@jbrowse/img 2.13.1 → 2.14.0

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Files changed (9) hide show
  1. package/dist/index.js +6 -5
  2. package/dist/renderRegion.js +39 -22
  3. package/dist/setupEnv.js +1 -1
  4. package/dist/util.js +1 -1
  5. package/esm/index.js +6 -5
  6. package/esm/renderRegion.js +39 -22
  7. package/esm/setupEnv.js +1 -1
  8. package/esm/util.js +1 -1
  9. package/package.json +4 -4
package/dist/index.js CHANGED
@@ -13,19 +13,20 @@ const setupEnv_1 = __importDefault(require("./setupEnv"));
13
13
  (0, setupEnv_1.default)();
14
14
  const err = console.error;
15
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  console.error = (...p) => {
16
- if (!`${p[0]}`.match('useLayoutEffect')) {
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+ if (!/useLayoutEffect/.exec(`${p[0]}`)) {
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17
  err(p);
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18
  }
19
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  };
20
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  const warn = console.warn;
21
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  console.warn = (...p) => {
22
- if (!`${p[0]}`.match('estimation reached timeout')) {
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+ if (!/estimation reached timeout/.exec(`${p[0]}`)) {
23
23
  warn(p);
24
24
  }
25
25
  };
26
- // note: yargs is actually unused except for printing help
27
- // we do custom command line parsing, see parseArgv.ts
28
- // eslint-disable-next-line @typescript-eslint/no-floating-promises
26
+ // note: yargs is actually unused except for printing help we do custom command
27
+ // line parsing, see parseArgv.ts
28
+ //
29
+ // eslint-disable-next-line @typescript-eslint/no-floating-promises,@typescript-eslint/no-unused-expressions
29
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  yargs_1.default
30
31
  .command('jb2export', 'Creates a jbrowse 2 image snapshot')
31
32
  .option('config', {
package/dist/renderRegion.js CHANGED
@@ -17,7 +17,7 @@ function read(file) {
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  res = JSON.parse(fs_1.default.readFileSync(file, 'utf8'));
18
18
  }
19
19
  catch (e) {
20
- throw new Error(`Failed to parse ${file} as JSON, use --fasta if you mean to pass a FASTA file`);
20
+ throw new Error(`Failed to parse ${file} as JSON, use --fasta if you mean to pass a FASTA file`, { cause: e });
21
21
  }
22
22
  return res;
23
23
  }
@@ -40,8 +40,10 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
40
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  var _a;
41
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  const assemblyData = asm && fs_1.default.existsSync(asm) ? read(asm) : undefined;
42
42
  const tracksData = tracks ? read(tracks) : undefined;
43
- const configData = (config ? read(config) : {});
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- let sessionData = session ? read(session) : undefined;
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+ const configData = config ? read(config) : {};
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+ let sessionData = session
45
+ ? read(session)
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+ : undefined;
45
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  if (config) {
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  addRelativePaths(configData, path_1.default.dirname(path_1.default.resolve(config)));
47
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  }
@@ -60,6 +62,7 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
60
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  configData.assembly = assemblyData;
61
63
  }
62
64
  // else check if it was an assembly name in a config file
65
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
63
66
  else if ((_a = configData.assemblies) === null || _a === void 0 ? void 0 : _a.length) {
64
67
  configData.assemblies.find(entry => entry.name === asm);
