Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
Description
Bookmarks does not check if file type is supported in IGB or not.
1. Open IGB to homo sapiens, chr20. In plug in panel, activate the VCFHandler plug in.
2. Download BOTH attached files to desktop. Load only the main file (NOT the .tbi) - it does NOT need to be unzipped. Click load data.
3. Make a bookmark. Close but do NOT reset IGB.
4 Reopen IGB, in the plug-in panel, unclick VCFHandler. Double click bookmark. See that it reports that IGB does not recognize the file type.
5. Reactivate the VCFHandler plugin. Double click the bookmark. Everything should load without problems.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | Katharine Kubiak [ kkubiak ] |
| Assignee | Katharine Kubiak [ kkubiak ] | Alyssa Gulledge [ alyssa ] |
IGB reports that the file type is not supported (twice) but then loads the other files. Console reports warnings but no errors.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Attachment | ALL.chr20.vqsr_2of5_union_200_sites_for_validation.20101123.indels.genotypes.vcf.gz [ 10654 ] | |
| Attachment | ALL.chr20.vqsr_2of5_union_200_sites_for_validation.20101123.indels.genotypes.vcf.gz.tbi [ 10655 ] |
| Description | Bookmarks does not check if file type is supported in IGB or not. |
Bookmarks does not check if file type is supported in IGB or not. 1. Open IGB to homo sapiens, chr20. In plug in panel, activate the VCFHandler plug in. 2. Download BOTH attached files to desktop. Load only the main file (NOT the .tbi) - it does NOT need to be unzipped. Click load data. 3. Make a bookmark. Close but do NOT reset IGB. 4 Reopen IGB, in the plug-in panel, unclick VCFHandler. Double click bookmark. See that it reports that IGB does not recognize the file type. 5. Reactivate the VCFHandler plugin. Double click the bookmark. Everything should load without problems. |
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
VCFHandler plugin NO LONGER EXISTS in IGB 7.0 (V.13526).
Passed V.13526, Mac, Java 1.06.0_37
Tested bookmarking .vcf file, closing IGB, and repoening bookmark and no issues occurred.
| Assignee | Alyssa Gulledge [ alyssa ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
Fixed in r8878.
Check if combination of supported and unsupported file works or not.