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
Add to User Guide
BNIB files can also be partially loaded for the range of the chromosome in view. Since BNIB files use a lot of memory, partial loading can be useful if you have many tracks open at once.
Open IGB, do NOT choose a species. Download the attached file to desktop, then drag into IGB. Chose 'Load region in view' and Zoom in entirely. click Load Data. Now zoom out slightly to see that only the selected portion of the file loaded (sequence) and not the whole track. This method will load the sequence file as a track and NOT as a reference sequence (this is correct).
Test Case Results
Oct 1, 2010 - Alyssa Gulledge
version 6.4 (6969) This is working exactly as described. Picture 1 shows the gray bar that was partially loaded (then zoomed out a bit.)
Attachments
Issue Links
- relates to
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BUG-622 File format issues
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | vikram bishnoi [ vbishnoi ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Anuj Puram [ anuj ] |
| Assignee | Anuj Puram [ anuj ] | Alyssa Gulledge [ alyssa ] |
| Attachment | chr1.bnib.zip [ 10568 ] | |
| Description |
Add to User Guide BNIB files can also be partially loaded for the range of the chromosome in view. Since BNIB files use a lot of memory, partial loading can be useful if you have many tracks open at once. Test Case Description Open A Thaliana, genome 2008. Zoom in on a region. Load from URL http://www.bioviz.org/quickload/A_thaliana_Apr_2008/chr1.bnib Chose 'Load region in view' and refresh Zoom out slightly to see the gray bar indicating loaded sequence is only a region and not the whole chromosome. Zoom in entirely to ensure that the sequence did load properly. Open the 'Show Console' selection under the 'Help' tab. Confirm that the last line(s) contain Response Code 20X (ie, 200, 206, etc.) Test Case Results Oct 1, 2010 - Alyssa Gulledge version 6.4 (6969) This is working exactly as described. Picture 1 shows the gray bar that was partially loaded (then zoomed out a bit.) |
Add to User Guide BNIB files can also be partially loaded for the range of the chromosome in view. Since BNIB files use a lot of memory, partial loading can be useful if you have many tracks open at once. Open IGB, do NOT choose a species. Download the attached file to desktop, then drag into IGB. Chose 'Load region in view' and Zoom in entirely. click Load Data. Now zoom out slightly to see that only the selected portion of the file loaded (sequence) and not the whole track. This method will load the sequence file as a track and NOT as a reference sequence (this is correct). Test Case Results Oct 1, 2010 - Alyssa Gulledge version 6.4 (6969) This is working exactly as described. Picture 1 shows the gray bar that was partially loaded (then zoomed out a bit.) |
| Assignee | Alyssa Gulledge [ alyssa ] | Anuj Puram [ anuj ] |
| Comment |
[ The link http://www.bioviz.org/quickload/A_thaliana_Apr_2008/chr1.bnib is not found ] |
| Assignee | Anuj Puram [ anuj ] | Katharine Kubiak [ kkubiak ] |
| Attachment | issue_bnib.bmp [ 10572 ] |
I followed the description and ended up with a light grey bar. I took a screen shot (attached issue_bnib.bmp).
| Assignee | Katharine Kubiak [ kkubiak ] | Alyssa Gulledge [ alyssa ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Vineeth Mylapur [ smylapur ] |
| Assignee | Vineeth Mylapur [ smylapur ] |
| Status | Reopened [ 4 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
Passed V.13526, Mac, Java 1.06.0_37
'Load Region in View' NO LONGER EXISTS in IGB 7.0.0 (13526). BNIB sequence files are loaded as their own track and if user zooms in to a certain region and clicks 'Load Data' at the top of the main viewer, only that region will load. 'Load Mode' is automatically set to Manual to allow for partial loading of data.
| Assignee | Alyssa Gulledge [ alyssa ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
Passed v9906 on Mac