65
68
  if (asm) {
@@ -84,8 +87,8 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
84
87
  adapter: {
85
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  type: bgzip ? 'BgzipFastaAdapter' : 'IndexedFastaAdapter',
86
89
  fastaLocation: makeLocation(fasta),
87
- faiLocation: makeLocation(fasta + '.fai'),
88
- gziLocation: bgzip ? makeLocation(fasta + '.gzi') : undefined,
90
+ faiLocation: makeLocation(`${fasta}.fai`),
91
+ gziLocation: bgzip ? makeLocation(`${fasta}.gzi`) : undefined,
89
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  },
90
93
  },
91
94
  };
@@ -107,12 +110,14 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
107
110
  }
108
111
  }
109
112
  // throw if still no assembly
113
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
110
114
  if (!configData.assembly) {
111
115
  throw new Error('no assembly specified, use --fasta to supply an indexed FASTA file (generated with samtools faidx yourfile.fa). see README for alternatives with --assembly and --config');
112
116
  }
113
117
  if (tracksData) {
114
118
  configData.tracks = tracksData;
115
119
  }
120
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
116
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  else if (!configData.tracks) {
117
122
  configData.tracks = [];
118
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  }
@@ -121,6 +126,9 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
121
126
  const [type, opts] = track;
122
127
  const [file, ...rest] = opts;
123
128
  const index = (_a = rest.find(r => r.startsWith('index:'))) === null || _a === void 0 ? void 0 : _a.replace('index:', '');
129
+ if (!file) {
130
+ throw new Error('no file specified');
131
+ }
124
132
  if (type === 'bam') {
125
133
  configData.tracks = [
126
134
  ...configData.tracks,
@@ -133,7 +141,7 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
133
141
  type: 'BamAdapter',
134
142
  bamLocation: makeLocation(file),
135
143
  index: {
136
- location: makeLocation(index || file + '.bai'),
144
+ location: makeLocation(index || `${file}.bai`),
137
145
  indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'BAI',
138
146
  },
139
147
  sequenceAdapter: configData.assembly.sequence.adapter,
@@ -143,7 +151,7 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
143
151
  displays: [
144
152
  {
145
153
  type: 'LinearSNPCoverageDisplay',
146
- displayId: path_1.default.basename(file) + '-' + Math.random(),
154
+ displayId: `${path_1.default.basename(file)}-${Math.random()}`,
147
155
  },
148
156
  ],
149
157
  }
@@ -162,7 +170,7 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
162
170
  adapter: {
163
171
  type: 'CramAdapter',
164
172
  cramLocation: makeLocation(file),
165
- craiLocation: makeLocation(index || file + '.crai'),
173
+ craiLocation: makeLocation(index || `${file}.crai`),
166
174
  sequenceAdapter: configData.assembly.sequence.adapter,
167
175
  },
168
176
  ...(opts.includes('snpcov')
@@ -170,7 +178,7 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
170
178
  displays: [
171
179
  {
172
180
  type: 'LinearSNPCoverageDisplay',
173
- displayId: path_1.default.basename(file) + '-' + Math.random(),
181
+ displayId: `${path_1.default.basename(file)}-${Math.random()}`,
174
182
  },
175
183
  ],
176
184
  }
@@ -205,7 +213,7 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
205
213
  type: 'VcfTabixAdapter',
206
214
  vcfGzLocation: makeLocation(file),
207
215
  index: {
208
- location: makeLocation(index || file + '.tbi'),
216
+ location: makeLocation(index || `${file}.tbi`),
209
217
  indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
210
218
  },
211
219
  },
@@ -224,7 +232,7 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
224
232
  type: 'Gff3TabixAdapter',
225
233
  gffGzLocation: makeLocation(file),
226
234
  index: {
227
- location: makeLocation(index || file + '.tbi'),
235
+ location: makeLocation(index || `${file}.tbi`),
228
236
  indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
229
237
  },
230
238
  },
@@ -273,7 +281,7 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
273
281
  type: 'BedTabixAdapter',
274
282
  bedGzLocation: makeLocation(file),
275
283
  index: {
276
- location: makeLocation(index || file + '.tbi'),
284
+ location: makeLocation(index || `${file}.tbi`),
277
285
  indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
278
286
  },
279
287
  },
@@ -284,7 +292,7 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
284
292
  if (!defaultSession) {
285
293
  // don't use defaultSession from config.json file, can result in assembly
286
294
  // name confusion
287
- delete configData.defaultSession;
295
+ configData.defaultSession = undefined;
288
296
  }
289
297
  // only allow an external manually specified session
290
298
  if (sessionData) {
@@ -294,13 +302,18 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
294
302
  }
295
303
  function process(trackEntry, view, extra = c => c) {
296
304
  const [, [track, ...opts]] = trackEntry;
305
+ if (!track) {
306
+ throw new Error('invalid command line args');
307
+ }
297
308
  const currentTrack = view.showTrack(extra(track));
298
309
  const display = currentTrack.displays[0];
299
310
  opts.forEach(opt => {
300
311
  // apply height to any track
301
312
  if (opt.startsWith('height:')) {
302
313
  const [, height] = opt.split(':');
303
- display.setHeight(+height);
314
+ if (height) {
315
+ display.setHeight(+height);
316
+ }
304
317
  }
305
318
  // apply sort to pileup
306
319
  else if (opt.startsWith('sort:')) {
@@ -332,8 +345,12 @@ function process(trackEntry, view, extra = c => c) {
332
345
  // apply min and max score to wiggle
333
346
  else if (opt.startsWith('minmax:')) {
334
347
  const [, min, max] = opt.split(':');
335
- display.setMinScore(+min);
336
- display.setMaxScore(+max);
348
+ if (min) {
349
+ display.setMinScore(+min);
350
+ }
351
+ if (max) {
352
+ display.setMaxScore(+max);
353
+ }
337
354
  }
338
355
  // apply linear or log scale to wiggle
339
356
  else if (opt.startsWith('scaletype:')) {
@@ -342,17 +359,17 @@ function process(trackEntry, view, extra = c => c) {
342
359
  }
343
360
  // draw crosshatches on wiggle
344
361
  else if (opt.startsWith('crosshatch:')) {
345
- const [, val] = opt.split(':');
362
+ const [, val = 'false'] = opt.split(':');
346
363
  display.setCrossHatches((0, util_1.booleanize)(val));
347
364
  }
348
365
  // turn off fill on bigwig with fill:false
349
366
  else if (opt.startsWith('fill:')) {
350
- const [, val] = opt.split(':');
367
+ const [, val = 'true'] = opt.split(':');
351
368
  display.setFill((0, util_1.booleanize)(val));
352
369
  }
353
370
  // set resolution:superfine to use finer bigwig bin size
354
371
  else if (opt.startsWith('resolution:')) {
355
- let [, val] = opt.split(':');
372
+ let [, val = 1] = opt.split(':');
356
373
  if (val === 'fine') {
357
374
  val = '10';
358
375
  }
@@ -374,12 +391,12 @@ async function renderRegion(opts) {
374
391
  const { assemblyManager } = model;
375
392
  view.setWidth(width);
376
393
  if (loc) {
377
- const [assembly] = assemblyManager.assemblies;
394
+ const { name } = assemblyManager.assemblies[0];
378
395
  if (loc === 'all') {
379
- view.showAllRegionsInAssembly(assembly.name);
396
+ view.showAllRegionsInAssembly(name);
380
397
  }
381
398
  else {
382
- await view.navToLocString(loc, assembly.name);
399
+ await view.navToLocString(loc, name);
383
400
  }
384
401
  }
385
402
  else if (!sessionParam && !defaultSession) {
package/dist/setupEnv.js CHANGED
@@ -32,7 +32,7 @@ function setupEnv() {
32
32
  global.nodeImage = canvas_1.Image;
33
33
  // @ts-expect-error
34
34
  global.nodeCreateCanvas = canvas_1.createCanvas;
35
- const window = new jsdom_1.JSDOM(`...`).window;
35
+ const window = new jsdom_1.JSDOM('...').window;
36
36
  global.document = window.document;
37
37
  // @ts-expect-error
38
38
  global.window = window;
package/dist/util.js CHANGED
