6
|
1 {
|
|
2 "configuration": {
|
|
3 "rpc": {
|
|
4 "defaultDriver": "WebWorkerRpcDriver",
|
|
5 "drivers": {
|
|
6 "MainThreadRpcDriver": {},
|
|
7 "WebWorkerRpcDriver": {}
|
|
8 }
|
|
9 },
|
|
10 "logoPath": {
|
|
11 "locationType": "UriLocation",
|
|
12 "uri": ""
|
|
13 }
|
|
14 },
|
|
15 "plugins": [],
|
|
16 "assemblies": [
|
|
17 {
|
|
18 "name": "Merlin",
|
|
19 "sequence": {
|
|
20 "type": "ReferenceSequenceTrack",
|
|
21 "trackId": "Merlin-1704349310829",
|
|
22 "adapter": {
|
|
23 "type": "IndexedFastaAdapter",
|
|
24 "fastaLocation": {
|
|
25 "locationType": "LocalPathLocation",
|
|
26 "localPath": "/home/ross/rossgit/tools-iuc/tools/jbrowse2/test-data/merlin.fa"
|
|
27 },
|
|
28 "faiLocation": {
|
|
29 "locationType": "LocalPathLocation",
|
|
30 "localPath": "/tmp/complete/Merlin.fasta.fai"
|
|
31 },
|
|
32 "metadataLocation": {
|
|
33 "locationType": "UriLocation",
|
|
34 "uri": "/path/to/fa.metadata.yaml"
|
|
35 }
|
|
36 },
|
|
37 "displays": [
|
|
38 {
|
|
39 "type": "LinearReferenceSequenceDisplay",
|
|
40 "displayId": "Merlin-1704349310829-LinearReferenceSequenceDisplay"
|
|
41 },
|
|
42 {
|
|
43 "type": "LinearGCContentDisplay",
|
|
44 "displayId": "Merlin-1704349310829-LinearGCContentDisplay"
|
|
45 }
|
|
46 ]
|
|
47 }
|
|
48 }
|
|
49 ],
|
|
50 "tracks": [
|
|
51 {
|
|
52 "type": "FeatureTrack",
|
|
53 "trackId": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz-1704349390805",
|
|
54 "name": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz",
|
|
55 "assemblyNames": [
|
|
56 "Merlin"
|
|
57 ],
|
|
58 "adapter": {
|
|
59 "type": "BedTabixAdapter",
|
|
60 "bedGzLocation": {
|
|
61 "locationType": "LocalPathLocation",
|
|
62 "localPath": "/tmp/complete/3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz"
|
|
63 },
|
|
64 "index": {
|
|
65 "location": {
|
|
66 "locationType": "LocalPathLocation",
|
|
67 "localPath": "/tmp/complete/3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz.tbi"
|
|
68 }
|
|
69 }
|
|
70 },
|
|
71 "displays": [
|
|
72 {
|
|
73 "type": "LinearBasicDisplay",
|
|
74 "displayId": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz-1704349390805-LinearBasicDisplay"
|
|
75 },
|
|
76 {
|
|
77 "type": "LinearArcDisplay",
|
|
78 "displayId": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz-1704349390805-LinearArcDisplay"
|
|
79 }
|
|
80 ]
|
|
81 },
|
|
82 {
|
|
83 "type": "VariantTrack",
|
|
84 "trackId": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277",
|
|
85 "name": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz",
|
|
86 "assemblyNames": [
|
|
87 "Merlin"
|
|
88 ],
|
|
89 "adapter": {
|
|
90 "type": "VcfTabixAdapter",
|
|
91 "vcfGzLocation": {
|
|
92 "locationType": "LocalPathLocation",
|
|
93 "localPath": "/tmp/complete/8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz"
|
|
94 },
|
|
95 "index": {
|
|
96 "location": {
|
|
97 "locationType": "LocalPathLocation",
|
|
98 "localPath": "/tmp/complete/8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz.tbi"
|
|
99 }
|
|
100 }
|
|
101 },
