Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5
Description
Please see attached image.
Explain in the comments here how I can select the index file for running a coverage graph analysis.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2376 [ 18533 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Story Points | 0.25 | 2 |
| Sprint | Winter 4 Feb 8 - Feb 19 [ 114 ] | Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 114, 115 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Tested:
1) Only the file names are required instead of the full path.
2) The bai name is autofilled unless no bai is found.
3) The "Select a file" tooltip has been updated to "Enter the name of your BAM file"
Closing issue.
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
Notes: The Create Scaled Coverage Graph app requires the user select a bai index file. Currently, the user must provide the full path to the index file.
Possible improvements:
1) Only require the name of the file for both the bam and bai index. Assume that the files are located in the user's current working directory and use that path + filename when submitting the analysis.
2) Attempt to automatically fill the index. Bai indexes should be one of two options: the exampleBam.bam.bai or exampleBam.bai. If neither is found in the current working directory then allow the user to fill in the name of the bai index (technically the bai index can be named anything.bai or anything.bam.bai).
3) Improve the default values shown. "Select a file" is misleading and should be changed to: "Enter the file name".