@@ -26,6 +26,6 @@ function convert(result, args, spawnArgs = []) {
26
26
  const a = ['-w', pngwidth, name, '-o', out, ...spawnArgs];
27
27
  const ls = (0, child_process_1.spawnSync)('rsvg-convert', a);
28
28
  console.error(`rsvg-convert stderr: ${ls.stderr.toString()}`);
29
- console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`); // eslint-disable-line no-console
29
+ console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`);
30
30
  fs_1.default.unlinkSync(name);
31
31
  }
package/esm/index.js CHANGED
@@ -8,19 +8,20 @@ import setupEnv from './setupEnv';
8
8
  setupEnv();
9
9
  const err = console.error;
10
10
  console.error = (...p) => {
11
- if (!`${p[0]}`.match('useLayoutEffect')) {
11
+ if (!/useLayoutEffect/.exec(`${p[0]}`)) {
12
12
  err(p);
13
13
  }
14
14
  };
15
15
  const warn = console.warn;
16
16
  console.warn = (...p) => {
17
- if (!`${p[0]}`.match('estimation reached timeout')) {
17
+ if (!/estimation reached timeout/.exec(`${p[0]}`)) {
18
18
  warn(p);
19
19
  }
20
20
  };
21
- // note: yargs is actually unused except for printing help
22
- // we do custom command line parsing, see parseArgv.ts
23
- // eslint-disable-next-line @typescript-eslint/no-floating-promises
21
+ // note: yargs is actually unused except for printing help we do custom command
22
+ // line parsing, see parseArgv.ts
23
+ //
24
+ // eslint-disable-next-line @typescript-eslint/no-floating-promises,@typescript-eslint/no-unused-expressions
24
25
  yargs
25
26
  .command('jb2export', 'Creates a jbrowse 2 image snapshot')
26
27
  .option('config', {
package/esm/renderRegion.js CHANGED
@@ -10,7 +10,7 @@ function read(file) {
10
10
  res = JSON.parse(fs.readFileSync(file, 'utf8'));
11
11
  }
12
12
  catch (e) {
13
- throw new Error(`Failed to parse ${file} as JSON, use --fasta if you mean to pass a FASTA file`);
13
+ throw new Error(`Failed to parse ${file} as JSON, use --fasta if you mean to pass a FASTA file`, { cause: e });
14
14
  }
15
15
  return res;
16
16
  }
@@ -33,8 +33,10 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
33
33
  var _a;
34
34
  const assemblyData = asm && fs.existsSync(asm) ? read(asm) : undefined;
35
35
  const tracksData = tracks ? read(tracks) : undefined;
36
- const configData = (config ? read(config) : {});
37
- let sessionData = session ? read(session) : undefined;
36
+ const configData = config ? read(config) : {};
37
+ let sessionData = session
38
+ ? read(session)
39
+ : undefined;
38
40
  if (config) {
39
41
  addRelativePaths(configData, path.dirname(path.resolve(config)));
40
42
  }
@@ -53,6 +55,7 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
53
55
  configData.assembly = assemblyData;
54
56
  }
55
57
  // else check if it was an assembly name in a config file
58
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
56
59
  else if ((_a = configData.assemblies) === null || _a === void 0 ? void 0 : _a.length) {
57
60
  configData.assemblies.find(entry => entry.name === asm);
58
61
  if (asm) {
@@ -77,8 +80,8 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
77
80
  adapter: {
78
81
  type: bgzip ? 'BgzipFastaAdapter' : 'IndexedFastaAdapter',
79
82
  fastaLocation: makeLocation(fasta),
80
- faiLocation: makeLocation(fasta + '.fai'),
81
- gziLocation: bgzip ? makeLocation(fasta + '.gzi') : undefined,
83
+ faiLocation: makeLocation(`${fasta}.fai`),
84
+ gziLocation: bgzip ? makeLocation(`${fasta}.gzi`) : undefined,
82
85
  },
83
86
  },
84
87
  };
@@ -100,12 +103,14 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
100
103
  }
101
104
  }
102
105
  // throw if still no assembly
106
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
103
107
  if (!configData.assembly) {
104
108
  throw new Error('no assembly specified, use --fasta to supply an indexed FASTA file (generated with samtools faidx yourfile.fa). see README for alternatives with --assembly and --config');
105
109
  }
106
110
  if (tracksData) {
107
111
  configData.tracks = tracksData;
108
112
