Details
-
Type:
Bug
-
Status: Closed (View Workflow)
-
Priority:
Minor
-
Resolution: Fixed
-
Labels:None
Description
make sure IGB can handle VCF files
Attachments
Issue Links
- relates to
-
BUG-622 File format issues
-
- Closed
-
Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Lance Frohman [ lfrohman ] | Michael Lawrence [ michafla ] |
ready to test
| Assignee | Michael Lawrence [ michafla ] | Alyssa Gulledge [ alyssa ] |
| Attachment | ALL.chr20.vqsr_2of5_union_200_sites_for_validation.20101123.indels.genotypes.vcf.gz [ 11097 ] | |
| Attachment | ALL.chr20.vqsr_2of5_union_200_sites_for_validation.20101123.indels.genotypes.vcf.gz.tbi [ 11098 ] |
To test - do NOT load the vcf plug-in. See that the error message properly pops-up. Then load the vcf plug-in. Make sure there is no pop-up error and make sure the vcf file loads (H. sapiens, chr20)
| Assignee | Alyssa Gulledge [ alyssa ] | Katharine Kubiak [ kkubiak ] |
Is the VCF plug-in updated for 7.0?
| Assignee | Katharine Kubiak [ kkubiak ] | Lance Frohman [ lfrohman ] |
yes, VCF plugin for 7.0 is ready
| Assignee | Lance Frohman [ lfrohman ] | Katharine Kubiak [ kkubiak ] |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Assignee | Katharine Kubiak [ kkubiak ] | |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Summary | error with no VCF plugin | Handle VCF files without plug in |
| Reporter | Lance Frohman [ lfrohman ] | Alyssa Gulledge [ alyssa ] |
| Description | I rebuilt the trunk fresh, and the VCF plugin is apparently not loaded. Despite that, the dbSNP track showed up from our Quickload site. When I tried to load it, I got "SEVERE: no handler for file type vcf", which was not surprising. However, IGB keeps working (progress bar keeps going) forever after that, and the cancel button does not stop it. | make sure IGB can handle VCF files |
| Status | Reopened [ 4 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] |
Now it will popup with an error message