@jbrowse/plugin-gtf 1.7.10 → 1.7.11

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Files changed (4) hide show
  1. package/dist/GtfAdapter/GtfAdapter.js +62 -23
  2. package/package.json +2 -2
  3. package/src/GtfAdapter/GtfAdapter.ts +13 -10
  4. package/src/GtfAdapter/__snapshots__/GtfAdapter.test.ts.snap +99 -99
package/dist/GtfAdapter/GtfAdapter.js CHANGED
@@ -73,44 +73,57 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
73
73
  key: "loadDataP",
74
74
  value: function () {
75
75
  var _loadDataP = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
76
- var buffer, buf, data, lines, feats, i, refName;
76
+ var opts,
77
+ gtfLoc,
78
+ buffer,
79
+ buf,
80
+ data,
81
+ lines,
82
+ feats,
83
+ i,
84
+ line,
85
+ tab,
86
+ refName,
87
+ _args = arguments;
77
88
  return _regenerator.default.wrap(function _callee$(_context) {
78
89
  while (1) {
79
90
  switch (_context.prev = _context.next) {
80
91
  case 0:
81
- _context.next = 2;
82
- return (0, _io.openLocation)(this.getConf('gtfLocation'), this.pluginManager).readFile();
92
+ opts = _args.length > 0 && _args[0] !== undefined ? _args[0] : {};
93
+ gtfLoc = this.getConf('gtfLocation');
94
+ _context.next = 4;
95
+ return (0, _io.openLocation)(gtfLoc, this.pluginManager).readFile(opts);
83
96
 
84
- case 2:
97
+ case 4:
85
98
  buffer = _context.sent;
86
99
 
87
100
  if (!isGzip(buffer)) {
88
- _context.next = 9;
101
+ _context.next = 11;
89
102
  break;
90
103
  }
91
104
 
92
- _context.next = 6;
105
+ _context.next = 8;
93
106
  return (0, _bgzfFilehandle.unzip)(buffer);
94
107
 
95
- case 6:
108
+ case 8:
96
109
  _context.t0 = _context.sent;
97
- _context.next = 10;
110
+ _context.next = 12;
98
111
  break;
99
112
 
100
- case 9:
113
+ case 11:
101
114
  _context.t0 = buffer;
102
115
 
103
- case 10:
116
+ case 12:
104
117
  buf = _context.t0;
105
118
 
106
119
  if (!(buf.length > 536870888)) {
107
- _context.next = 13;
120
+ _context.next = 15;
108
121
  break;
109
122
  }
110
123
 
111
124
  throw new Error('Data exceeds maximum string length (512MB)');
112
125
 
113
- case 13:
126
+ case 15:
114
127
  data = new TextDecoder('utf8', {
115
128
  fatal: true
116
129
  }).decode(buf);
@@ -118,22 +131,44 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
118
131
  return !!f && !f.startsWith('#');
119
132
  });
120
133
  feats = {};
134
+ i = 0;
135
+
136
+ case 19:
137
+ if (!(i < lines.length)) {
138
+ _context.next = 30;
139
+ break;
140
+ }
141
+
142
+ line = lines[i];
143
+
144
+ if (!line.startsWith('#')) {
145
+ _context.next = 23;
146
+ break;
147
+ }
121
148
 
122
- for (i = 0; i < lines.length; i++) {
123
- refName = lines[i].split('\t')[0];
149
+ return _context.abrupt("continue", 27);
124
150
 
125
- if (!feats[refName]) {
126
- feats[refName] = [];
127
- }
151
+ case 23:
152
+ tab = line.indexOf('\t');
153
+ refName = line.slice(0, tab);
128
154
 
129
- feats[refName].push(lines[i]);
155
+ if (!feats[refName]) {
156
+ feats[refName] = [];
130
157
  }
131
158
 
159
+ feats[refName].push(lines[i]);
160
+
161
+ case 27:
162
+ i++;
163
+ _context.next = 19;
164
+ break;
165
+
166
+ case 30:
132
167
  return _context.abrupt("return", {
133
168
  feats: feats
134
169
  });
135
170
 
136
- case 18:
171
+ case 31:
137
172
  case "end":
138
173
  return _context.stop();
139
174
  }
@@ -153,12 +188,16 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
153
188
  var _loadData = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
154
189
  var _this2 = this;
155
190
 
191
+ var opts,
192
+ _args2 = arguments;
156
193
  return _regenerator.default.wrap(function _callee2$(_context2) {
157
194
  while (1) {
158
195
  switch (_context2.prev = _context2.next) {
159
196
  case 0:
197
+ opts = _args2.length > 0 && _args2[0] !== undefined ? _args2[0] : {};
198
+
160
199
  if (!this.gtfFeatures) {
161
- this.gtfFeatures = this.loadDataP().catch(function (e) {
200
+ this.gtfFeatures = this.loadDataP(opts).catch(function (e) {
162
201
  _this2.gtfFeatures = undefined;
163
202
  throw e;
164
203
  });
@@ -166,7 +205,7 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
166
205
 
167
206
  return _context2.abrupt("return", this.gtfFeatures);
168
207
 
169
- case 2:
208
+ case 3:
170
209
  case "end":
171
210
  return _context2.stop();
172
211
  }
@@ -195,7 +234,7 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
195
234
  case 0:
196
235
  opts = _args3.length > 0 && _args3[0] !== undefined ? _args3[0] : {};
197
236
  _context3.next = 3;
198
- return this.loadData();
237
+ return this.loadData(opts);
199
238
 