  }
113
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
109
114
  else if (!configData.tracks) {
110
115
  configData.tracks = [];
111
116
  }
@@ -114,6 +119,9 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
114
119
  const [type, opts] = track;
115
120
  const [file, ...rest] = opts;
116
121
  const index = (_a = rest.find(r => r.startsWith('index:'))) === null || _a === void 0 ? void 0 : _a.replace('index:', '');
122
+ if (!file) {
123
+ throw new Error('no file specified');
124
+ }
117
125
  if (type === 'bam') {
118
126
  configData.tracks = [
119
127
  ...configData.tracks,
@@ -126,7 +134,7 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
126
134
  type: 'BamAdapter',
127
135
  bamLocation: makeLocation(file),
128
136
  index: {
129
- location: makeLocation(index || file + '.bai'),
137
+ location: makeLocation(index || `${file}.bai`),
130
138
  indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'BAI',
131
139
  },
132
140
  sequenceAdapter: configData.assembly.sequence.adapter,
@@ -136,7 +144,7 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
136
144
  displays: [
137
145
  {
138
146
  type: 'LinearSNPCoverageDisplay',
139
- displayId: path.basename(file) + '-' + Math.random(),
147
+ displayId: `${path.basename(file)}-${Math.random()}`,
140
148
  },
141
149
  ],
142
150
  }
@@ -155,7 +163,7 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
155
163
  adapter: {
156
164
  type: 'CramAdapter',
157
165
  cramLocation: makeLocation(file),
158
- craiLocation: makeLocation(index || file + '.crai'),
166
+ craiLocation: makeLocation(index || `${file}.crai`),
159
167
  sequenceAdapter: configData.assembly.sequence.adapter,
160
168
  },
161
169
  ...(opts.includes('snpcov')
@@ -163,7 +171,7 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
163
171
  displays: [
164
172
  {
165
173
  type: 'LinearSNPCoverageDisplay',
166
- displayId: path.basename(file) + '-' + Math.random(),
174
+ displayId: `${path.basename(file)}-${Math.random()}`,
167
175
  },
168
176
  ],
169
177
  }
@@ -198,7 +206,7 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
198
206
  type: 'VcfTabixAdapter',
199
207
  vcfGzLocation: makeLocation(file),
200
208
  index: {
201
- location: makeLocation(index || file + '.tbi'),
209
+ location: makeLocation(index || `${file}.tbi`),
202
210
  indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
203
211
  },
204
212
  },
@@ -217,7 +225,7 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
217
225
  type: 'Gff3TabixAdapter',
218
226
  gffGzLocation: makeLocation(file),
219
227
  index: {
220
- location: makeLocation(index || file + '.tbi'),
228
+ location: makeLocation(index || `${file}.tbi`),
221
229
  indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
222
230
  },
223
231
  },
@@ -266,7 +274,7 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
266
274
  type: 'BedTabixAdapter',
267
275
  bedGzLocation: makeLocation(file),
268
276
  index: {
269
- location: makeLocation(index || file + '.tbi'),
277
+ location: makeLocation(index || `${file}.tbi`),
270
278
  indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
271
279
  },
272
280
  },
@@ -277,7 +285,7 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
277
285
  if (!defaultSession) {
278
286
  // don't use defaultSession from config.json file, can result in assembly
279
287
  // name confusion
280
- delete configData.defaultSession;
288
+ configData.defaultSession = undefined;
281
289
  }
282
290
  // only allow an external manually specified session
283
291
  if (sessionData) {
@@ -287,13 +295,18 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
287
295
  }
288
296
  function process(trackEntry, view, extra = c => c) {
289
297
  const [, [track, ...opts]] = trackEntry;
298
+ if (!track) {
299
+ throw new Error('invalid command line args');
300
+ }
290
301
  const currentTrack = view.showTrack(extra(track));
291
302
  const display = currentTrack.displays[0];
292
303
  opts.forEach(opt => {