|
|
102 "textSearching": {
|
|
103 "textSearchAdapter": {
|
|
104 "type": "TrixTextSearchAdapter",
|
|
105 "textSearchAdapterId": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-index",
|
|
106 "ixFilePath": {
|
|
107 "locationType": "LocalPathLocation",
|
|
108 "localPath": "/home/ross/.config/@jbrowse/desktop/autosaved/trix/8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-index.ix"
|
|
109 },
|
|
110 "ixxFilePath": {
|
|
111 "locationType": "LocalPathLocation",
|
|
112 "localPath": "/home/ross/.config/@jbrowse/desktop/autosaved/trix/8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-index.ixx"
|
|
113 },
|
|
114 "metaFilePath": {
|
|
115 "locationType": "LocalPathLocation",
|
|
116 "localPath": "/home/ross/.config/@jbrowse/desktop/autosaved/trix/8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-index.json"
|
|
117 },
|
|
118 "tracks": [
|
|
119 "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277"
|
|
120 ],
|
|
121 "assemblyNames": [
|
|
122 "Merlin"
|
|
123 ]
|
|
124 }
|
|
125 },
|
|
126 "displays": [
|
|
127 {
|
|
128 "type": "LinearVariantDisplay",
|
|
129 "displayId": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-LinearVariantDisplay"
|
|
130 },
|
|
131 {
|
|
132 "type": "ChordVariantDisplay",
|
|
133 "displayId": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-ChordVariantDisplay"
|
|
134 },
|
|
135 {
|
|
136 "type": "LinearPairedArcDisplay",
|
|
137 "displayId": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-LinearPairedArcDisplay"
|
|
138 }
|
|
139 ]
|
|
140 },
|
|
141 {
|
|
142 "type": "AlignmentsTrack",
|
|
143 "trackId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556",
|
|
144 "name": "859509e7a79c8f48992e130a2a79b36e_0.bam",
|
|
145 "assemblyNames": [
|
|
146 "Merlin"
|
|
147 ],
|
|
148 "adapter": {
|
|
149 "type": "BamAdapter",
|
|
150 "bamLocation": {
|
|
151 "locationType": "LocalPathLocation",
|
|
152 "localPath": "/tmp/complete/859509e7a79c8f48992e130a2a79b36e_0.bam"
|
|
153 },
|
|
154 "index": {
|
|
155 "location": {
|
|
156 "locationType": "LocalPathLocation",
|
|
157 "localPath": "/tmp/complete/859509e7a79c8f48992e130a2a79b36e_0.bam.bai"
|
|
158 }
|
|
159 },
|
|
160 "sequenceAdapter": {
|
|
161 "type": "IndexedFastaAdapter",
|
|
162 "fastaLocation": {
|
|
163 "locationType": "LocalPathLocation",
|
|
164 "localPath": "/home/ross/rossgit/tools-iuc/tools/jbrowse2/test-data/merlin.fa"
|
|
165 },
|
|
166 "faiLocation": {
|
|
167 "locationType": "LocalPathLocation",
|
|
168 "localPath": "/tmp/complete/Merlin.fasta.fai"
|
|
169 },
|
|
170 "metadataLocation": {
|
|
171 "locationType": "UriLocation",
|
|
172 "uri": "/path/to/fa.metadata.yaml"
|
|
173 }
|
|
174 }
|
|
175 },
|
|
176 "displays": [
|
|
177 {
|
|
178 "type": "LinearAlignmentsDisplay",
|
|
179 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearAlignmentsDisplay"
|
|
180 },
|
|
181 {
|
|
182 "type": "LinearPileupDisplay",
|
|
183 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearPileupDisplay"
|
|
184 },
|
|
185 {
|
|