200
239
  case 3:
201
240
  _yield$this$loadData = _context3.sent;
@@ -254,7 +293,7 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
254
293
  ret = data.flat().map(function (f, i) {
255
294
  return new _simpleFeature.default({
256
295
  data: (0, _util.featureData)(f),
257
- id: "".concat(_this3.id, "-offset-").concat(i)
296
+ id: "".concat(_this3.id, "-").concat(refName, "-").concat(i)
258
297
  });
259
298
  });
260
299
 
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-gtf",
3
- "version": "1.7.10",
3
+ "version": "1.7.11",
4
4
  "description": "JBrowse 2 gtf feature adapter",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -51,5 +51,5 @@
51
51
  "publishConfig": {
52
52
  "access": "public"
53
53
  },
54
- "gitHead": "02d8c1e88e5603ea5855faed4ccb814e28071b32"
54
+ "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
55
55
  }
package/src/GtfAdapter/GtfAdapter.ts CHANGED
@@ -23,11 +23,9 @@ export default class extends BaseFeatureDataAdapter {
23
23
  [key: string]: Promise<IntervalTree | undefined> | undefined
24
24
  } = {}
25
25
 
26
- private async loadDataP() {
27
- const buffer = await openLocation(
28
- this.getConf('gtfLocation'),
29
- this.pluginManager,
30
- ).readFile()
26
+ private async loadDataP(opts: BaseOptions = {}) {
27
+ const gtfLoc = this.getConf('gtfLocation')
28
+ const buffer = await openLocation(gtfLoc, this.pluginManager).readFile(opts)
31
29
 
32
30
  const buf = isGzip(buffer) ? await unzip(buffer) : buffer
33
31
  // 512MB max chrome string length is 512MB
@@ -39,7 +37,12 @@ export default class extends BaseFeatureDataAdapter {
39
37
  const lines = data.split('\n').filter(f => !!f && !f.startsWith('#'))
40
38
  const feats = {} as { [key: string]: string[] }
41
39
  for (let i = 0; i < lines.length; i++) {
42
- const refName = lines[i].split('\t')[0]
40
+ const line = lines[i]
41
+ if (line.startsWith('#')) {
42
+ continue
43
+ }
44
+ const tab = line.indexOf('\t')
45
+ const refName = line.slice(0, tab)
43
46
  if (!feats[refName]) {
44
47
  feats[refName] = []
45
48
  }
@@ -49,9 +52,9 @@ export default class extends BaseFeatureDataAdapter {
49
52
  return { feats }
50
53
  }
51
54
 
52
- private async loadData() {
55
+ private async loadData(opts: BaseOptions = {}) {
53
56
  if (!this.gtfFeatures) {
54
- this.gtfFeatures = this.loadDataP().catch(e => {
57
+ this.gtfFeatures = this.loadDataP(opts).catch(e => {
55
58
  this.gtfFeatures = undefined
56
59
  throw e
57
60
  })
@@ -61,7 +64,7 @@ export default class extends BaseFeatureDataAdapter {
61
64
  }
62
65
 
63
66
  public async getRefNames(opts: BaseOptions = {}) {
64
- const { feats } = await this.loadData()
67
+ const { feats } = await this.loadData(opts)
65
68
  return Object.keys(feats)
66
69
  }
67
70
 
@@ -83,7 +86,7 @@ export default class extends BaseFeatureDataAdapter {
83
86
  (f, i) =>
84
87
  new SimpleFeature({
85
88
  data: featureData(f),
86
- id: `${this.id}-offset-${i}`,
89
+ id: `${this.id}-${refName}-${i}`,
87
90
  }),
88
91
  )
89
92
 