293
304
  // apply height to any track
294
305
  if (opt.startsWith('height:')) {
295
306
  const [, height] = opt.split(':');
296
- display.setHeight(+height);
307
+ if (height) {
308
+ display.setHeight(+height);
309
+ }
297
310
  }
298
311
  // apply sort to pileup
299
312
  else if (opt.startsWith('sort:')) {
@@ -325,8 +338,12 @@ function process(trackEntry, view, extra = c => c) {
325
338
  // apply min and max score to wiggle
326
339
  else if (opt.startsWith('minmax:')) {
327
340
  const [, min, max] = opt.split(':');
328
- display.setMinScore(+min);
329
- display.setMaxScore(+max);
341
+ if (min) {
342
+ display.setMinScore(+min);
343
+ }
344
+ if (max) {
345
+ display.setMaxScore(+max);
346
+ }
330
347
  }
331
348
  // apply linear or log scale to wiggle
332
349
  else if (opt.startsWith('scaletype:')) {
@@ -335,17 +352,17 @@ function process(trackEntry, view, extra = c => c) {
335
352
  }
336
353
  // draw crosshatches on wiggle
337
354
  else if (opt.startsWith('crosshatch:')) {
338
- const [, val] = opt.split(':');
355
+ const [, val = 'false'] = opt.split(':');
339
356
  display.setCrossHatches(booleanize(val));
340
357
  }
341
358
  // turn off fill on bigwig with fill:false
342
359
  else if (opt.startsWith('fill:')) {
343
- const [, val] = opt.split(':');
360
+ const [, val = 'true'] = opt.split(':');
344
361
  display.setFill(booleanize(val));
345
362
  }
346
363
  // set resolution:superfine to use finer bigwig bin size
347
364
  else if (opt.startsWith('resolution:')) {
348
- let [, val] = opt.split(':');
365
+ let [, val = 1] = opt.split(':');
349
366
  if (val === 'fine') {
350
367
  val = '10';
351
368
  }
@@ -367,12 +384,12 @@ export async function renderRegion(opts) {
367
384
  const { assemblyManager } = model;
368
385
  view.setWidth(width);
369
386
  if (loc) {
370
- const [assembly] = assemblyManager.assemblies;
387
+ const { name } = assemblyManager.assemblies[0];
371
388
  if (loc === 'all') {
372
- view.showAllRegionsInAssembly(assembly.name);
389
+ view.showAllRegionsInAssembly(name);
373
390
  }
374
391
  else {
375
- await view.navToLocString(loc, assembly.name);
392
+ await view.navToLocString(loc, name);
376
393
  }
377
394
  }
378
395
  else if (!sessionParam && !defaultSession) {
package/esm/setupEnv.js CHANGED
@@ -6,7 +6,7 @@ export default function setupEnv() {
6
6
  global.nodeImage = Image;
7
7
  // @ts-expect-error
8
8
  global.nodeCreateCanvas = createCanvas;
9
- const window = new JSDOM(`...`).window;
9
+ const window = new JSDOM('...').window;
10
10
  global.document = window.document;
11
11
  // @ts-expect-error
12
12
  global.window = window;
package/esm/util.js CHANGED
@@ -19,6 +19,6 @@ export function convert(result, args, spawnArgs = []) {
19
19
  const a = ['-w', pngwidth, name, '-o', out, ...spawnArgs];
20
20
  const ls = spawnSync('rsvg-convert', a);
21
21
  console.error(`rsvg-convert stderr: ${ls.stderr.toString()}`);
22
- console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`); // eslint-disable-line no-console
22
+ console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`);
23
23
  fs.unlinkSync(name);
24
24
  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/img",
3
- "version": "2.13.1",
3
+ "version": "2.14.0",
4
4
  "main": "dist/index.js",
5
5
  "module": "esm/index.js",
6
6
  "author": "JBrowse Team",
@@ -27,8 +27,8 @@
27
27
  "@babel/runtime": "^7.17.9",
28
28
  "@emotion/cache": "^11.7.1",
29
29
  "@emotion/react": "^11.9.0",
30
- "@jbrowse/plugin-linear-genome-view": "^2.13.1",
31
- "@jbrowse/react-linear-genome-view": "^2.13.1",
30
+ "@jbrowse/plugin-linear-genome-view": "^2.14.0",
31
+ "@jbrowse/react-linear-genome-view": "^2.14.0",
32
32
  "canvas": "^2.9.1",
33
33
  "jsdom": "^24.0.0",
34
34
  "mobx": "^6.6.0",
@@ -41,5 +41,5 @@
41
41
  "publishConfig": {
42
42
  "access": "public"
43
43
  },
44
- "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
44
+ "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
45
45
  }