186 "type": "LinearSNPCoverageDisplay",
|
|
187 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearSNPCoverageDisplay"
|
|
188 },
|
|
189 {
|
|
190 "type": "LinearReadArcsDisplay",
|
|
191 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearReadArcsDisplay"
|
|
192 },
|
|
193 {
|
|
194 "type": "LinearReadCloudDisplay",
|
|
195 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearReadCloudDisplay"
|
|
196 }
|
|
197 ]
|
|
198 },
|
|
199 {
|
|
200 "type": "FeatureTrack",
|
|
201 "trackId": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492",
|
|
202 "name": "1838188642fecd9922f419a0e735e755_0.gff3.gz",
|
|
203 "assemblyNames": [
|
|
204 "Merlin"
|
|
205 ],
|
|
206 "adapter": {
|
|
207 "type": "Gff3TabixAdapter",
|
|
208 "gffGzLocation": {
|
|
209 "locationType": "LocalPathLocation",
|
|
210 "localPath": "/tmp/complete/1838188642fecd9922f419a0e735e755_0.gff3.gz"
|
|
211 },
|
|
212 "index": {
|
|
213 "location": {
|
|
214 "locationType": "LocalPathLocation",
|
|
215 "localPath": "/tmp/complete/1838188642fecd9922f419a0e735e755_0.gff3.gz.tbi"
|
|
216 }
|
|
217 }
|
|
218 },
|
|
219 "displays": [
|
|
220 {
|
|
221 "type": "LinearBasicDisplay",
|
|
222 "displayId": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492-LinearBasicDisplay"
|
|
223 },
|
|
224 {
|
|
225 "type": "LinearArcDisplay",
|
|
226 "displayId": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492-LinearArcDisplay"
|
|
227 }
|
|
228 ]
|
|
229 },
|
|
230 {
|
|
231 "type": "QuantitativeTrack",
|
|
232 "trackId": "merlin.bw-1704349777260",
|
|
233 "name": "merlin.bw",
|
|
234 "assemblyNames": [
|
|
235 "Merlin"
|
|
236 ],
|
|
237 "adapter": {
|
|
238 "type": "BigWigAdapter",
|
|
239 "bigWigLocation": {
|
|
240 "locationType": "LocalPathLocation",
|
|
241 "localPath": "/home/ross/rossgit/tools-iuc/tools/jbrowse2/test-data/bw/merlin.bw"
|
|
242 }
|
|
243 },
|
|
244 "displays": [
|
|
245 {
|
|
246 "type": "LinearWiggleDisplay",
|
|
247 "displayId": "merlin.bw-1704349777260-LinearWiggleDisplay"
|
|
248 }
|
|
249 ]
|
|
250 }
|
|
251 ],
|
|
252 "internetAccounts": [
|
|
253 {
|
|
254 "type": "DropboxOAuthInternetAccount",
|
|
255 "internetAccountId": "dropboxOAuth",
|
|
256 "name": "Dropbox",
|
|
257 "description": "Account to access Dropbox files",
|
|
258 "clientId": "ykjqg1kr23pl1i7"
|
|
259 },
|
|
260 {
|
|
261 "type": "GoogleDriveOAuthInternetAccount",
|
|
262 "internetAccountId": "googleOAuth",
|
|
263 "name": "Google Drive",
|
|
264 "description": "Account to access Google Drive files",
|
|
265 "clientId": "109518325434-m86s8a5og8ijc5m6n7n8dk7e9586bg9i.apps.googleusercontent.com"
|
|
266 }
|
|
267 ],
|
|
268 "aggregateTextSearchAdapters": [],
|
|
269 "connections": [],
|
|
270 "defaultSession": {
|
|
271 "connectionInstances": [],
|
|
272 "drawerPosition": "right",
|
|
273 "drawerWidth": 384,
|
|
274 "widgets": {
|
|
275 "GridBookmark": {
|
|
276 "id": "GridBookmark",
|
|
277 "type": "GridBookmarkWidget"
|
|
278 },
|
|
279 "addTrackWidget": {
|
|
280 "id": "addTrackWidget",
|
|