package/src/GtfAdapter/__snapshots__/GtfAdapter.test.ts.snap CHANGED
@@ -18,7 +18,7 @@ Array [
18
18
  "gene_id": "EDEN",
19
19
  "gene_name": "EDEN",
20
20
  "name": "EDEN.1",
21
- "parentId": "test-offset-0",
21
+ "parentId": "test-ctgA-0",
22
22
  "phase": 0,
23
23
  "refName": "ctgA",
24
24
  "source": "example",
@@ -26,14 +26,14 @@ Array [
26
26
  "strand": 1,
27
27
  "transcript_id": "EDEN.1",
28
28
  "type": "exon",
29
- "uniqueId": "test-offset-0-0",
29
+ "uniqueId": "test-ctgA-0-0",
30
30
  },
31
31
  Object {
32
32
  "end": 1200,
33
33
  "gene_id": "EDEN",
34
34
  "gene_name": "EDEN",
35
35
  "name": "EDEN.1",
36
- "parentId": "test-offset-0",
36
+ "parentId": "test-ctgA-0",
37
37
  "phase": 0,
38
38
  "refName": "ctgA",
39
39
  "source": "example",
@@ -41,14 +41,14 @@ Array [
41
41
  "strand": 1,
42
42
  "transcript_id": "EDEN.1",
43
43
  "type": "five_prime_UTR",
44
- "uniqueId": "test-offset-0-1",
44
+ "uniqueId": "test-ctgA-0-1",
45
45
  },
46
46
  Object {
47
47
  "end": 1500,
48
48
  "gene_id": "EDEN",
49
49
  "gene_name": "EDEN",
50
50
  "name": "EDEN.1",
51
- "parentId": "test-offset-0",
51
+ "parentId": "test-ctgA-0",
52
52
  "phase": 0,
53
53
  "refName": "ctgA",
54
54
  "source": "example",
@@ -56,14 +56,14 @@ Array [
56
56
  "strand": 1,
57
57
  "transcript_id": "EDEN.1",
58
58
  "type": "CDS",
59
- "uniqueId": "test-offset-0-2",
59
+ "uniqueId": "test-ctgA-0-2",
60
60
  },
61
61
  Object {
62
62
  "end": 3902,
63
63
  "gene_id": "EDEN",
64
64
  "gene_name": "EDEN",
65
65
  "name": "EDEN.1",
66
- "parentId": "test-offset-0",
66
+ "parentId": "test-ctgA-0",
67
67
  "phase": 0,
68
68
  "refName": "ctgA",
69
69
  "source": "example",
@@ -71,14 +71,14 @@ Array [
71
71
  "strand": 1,
72
72
  "transcript_id": "EDEN.1",
73
73
  "type": "CDS",
74
- "uniqueId": "test-offset-0-3",
74
+ "uniqueId": "test-ctgA-0-3",
75
75
  },
76
76
  Object {
77
77
  "end": 3902,
78
78
  "gene_id": "EDEN",
79
79
  "gene_name": "EDEN",
80
80
  "name": "EDEN.1",
81
- "parentId": "test-offset-0",
81
+ "parentId": "test-ctgA-0",
82
82
  "phase": 0,
83
83
  "refName": "ctgA",
84
84
  "source": "example",
@@ -86,14 +86,14 @@ Array [
86
86
  "strand": 1,
87
87
  "transcript_id": "EDEN.1",
88
88
  "type": "exon",
89
- "uniqueId": "test-offset-0-4",
89
+ "uniqueId": "test-ctgA-0-4",
90
90
  },
91
91
  Object {
92
92
  "end": 5500,
93
93
  "gene_id": "EDEN",
94
94
  "gene_name": "EDEN",
95
95
  "name": "EDEN.1",
96
- "parentId": "test-offset-0",
96
+ "parentId": "test-ctgA-0",
97
97
  "phase": 0,
98
98
  "refName": "ctgA",
99
99
  "source": "example",
@@ -101,14 +101,14 @@ Array [
101
101
  "strand": 1,
102
102
  "transcript_id": "EDEN.1",
103
103
  "type": "CDS",
104
- "uniqueId": "test-offset-0-5",
104
+ "uniqueId": "test-ctgA-0-5",
105
105
  },
106
106
  Object {
107
107
  "end": 5500,
108
108
  "gene_id": "EDEN",
109
109
  "gene_name": "EDEN",
110
110
  "name": "EDEN.1",
111
- "parentId": "test-offset-0",
111
+ "parentId": "test-ctgA-0",
112
112
  "phase": 0,
113
113
  "refName": "ctgA",
114
114
  "source": "example",
@@ -116,14 +116,14 @@ Array [
116
116
  "strand": 1,
117
117
  "transcript_id": "EDEN.1",
118
118
  "type": "exon",
119
- "uniqueId": "test-offset-0-6",
119
+ "uniqueId": "test-ctgA-0-6",
120
120
  },
121
121
  Object {
122
122
  "end": 7608,
123
123
  "gene_id": "EDEN",
124
124
  "gene_name": "EDEN",
125
125
  "name": "EDEN.1",
126
- "parentId": "test-offset-0",
126
+ "parentId": "test-ctgA-0",
127
127
  "phase": 0,
128
128
  "refName": "ctgA",
129
129
  "source": "example",
@@ -131,14 +131,14 @@ Array [
131
131
  "strand": 1,
132
132
  "transcript_id": "EDEN.1",
133
133
  "type": "CDS",
134
- "uniqueId": "test-offset-0-7",
134
+ "uniqueId": "test-ctgA-0-7",
135
135
  },
136
136
  Object {
137
137
  "end": 9000,
138
138
  "gene_id": "EDEN",
139
139
  "gene_name": "EDEN",
140
140
  "name": "EDEN.1",
141
- "parentId": "test-offset-0",
141
+ "parentId": "test-ctgA-0",
142
142
  "phase": 0,
143
143
  "refName": "ctgA",
144
144
  "source": "example",
@@ -146,14 +146,14 @@ Array [
146
146
  "strand": 1,
147
147
  "transcript_id": "EDEN.1",
148
148
  "type": "exon",
149
- "uniqueId": "test-offset-0-8",
149
+ "uniqueId": "test-ctgA-0-8",
150
150
  },
151
151
  Object {
