jbrowse/core/util';
2
2
  export function ucscProcessedTranscript(feature) {
3
- const children = feature.children();
4
- // split the blocks into UTR, CDS, and exons
5
- const thickStart = feature.get('thickStart');
6
- const thickEnd = feature.get('thickEnd');
7
- const refName = feature.get('refName');
8
- if (!thickStart && !thickEnd) {
3
+ var _a;
4
+ const { subfeatures: oldSubfeatures, thickStart, thickEnd, blockCount, blockSizes, chromStarts, refName, strand = 0, ...rest } = feature;
5
+ if (!thickStart || !thickEnd || !strand) {
9
6
  return feature;
10
7
  }
11
- const blocks = children
12
- ? children
13
- .filter(child => child.get('type') === 'block')
14
- .sort((a, b) => a.get('start') - b.get('start'))
15
- : [];
16
- const newChildren = [];
17
- blocks.forEach(block => {
18
- const start = block.get('start');
19
- const end = block.get('end');
8
+ const subfeatures = [];
9
+ (_a = oldSubfeatures
10
+ .filter(child => child.type === 'block')
11
+ .sort((a, b) => a.start - b.start)) === null || _a === void 0 ? void 0 : _a.forEach(block => {
12
+ const start = block.start;
13
+ const end = block.end;
20
14
  if (thickStart >= end) {
21
15
  // left-side UTR
22
- const prime = feature.get('strand') > 0 ? 'five' : 'three';
23
- newChildren.push({
16
+ const prime = strand > 0 ? 'five' : 'three';
17
+ subfeatures.push({
24
18
  type: `${prime}_prime_UTR`,
25
19
  start,
26
20
  end,
@@ -29,8 +23,8 @@ export function ucscProcessedTranscript(feature) {
29
23
  }
30
24
  else if (thickStart > start && thickStart < end && thickEnd >= end) {
31
25
  // UTR | CDS
32
- const prime = feature.get('strand') > 0 ? 'five' : 'three';
33
- newChildren.push({
26
+ const prime = strand > 0 ? 'five' : 'three';
27
+ subfeatures.push({
34
28
  type: `${prime}_prime_UTR`,
35
29
  start,
36
30
  end: thickStart,
@@ -44,7 +38,7 @@ export function ucscProcessedTranscript(feature) {
44
38
  }
45
39
  else if (thickStart <= start && thickEnd >= end) {
46
40
  // CDS
47
- newChildren.push({
41
+ subfeatures.push({
48
42
  type: 'CDS',
49
43
  start,
50
44
  end,
@@ -53,9 +47,9 @@ export function ucscProcessedTranscript(feature) {
53
47
  }
54
48
  else if (thickStart > start && thickStart < end && thickEnd < end) {
55
49
  // UTR | CDS | UTR
56
- const leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
57
- const rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
58
- newChildren.push({
50
+ const leftPrime = strand > 0 ? 'five' : 'three';
51
+ const rightPrime = strand > 0 ? 'three' : 'five';
52
+ subfeatures.push({
59
53
  type: `${leftPrime}_prime_UTR`,
60
54
  start,
61
55
  end: thickStart,
@@ -74,8 +68,8 @@ export function ucscProcessedTranscript(feature) {
74
68
  }
75
69
  else if (thickStart <= start && thickEnd > start && thickEnd < end) {
76
70
  // CDS | UTR
77
- const prime = feature.get('strand') > 0 ? 'three' : 'five';
78
- newChildren.push({
71
+ const prime = strand > 0 ? 'three' : 'five';
72
+ subfeatures.push({
79
73
  type: `CDS`,
80
74
  start,
81
75
  end: thickEnd,
@@ -89,8 +83,8 @@ export function ucscProcessedTranscript(feature) {
89
83
  }
90
84
  else if (thickEnd <= start) {
91
85
  // right-side UTR
92
- const prime = feature.get('strand') > 0 ? 'three' : 'five';
93
- newChildren.push({
86
+ const prime = strand > 0 ? 'three' : 'five';
87
+ subfeatures.push({
94
88
  type: `${prime}_prime_UTR`,
95
89
  start,
96
90
  end,
@@ -98,26 +92,35 @@ export function ucscProcessedTranscript(feature) {
98
92
  });
99
93
  }
100
94
  });
101
- const newData = Object.fromEntries(feature.tags().map(tag => [tag, feature.get(tag)]));
102
- newData.subfeatures = newChildren;
103
- newData.type = 'mRNA';
104
- newData.uniqueId = feature.id();
105
- delete newData.chromStarts;
106
- delete newData.chromStart;
107
- delete newData.chromEnd;
108
- delete newData.chrom;
109
- delete newData.blockStarts;
110
- delete newData.blockSizes;
111
- delete newData.blockCount;