281 "type": "AddTrackWidget",
|
|
282 "view": "oATIzuZAL61OxOyGsWP1l"
|
|
283 },
|
|
284 "JobsList": {
|
|
285 "id": "JobsList",
|
|
286 "type": "JobsListWidget",
|
|
287 "jobs": [],
|
|
288 "finished": [
|
|
289 {
|
|
290 "name": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-index",
|
|
291 "statusMessage": "done",
|
|
292 "progressPct": 100
|
|
293 }
|
|
294 ],
|
|
295 "queued": [],
|
|
296 "aborted": []
|
|
297 },
|
|
298 "configEditor": {
|
|
299 "id": "configEditor",
|
|
300 "type": "ConfigurationEditorWidget",
|
|
301 "target": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492"
|
|
302 },
|
|
303 "hierarchicalTrackSelector": {
|
|
304 "id": "hierarchicalTrackSelector",
|
|
305 "type": "HierarchicalTrackSelectorWidget",
|
|
306 "initialized": true,
|
|
307 "collapsed": {},
|
|
308 "view": "oATIzuZAL61OxOyGsWP1l",
|
|
309 "faceted": {
|
|
310 "filterText": "",
|
|
311 "showSparse": false,
|
|
312 "showFilters": true,
|
|
313 "showOptions": false,
|
|
314 "panelWidth": 400
|
|
315 }
|
|
316 }
|
|
317 },
|
|
318 "activeWidgets": {
|
|
319 "hierarchicalTrackSelector": "hierarchicalTrackSelector"
|
|
320 },
|
|
321 "minimized": false,
|
|
322 "id": "0RCNRFfuiied_MUxKv21r",
|
|
323 "name": "New Session 1/4/2024, 5:21:50 PM",
|
|
324 "margin": 0,
|
|
325 "views": [
|
|
326 {
|
|
327 "id": "oATIzuZAL61OxOyGsWP1l",
|
|
328 "minimized": false,
|
|
329 "type": "LinearGenomeView",
|
|
330 "offsetPx": 0,
|
|
331 "bpPerPx": 113.22935779816514,
|
|
332 "displayedRegions": [
|
|
333 {
|
|
334 "refName": "Merlin",
|
|
335 "start": 0,
|
|
336 "end": 172788,
|
|
337 "reversed": false,
|
|
338 "assemblyName": "Merlin"
|
|
339 }
|
|
340 ],
|
|
341 "tracks": [
|
|
342 {
|
|
343 "id": "6q8cZDkFnpribnYm8CCn5",
|
|
344 "type": "FeatureTrack",
|
|
345 "configuration": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz-1704349390805",
|
|
346 "minimized": false,
|
|
347 "displays": [
|
|
348 {
|
|
349 "id": "5lTYaGmlQD_RJMDpG-Mol",
|
|
350 "type": "LinearBasicDisplay",
|
|
351 "configuration": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz-1704349390805-LinearBasicDisplay"
|
|
352 }
|
|
353 ]
|
|
354 },
|
|
355 {
|
|
356 "id": "O9bSW2YKphod5uuN1za6E",
|
|
357 "type": "VariantTrack",
|
|
358 "configuration": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277",
|
|
359 "minimized": false,
|
|
360 "displays": [
|
|
361 {
|
|
362 "id": "31Hdn7-9Dnr0L6PSxiDmf",
|
|
363 "type": "LinearVariantDisplay",
|
|
364 "configuration": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-LinearVariantDisplay"
|
|
365 }
|
|
366 ]
|
|
367 },
|
|
368 {
|
|
369 "id": "IcnRsR2AjMxQq6wiOT9Vi",
|
|
370 "type": "AlignmentsTrack",
|
|
371 "configuration": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556",
|
|
372 "minimized": false,
|
|
373 "displays": [
|
|
374 {
|
|
375 "id": "Dvu0sQCwrUmkze6Zua8JY",
|
|
376 "type": "LinearAlignmentsDisplay",
|
|
377 "PileupDisplay": {
|
|
378 "id": "ulHQgd0Omh3VttUCKyvPi",
|
|
379 "type": "LinearPileupDisplay",
|
|
380 "heightPreConfig": 205,
|
|