152
152
  "end": 9000,
153
153
  "gene_id": "EDEN",
154
154
  "gene_name": "EDEN",
155
155
  "name": "EDEN.1",
156
- "parentId": "test-offset-0",
156
+ "parentId": "test-ctgA-0",
157
157
  "phase": 0,
158
158
  "refName": "ctgA",
159
159
  "source": "example",
@@ -161,12 +161,12 @@ Array [
161
161
  "strand": 1,
162
162
  "transcript_id": "EDEN.1",
163
163
  "type": "three_prime_UTR",
164
- "uniqueId": "test-offset-0-9",
164
+ "uniqueId": "test-ctgA-0-9",
165
165
  },
166
166
  ],
167
167
  "transcript_id": "EDEN.1",
168
168
  "type": "transcript",
169
- "uniqueId": "test-offset-0",
169
+ "uniqueId": "test-ctgA-0",
170
170
  },
171
171
  Object {
172
172
  "end": 9000,
@@ -184,7 +184,7 @@ Array [
184
184
  "gene_id": "EDEN",
185
185
  "gene_name": "EDEN",
186
186
  "name": "EDEN.2",
187
- "parentId": "test-offset-1",
187
+ "parentId": "test-ctgA-1",
188
188
  "phase": 0,
189
189
  "refName": "ctgA",
190
190
  "source": "example",
@@ -192,14 +192,14 @@ Array [
192
192
  "strand": 1,
193
193
  "transcript_id": "EDEN.2",
194
194
  "type": "exon",
195
- "uniqueId": "test-offset-1-0",
195
+ "uniqueId": "test-ctgA-1-0",
196
196
  },
197
197
  Object {
198
198
  "end": 1200,
199
199
  "gene_id": "EDEN",
200
200
  "gene_name": "EDEN",
201
201
  "name": "EDEN.2",
202
- "parentId": "test-offset-1",
202
+ "parentId": "test-ctgA-1",
203
203
  "phase": 0,
204
204
  "refName": "ctgA",
205
205
  "source": "example",
@@ -207,14 +207,14 @@ Array [
207
207
  "strand": 1,
208
208
  "transcript_id": "EDEN.2",
209
209
  "type": "five_prime_UTR",
210
- "uniqueId": "test-offset-1-1",
210
+ "uniqueId": "test-ctgA-1-1",
211
211
  },
212
212
  Object {
213
213
  "end": 1500,
214
214
  "gene_id": "EDEN",
215
215
  "gene_name": "EDEN",
216
216
  "name": "EDEN.2",
217
- "parentId": "test-offset-1",
217
+ "parentId": "test-ctgA-1",
218
218
  "phase": 0,
219
219
  "refName": "ctgA",
220
220
  "source": "example",
@@ -222,14 +222,14 @@ Array [
222
222
  "strand": 1,
223
223
  "transcript_id": "EDEN.2",
224
224
  "type": "CDS",
225
- "uniqueId": "test-offset-1-2",
225
+ "uniqueId": "test-ctgA-1-2",
226
226
  },
227
227
  Object {
228
228
  "end": 5500,
229
229
  "gene_id": "EDEN",
230
230
  "gene_name": "EDEN",
231
231
  "name": "EDEN.2",
232
- "parentId": "test-offset-1",
232
+ "parentId": "test-ctgA-1",
233
233
  "phase": 0,
234
234
  "refName": "ctgA",
235
235
  "source": "example",
@@ -237,14 +237,14 @@ Array [
237
237
  "strand": 1,
238
238
  "transcript_id": "EDEN.2",
239
239
  "type": "CDS",
240
- "uniqueId": "test-offset-1-3",
240
+ "uniqueId": "test-ctgA-1-3",
241
241
  },
242
242
  Object {
243
243
  "end": 5500,
244
244
  "gene_id": "EDEN",
245
245
  "gene_name": "EDEN",
246
246
  "name": "EDEN.2",
247
- "parentId": "test-offset-1",
247
+ "parentId": "test-ctgA-1",
248
248
  "phase": 0,
249
249
  "refName": "ctgA",
250
250
  "source": "example",
@@ -252,14 +252,14 @@ Array [
252
252
  "strand": 1,
253
253
  "transcript_id": "EDEN.2",
254
254
  "type": "exon",
255
- "uniqueId": "test-offset-1-4",
255
+ "uniqueId": "test-ctgA-1-4",
256
256
  },
257
257
  Object {
258
258
  "end": 7608,
259
259
  "gene_id": "EDEN",
260
260
  "gene_name": "EDEN",
261
261
  "name": "EDEN.2",
262
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262
+ "parentId": "test-ctgA-1",
263
263
  "phase": 0,
264
264
  "refName": "ctgA",
265
265
  "source": "example",
@@ -267,14 +267,14 @@ Array [
267
267
  "strand": 1,
268
268
  "transcript_id": "EDEN.2",
269
269
  "type": "CDS",
270
- "uniqueId": "test-offset-1-5",
270
+ "uniqueId": "test-ctgA-1-5",
271
271
  },
272
272
  Object {
273
273
  "end": 9000,
274
274
  "gene_id": "EDEN",
275
275
  "gene_name": "EDEN",
276
276
  "name": "EDEN.2",
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- "parentId": "test-offset-1",
277
+ "parentId": "test-ctgA-1",
278
278
  "phase": 0,
279
279
  "refName": "ctgA",
280
280
  "source": "example",
@@ -282,14 +282,14 @@ Array [
282
282
  "strand": 1,
283
283
  "transcript_id": "EDEN.2",
284
284
  "type": "exon",
285
- "uniqueId": "test-offset-1-6",
285
+ "uniqueId": "test-ctgA-1-6",
286
286
  },
287
287
  Object {
288
288
  "end": 9000,
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289
  "gene_id": "EDEN",
290
290