112
- delete newData.thickStart;
113
- delete newData.thickEnd;
114
- return new SimpleFeature({
115
- data: newData,
116
- id: feature.id(),
117
- });
95
+ return { ...rest, strand, type: 'mRNA', refName, subfeatures };
118
96
  }
119
97
  function defaultParser(fields, line) {
120
- return Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
98
+ const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
99
+ return {
100
+ ...rest,
101
+ blockStarts: blockStarts === null || blockStarts === void 0 ? void 0 : blockStarts.split(',').map(r => +r),
102
+ chromStarts: chromStarts === null || chromStarts === void 0 ? void 0 : chromStarts.split(',').map(r => +r),
103
+ blockSizes: blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes.split(',').map(r => +r),
104
+ thickStart: +thickStart,
105
+ thickEnd: +thickEnd,
106
+ blockCount: +blockCount,
107
+ };
108
+ }
109
+ export function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }) {
110
+ const subfeatures = [];
111
+ const starts = chromStarts || blockStarts || [];
112
+ for (let b = 0; b < blockCount; b++) {
113
+ const bmin = (starts[b] || 0) + start;
114
+ const bmax = bmin + ((blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes[b]) || 0);
115
+ subfeatures.push({
116
+ uniqueId: `${uniqueId}-${b}`,
117
+ start: bmin,
118
+ end: bmax,
119
+ refName,
120
+ type: 'block',
121
+ });
122
+ }
123
+ return subfeatures;
121
124
  }
122
125
  export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names) {
123
126
  const l = line.split('\t');
@@ -128,36 +131,42 @@ export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser,
128
131
  const data = names
129
132
  ? defaultParser(names, line)
130
133
  : parser.parseLine(line, { uniqueId });
131
- const { blockCount, blockSizes, blockStarts, chromStarts } = data;
132
- if (blockCount) {
133
- const starts = chromStarts || blockStarts || [];
134
- const sizes = blockSizes;
135
- const blocksOffset = start;
136
- data.subfeatures = [];
137
- for (let b = 0; b < blockCount; b += 1) {
138
- const bmin = (starts[b] || 0) + blocksOffset;
139
- const bmax = bmin + (sizes[b] || 0);
140
- data.subfeatures.push({
141
- uniqueId: `${uniqueId}-${b}`,
142
- start: bmin,
143
- end: bmax,
144
- refName,
145
- type: 'block',
146
- });
147
- }
148
- }
149
- if (scoreColumn) {
150
- data.score = +data[scoreColumn];
151
- }
152
- delete data.chrom;
153
- delete data.chromStart;
154
- delete data.chromEnd;
155
- const f = new SimpleFeature({
156
- ...data,
134
+ const { blockCount, blockSizes, blockStarts, chromStarts, thickStart, thickEnd, type, score, chrom: _1, chromStart: _2, chromEnd: _3, ...rest } = data;
135
+ const subfeatures = blockCount
136
+ ? makeBlocks({
137
+ start,
138
+ uniqueId,
139
+ refName,
140
+ chromStarts,
141
+ blockCount,
142
+ blockSizes,
143
+ blockStarts,
144
+ })
145
+ : [];
146
+ const f = {
147
+ ...rest,
148
+ type,
149
+ score: scoreColumn ? +data[scoreColumn] : score,
157
150
  start,
158
151
  end,
159
152
  refName,
160
153
  uniqueId,
154
+ subfeatures,
155
+ };
156
+ return new SimpleFeature({
157
+ id: uniqueId,
158
+ data: isUCSC(data)
159
+ ? ucscProcessedTranscript({
160
+ thickStart,
161
+ thickEnd,
162
+ blockCount,
163
+ blockSizes,
164
+ chromStarts,
165
+ ...f,
166
+ })
167
+ : f,
161
168
  });
162
- return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
169
+ }
170
+ export function isUCSC(f) {
171
+ return f.thickStart && f.blockCount && f.strand !== 0;
163
172
  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-bed",
3
- "version": "2.10.3",
3
+ "version": "2.11.0",
4
4
  "description": "JBrowse 2 bed adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -55,5 +55,5 @@
55
55
  "distModule": "esm/index.js",
56
56
  "srcModule": "src/index.ts",
57
57
  "module": "esm/index.js",
58
- "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
58
+ "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
59
59
  }