381 "configuration": {
|
|
382 "type": "LinearPileupDisplay",
|
|
383 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearAlignmentsDisplay_LinearPileupDisplay_xyz"
|
|
384 },
|
|
385 "filterBy": {
|
|
386 "flagInclude": 0,
|
|
387 "flagExclude": 1540
|
|
388 },
|
|
389 "jexlFilters": [],
|
|
390 "showSoftClipping": false
|
|
391 },
|
|
392 "SNPCoverageDisplay": {
|
|
393 "id": "z_mkwAGHGZCZpvqG0AEMg",
|
|
394 "type": "LinearSNPCoverageDisplay",
|
|
395 "heightPreConfig": 45,
|
|
396 "configuration": {
|
|
397 "type": "LinearSNPCoverageDisplay",
|
|
398 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearAlignmentsDisplay_snpcoverage_xyz"
|
|
399 },
|
|
400 "selectedRendering": "",
|
|
401 "resolution": 1,
|
|
402 "constraints": {},
|
|
403 "filterBy": {
|
|
404 "flagInclude": 0,
|
|
405 "flagExclude": 1540
|
|
406 },
|
|
407 "jexlFilters": []
|
|
408 },
|
|
409 "snpCovHeight": 45,
|
|
410 "configuration": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearAlignmentsDisplay",
|
|
411 "lowerPanelType": "LinearPileupDisplay"
|
|
412 }
|
|
413 ]
|
|
414 },
|
|
415 {
|
|
416 "id": "sqXxD9i7mkIgJX9bStLFp",
|
|
417 "type": "FeatureTrack",
|
|
418 "configuration": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492",
|
|
419 "minimized": false,
|
|
420 "displays": [
|
|
421 {
|
|
422 "id": "ot2hxRedj7L-2eOtTfj47",
|
|
423 "type": "LinearBasicDisplay",
|
|
424 "configuration": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492-LinearBasicDisplay"
|
|
425 }
|
|
426 ]
|
|
427 },
|
|
428 {
|
|
429 "id": "w8XYtNAPQ77lYiJ4yfTc_",
|
|
430 "type": "QuantitativeTrack",
|
|
431 "configuration": "merlin.bw-1704349777260",
|
|
432 "minimized": false,
|
|
433 "displays": [
|
|
434 {
|
|
435 "id": "R7aBFiHHKrly_WAFzxdcN",
|
|
436 "type": "LinearWiggleDisplay",
|
|
437 "configuration": "merlin.bw-1704349777260-LinearWiggleDisplay",
|
|
438 "selectedRendering": "",
|
|
439 "resolution": 1,
|
|
440 "constraints": {}
|
|
441 }
|
|
442 ]
|
|
443 },
|
|
444 {
|
|
445 "id": "vCT2YxTb4kbBwbjU7y0Nw",
|
|
446 "type": "ReferenceSequenceTrack",
|
|
447 "configuration": "Merlin-1704349310829",
|
|
448 "minimized": false,
|
|
449 "displays": [
|
|
450 {
|
|
451 "id": "1hj13cpwWU1pHF9KyXyYA",
|
|
452 "type": "LinearReferenceSequenceDisplay",
|
|
453 "heightPreConfig": 50,
|
|
454 "configuration": "Merlin-1704349310829-LinearReferenceSequenceDisplay",
|
|
455 "showForward": true,
|
|
456 "showReverse": true,
|
|
457 "showTranslation": true
|
|
458 }
|
|
459 ]
|
|
460 }
|
|
461 ],
|
|
462 "hideHeader": false,
|
|
463 "hideHeaderOverview": false,
|
|
464 "hideNoTracksActive": false,
|
|
465 "trackSelectorType": "hierarchical",
|
|
466 "showCenterLine": false,
|
|
467 "showCytobandsSetting": true,
|
|
468 "trackLabels": "",
|
|
469 "showGridlines": true,
|
|
470 "showBookmarkHighlights": true,
|
|
471 "showBookmarkLabels": true
|
|
472 }
|
|
473 ],
|
|
474 "sessionAssemblies": [],
|
|
475 "temporaryAssemblies": [],
|
|
476 "focusedViewId": "oATIzuZAL61OxOyGsWP1l"
|
|
477 }
|
|
478 } |