  "gene_name": "EDEN",
291
291
  "name": "EDEN.2",
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- "parentId": "test-offset-1",
292
+ "parentId": "test-ctgA-1",
293
293
  "phase": 0,
294
294
  "refName": "ctgA",
295
295
  "source": "example",
@@ -297,12 +297,12 @@ Array [
297
297
  "strand": 1,
298
298
  "transcript_id": "EDEN.2",
299
299
  "type": "three_prime_UTR",
300
- "uniqueId": "test-offset-1-7",
300
+ "uniqueId": "test-ctgA-1-7",
301
301
  },
302
302
  ],
303
303
  "transcript_id": "EDEN.2",
304
304
  "type": "transcript",
305
- "uniqueId": "test-offset-1",
305
+ "uniqueId": "test-ctgA-1",
306
306
  },
307
307
  Object {
308
308
  "end": 9000,
@@ -320,7 +320,7 @@ Array [
320
320
  "gene_id": "EDEN",
321
321
  "gene_name": "EDEN",
322
322
  "name": "EDEN.3",
323
- "parentId": "test-offset-2",
323
+ "parentId": "test-ctgA-2",
324
324
  "phase": 0,
325
325
  "refName": "ctgA",
326
326
  "source": "example",
@@ -328,14 +328,14 @@ Array [
328
328
  "strand": 1,
329
329
  "transcript_id": "EDEN.3",
330
330
  "type": "exon",
331
- "uniqueId": "test-offset-2-0",
331
+ "uniqueId": "test-ctgA-2-0",
332
332
  },
333
333
  Object {
334
334
  "end": 1500,
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335
  "gene_id": "EDEN",
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336
  "gene_name": "EDEN",
337
337
  "name": "EDEN.3",
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- "parentId": "test-offset-2",
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+ "parentId": "test-ctgA-2",
339
339
  "phase": 1,
340
340
  "refName": "ctgA",
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341
  "source": "example",
@@ -343,14 +343,14 @@ Array [
343
343
  "strand": 1,
344
344
  "transcript_id": "EDEN.3",
345
345
  "type": "five_prime_UTR",
346
- "uniqueId": "test-offset-2-1",
346
+ "uniqueId": "test-ctgA-2-1",
347
347
  },
348
348
  Object {
349
349
  "end": 3902,
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350
  "gene_id": "EDEN",
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351
  "gene_name": "EDEN",
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352
  "name": "EDEN.3",
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- "parentId": "test-offset-2",
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+ "parentId": "test-ctgA-2",
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354
  "phase": 0,
355
355
  "refName": "ctgA",
356
356
  "source": "example",
@@ -358,14 +358,14 @@ Array [
358
358
  "strand": 1,
359
359
  "transcript_id": "EDEN.3",
360
360
  "type": "exon",
361
- "uniqueId": "test-offset-2-2",
361
+ "uniqueId": "test-ctgA-2-2",
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362
  },
363
363
  Object {
364
364
  "end": 3300,
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365
  "gene_id": "EDEN",
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366
  "gene_name": "EDEN",
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367
  "name": "EDEN.3",
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- "parentId": "test-offset-2",
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+ "parentId": "test-ctgA-2",
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369
  "phase": 1,
370
370
  "refName": "ctgA",
371
371
  "source": "example",
@@ -373,14 +373,14 @@ Array [
373
373
  "strand": 1,
374
374
  "transcript_id": "EDEN.3",
375
375
  "type": "five_prime_UTR",
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- "uniqueId": "test-offset-2-3",
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+ "uniqueId": "test-ctgA-2-3",
377
377
  },
378
378
  Object {
379
379
  "end": 3902,
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380
  "gene_id": "EDEN",
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381
  "gene_name": "EDEN",
382
382
  "name": "EDEN.3",
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- "parentId": "test-offset-2",
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+ "parentId": "test-ctgA-2",
384
384
  "phase": 0,
385
385
  "refName": "ctgA",
386
386
  "source": "example",
@@ -388,14 +388,14 @@ Array [
388
388
  "strand": 1,
389
389
  "transcript_id": "EDEN.3",
390
390
  "type": "CDS",
391
- "uniqueId": "test-offset-2-4",
391
+ "uniqueId": "test-ctgA-2-4",
392
392
  },
393
393
  Object {
394
394
  "end": 5500,
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395
  "gene_id": "EDEN",
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396
  "gene_name": "EDEN",
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397
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- "parentId": "test-offset-2",
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+ "parentId": "test-ctgA-2",
399
399
  "phase": 1,
400
400
  "refName": "ctgA",
401
401
  "source": "example",
@@ -403,14 +403,14 @@ Array [
403
403
  "strand": 1,
404
404
  "transcript_id": "EDEN.3",
405
405
  "type": "CDS",
406
- "uniqueId": "test-offset-2-5",
406
+ "uniqueId": "test-ctgA-2-5",
407
407
  },
408
408
  Object {
409
409
  "end": 5500,
410
410
  "gene_id": "EDEN",
411
411
  "gene_name": "EDEN",
412
412
  "name": "EDEN.3",
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- "parentId": "test-offset-2",
413
+ "parentId": "test-ctgA-2",
414
414
  "phase": 0,
415
415
  "refName": "ctgA",
416
416
  "source": "example",
@@ -418,14 +418,14 @@ Array [
418
418
  "strand": 1,
419
419
  "transcript_id": "EDEN.3",
420
420
  "type": "exon",
421
- "uniqueId": "test-offset-2-6",
421
+ "uniqueId": "test-ctgA-2-6",
422
422
  },
423
423
  Object {
424
424
  "end": 7600,
425
425
  "gene_id": "EDEN",
426
426
  "gene_name": "EDEN",
427
427
  "name": "EDEN.3",
428
- "parentId": "test-offset-2",
428
+ "parentId": "test-ctgA-2",
429
429
  "phase": 1,
430
430
  "refName": "ctgA",
431
431
  "source": "example",
@@ -433,14 +433,14 @@ Array [
433
433
  "strand": 1,
434
434
  "transcript_id": "EDEN.3",
435
435
  "type": "CDS",
436
- "uniqueId": "test-offset-2-7",
436
+ "uniqueId": "test-ctgA-2-7",
437
437
  },
438
438
  Object {
439
439
  "end": 9000,
440
440
  "gene_id": "EDEN",
441
441
  "gene_name": "EDEN",
442
442
  "name": "EDEN.3",
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- "parentId": "test-offset-2",
443
+ "parentId": "test-ctgA-2",
444
444
  "phase": 0,
445
445
  "refName": "ctgA",
446
446
  "source": "example",
@@ -448,14 +448,14 @@ Array [
448
448
  "strand": 1,
449
449
  "transcript_id": "EDEN.3",
450
450
  "type": "exon",
451
- "uniqueId": "test-offset-2-8",
451
+ "uniqueId": "test-ctgA-2-8",
452
452
  },
453
453
  Object {
454
454
  "end": 9000,
455
455
  "gene_id": "EDEN",
456
456
  "gene_name": "EDEN",
457
457
  "name": "EDEN.3",
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- "parentId": "test-offset-2",
458
+ "parentId": "test-ctgA-2",
459
459
  "phase": 1,
460
460
  "refName": "ctgA",
461
461
  "source": "example",
@@ -463,12 +463,12 @@ Array [
463
463
  "strand": 1,
464
464
  "transcript_id": "EDEN.3",
465
465
  "type": "three_prime_UTR",
466
- "uniqueId": "test-offset-2-9",
466
+ "uniqueId": "test-ctgA-2-9",
467
467
  },
468
468
  ],
469
469
  "transcript_id": "EDEN.3",
470
470
  "type": "transcript",
471
- "uniqueId": "test-offset-2",
471
+ "uniqueId": "test-ctgA-2",
472
472
  },
473
473
  Object {
474
474
  "end": 11500,
@@ -482,7 +482,7 @@ Array [
482
482
  Object {
483
483
  "end": 11500,
484
484
  "name": "Apple1",
485
- "parentId": "test-offset-3",
485
+ "parentId": "test-ctgA-3",
486
486
  "phase": 0,
487
487
  "refName": "ctgA",
488
488
  "source": "bare_predicted",
@@ -490,12 +490,12 @@ Array [
490
490
  "strand": 1,
491
491
  "transcript_id": "Apple1",
492
492
  "type": "CDS",
493
- "uniqueId": "test-offset-3-0",
493
+ "uniqueId": "test-ctgA-3-0",
494
494
  },
495
495
  ],
496
496
  "transcript_id": "Apple1",
497
497
  "type": "transcript",
498
- "uniqueId": "test-offset-3",
498
+ "uniqueId": "test-ctgA-3",
499
499
  },
500
500
  Object {
501
501
  "end": 17000,
@@ -509,7 +509,7 @@ Array [
509
509
  Object {
510
510
  "end": 13800,
511
511
  "name": "cds-Apple2",
512
- "parentId": "test-offset-4",
512
+ "parentId": "test-ctgA-4",
513
513
  "phase": 0,
514
514
  "refName": "ctgA",
515
515
  "source": "predicted",
@@ -517,12 +517,12 @@ Array [
517
517
  "strand": 1,
518
518
  "transcript_id": "cds-Apple2",
519
519
  "type": "CDS",
520
- "uniqueId": "test-offset-4-0",
520
+ "uniqueId": "test-ctgA-4-0",
521
521
  },
522
522
  Object {
523
523
  "end": 15500,
524
524
  "name": "cds-Apple2",
525
- "parentId": "test-offset-4",
525
+ "parentId": "test-ctgA-4",
526
526
  "phase": 1,
527
527
  "refName": "ctgA",
528
528
  "source": "predicted",
@@ -530,12 +530,12 @@ Array [
530
530
  "strand": 1,
531
531
  "transcript_id": "cds-Apple2",
532
532
  "type": "CDS",
533
- "uniqueId": "test-offset-4-1",
533
+ "uniqueId": "test-ctgA-4-1",
534
534
  },
535
535
  Object {
536
536
  "end": 17000,
537
537
  "name": "cds-Apple2",
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- "parentId": "test-offset-4",
538
+ "parentId": "test-ctgA-4",
539
539
  "phase": 2,
540
540
  "refName": "ctgA",
541
541
  "source": "predicted",
@@ -543,12 +543,12 @@ Array [
543
543
  "strand": 1,
544
544
  "transcript_id": "cds-Apple2",
545
545
  "type": "CDS",
546
- "uniqueId": "test-offset-4-2",
546
+ "uniqueId": "test-ctgA-4-2",
547
547
  },
548
548
  ],
549
549
  "transcript_id": "cds-Apple2",
550
550
  "type": "transcript",
551
- "uniqueId": "test-offset-4",
551
+ "uniqueId": "test-ctgA-4",
552
552
  },
553
553
  Object {
554
554
  "end": 23000,
@@ -562,7 +562,7 @@ Array [
562
562
  Object {
563
563
  "end": 17999,
564
564
  "name": "rna-Apple3",
565
- "parentId": "test-offset-5",
565
+ "parentId": "test-ctgA-5",
566
566
  "phase": 0,
567
567
  "refName": "ctgA",
568
568
  "source": "exonerate",
@@ -570,12 +570,12 @@ Array [
570
570
  "strand": 1,
571
571
  "transcript_id": "rna-Apple3",
572
572
  "type": "UTR",
573
- "uniqueId": "test-offset-5-0",
573
+ "uniqueId": "test-ctgA-5-0",
574
574
  },
575
575
  Object {
576
576
  "end": 18800,
577
577
  "name": "rna-Apple3",
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- "parentId": "test-offset-5",
578
+ "parentId": "test-ctgA-5",
579
579
  "phase": 0,
580
580
  "refName": "ctgA",
581
581
  "source": "exonerate",
@@ -583,12 +583,12 @@ Array [
583
583
  "strand": 1,
584
584
  "transcript_id": "rna-Apple3",
585
585
  "type": "exon",
586
- "uniqueId": "test-offset-5-1",
586
+ "uniqueId": "test-ctgA-5-1",
587
587
  },
588
588
  Object {
589
589
  "end": 18800,
590
590
  "name": "rna-Apple3",
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- "parentId": "test-offset-5",
591
+ "parentId": "test-ctgA-5",
592
592
  "phase": 0,
593
593
  "refName": "ctgA",
594
594
  "source": "exonerate",
@@ -596,12 +596,12 @@ Array [
596
596
  "strand": 1,
597
597
  "transcript_id": "rna-Apple3",
598
598
  "type": "CDS",
599
- "uniqueId": "test-offset-5-2",
599
+ "uniqueId": "test-ctgA-5-2",
600
600
  },
601
601
  Object {
602
602
  "end": 19500,
603
603
  "name": "rna-Apple3",
604
- "parentId": "test-offset-5",
604
+ "parentId": "test-ctgA-5",
605
605
  "phase": 0,
606
606
  "refName": "ctgA",
607
607
  "source": "exonerate",
@@ -609,12 +609,12 @@ Array [
609
609
  "strand": 1,
610
610
  "transcript_id": "rna-Apple3",
611
611
  "type": "CDS",
612
- "uniqueId": "test-offset-5-3",
612
+ "uniqueId": "test-ctgA-5-3",
613
613
  },
614
614
  Object {
615
615
  "end": 19500,
616
616
  "name": "rna-Apple3",
617
- "parentId": "test-offset-5",
617
+ "parentId": "test-ctgA-5",
618
618
  "phase": 0,
619
619
  "refName": "ctgA",
620
620
  "source": "exonerate",
@@ -622,12 +622,12 @@ Array [
622
622
  "strand": 1,
623
623
  "transcript_id": "rna-Apple3",
624
624
  "type": "exon",
625
- "uniqueId": "test-offset-5-4",
625
+ "uniqueId": "test-ctgA-5-4",
626
626
  },
627
627
  Object {
628
628
  "end": 21200,
629
629
  "name": "rna-Apple3",
630
- "parentId": "test-offset-5",
630
+ "parentId": "test-ctgA-5",
631
631
  "phase": 0,
632
632
  "refName": "ctgA",
633
633
  "source": "exonerate",
@@ -635,12 +635,12 @@ Array [
635
635
  "strand": 1,
636
636
  "transcript_id": "rna-Apple3",
637
637
  "type": "CDS",
638
- "uniqueId": "test-offset-5-5",
638
+ "uniqueId": "test-ctgA-5-5",
639
639
  },
640
640
  Object {
641
641
  "end": 23000,
642
642
  "name": "rna-Apple3",
643
- "parentId": "test-offset-5",
643
+ "parentId": "test-ctgA-5",
644
644
  "phase": 0,
645
645
  "refName": "ctgA",
646
646
  "source": "exonerate",
@@ -648,12 +648,12 @@ Array [
648
648
  "strand": 1,
649
649
  "transcript_id": "rna-Apple3",
650
650
  "type": "exon",
651
- "uniqueId": "test-offset-5-6",
651
+ "uniqueId": "test-ctgA-5-6",
652
652
  },
653
653
  Object {
654
654
  "end": 23000,
655
655
  "name": "rna-Apple3",
656
- "parentId": "test-offset-5",
656
+ "parentId": "test-ctgA-5",
657
657
  "phase": 0,
658
658
  "refName": "ctgA",
659
659
  "source": "exonerate",
@@ -661,12 +661,12 @@ Array [
661
661
  "strand": 1,
662
662
  "transcript_id": "rna-Apple3",
663
663
  "type": "UTR",
664
- "uniqueId": "test-offset-5-7",
664
+ "uniqueId": "test-ctgA-5-7",
665
665
  },
666
666
  ],
667
667
  "transcript_id": "rna-Apple3",
668
668
  "type": "transcript",
669
- "uniqueId": "test-offset-5",
669
+ "uniqueId": "test-ctgA-5",
670
670
  },
671
671
  ]
672
672
  `;
@@ -696,7 +696,7 @@ Array [
696
696
  "gene_source": "ensembl",
697
697
  "gene_version": "1",
698
698
  "name": "ENSVPAT00000000407",
699
- "parentId": "test-offset-0",
699
+ "parentId": "test-GeneScaffold_1-0",
700
700
  "phase": 0,
701
701
  "refName": "GeneScaffold_1",
702
702
  "source": "ensembl",
@@ -707,7 +707,7 @@ Array [
707
707
  "transcript_source": "ensembl",
708
708
  "transcript_version": "1",
709
709
  "type": "exon",
710
- "uniqueId": "test-offset-0-0",
710
+ "uniqueId": "test-GeneScaffold_1-0-0",
711
711
  },
712
712
  Object {
713
713
  "end": 107812,
@@ -719,7 +719,7 @@ Array [
719
719
  "gene_source": "ensembl",
720
720
  "gene_version": "1",
721
721
  "name": "ENSVPAT00000000407",
722
- "parentId": "test-offset-0",
722
+ "parentId": "test-GeneScaffold_1-0",
723
723
  "phase": 0,
724
724
  "refName": "GeneScaffold_1",
725
725
  "source": "ensembl",
@@ -730,7 +730,7 @@ Array [
730
730
  "transcript_source": "ensembl",
731
731
  "transcript_version": "1",
732
732
  "type": "exon",
733
- "uniqueId": "test-offset-0-1",
733
+ "uniqueId": "test-GeneScaffold_1-0-1",
734
734
  },
735
735
  Object {
736
736
  "end": 107877,
@@ -742,7 +742,7 @@ Array [
742
742
  "gene_source": "ensembl",
743
743
  "gene_version": "1",
744
744
  "name": "ENSVPAT00000000407",
745
- "parentId": "test-offset-0",
745
+ "parentId": "test-GeneScaffold_1-0",
746
746
  "phase": 0,
747
747
  "refName": "GeneScaffold_1",
748
748
  "source": "ensembl",
@@ -753,7 +753,7 @@ Array [
753
753
  "transcript_source": "ensembl",
754
754
  "transcript_version": "1",
755
755
  "type": "exon",
756
- "uniqueId": "test-offset-0-2",
756
+ "uniqueId": "test-GeneScaffold_1-0-2",
757
757
  },
758
758
  Object {
759
759
  "end": 107895,
@@ -765,7 +765,7 @@ Array [
765
765
  "gene_source": "ensembl",
766
766
  "gene_version": "1",
767
767
  "name": "ENSVPAT00000000407",
768
- "parentId": "test-offset-0",
768
+ "parentId": "test-GeneScaffold_1-0",
769
769
  "phase": 0,
770
770
  "refName": "GeneScaffold_1",
771
771
  "source": "ensembl",
@@ -776,7 +776,7 @@ Array [
776
776
  "transcript_source": "ensembl",
777
777
  "transcript_version": "1",
778
778
  "type": "exon",
779
- "uniqueId": "test-offset-0-3",
779
+ "uniqueId": "test-GeneScaffold_1-0-3",
780
780
  },
781
781
  Object {
782
782
  "end": 107917,
@@ -788,7 +788,7 @@ Array [
788
788
  "gene_source": "ensembl",
789
789
  "gene_version": "1",
790
790
  "name": "ENSVPAT00000000407",
791
- "parentId": "test-offset-0",
791
+ "parentId": "test-GeneScaffold_1-0",
792
792
  "phase": 0,
793
793
  "refName": "GeneScaffold_1",
794
794
  "source": "ensembl",
@@ -799,7 +799,7 @@ Array [
799
799
  "transcript_source": "ensembl",
800
800
  "transcript_version": "1",
801
801
  "type": "exon",
802
- "uniqueId": "test-offset-0-4",
802
+ "uniqueId": "test-GeneScaffold_1-0-4",
803
803
  },
804
804
  Object {
805
805
  "end": 107987,
@@ -811,7 +811,7 @@ Array [
811
811
  "gene_source": "ensembl",
812
812
  "gene_version": "1",
813
813
  "name": "ENSVPAT00000000407",
814
- "parentId": "test-offset-0",
814
+ "parentId": "test-GeneScaffold_1-0",
815
815
  "phase": 0,
816
816
  "refName": "GeneScaffold_1",
817
817
  "source": "ensembl",
@@ -822,7 +822,7 @@ Array [
822
822
  "transcript_source": "ensembl",
823
823
  "transcript_version": "1",
824
824
  "type": "exon",
825
- "uniqueId": "test-offset-0-5",
825
+ "uniqueId": "test-GeneScaffold_1-0-5",
826
826
  },
827
827
  ],
828
828
  "transcript_biotype": "pseudogene",
@@ -830,7 +830,7 @@ Array [
830
830
  "transcript_source": "ensembl",
831
831
  "transcript_version": "1",
832
832
  "type": "transcript",
833
- "uniqueId": "test-offset-0",
833
+ "uniqueId": "test-GeneScaffold_1-0",
834
834
  },
835
835
  ]
836
836
  `;