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:Spring 1 : 25 Dec to 17 Jan, Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb
Description
Situation: Because the bai file does not include the chromosome information, we have been assuming that the order of the bai file chromosomes are the same as that in IGB. However, many bai files are not ordered exactly the same as IGB. The only way to know for sure the order of the bai file is to look at the header of the bam file. However, because we allow the user to load a bai file directly, there may not be a readable bam file.
Task: Within the BAI index visualization handler plugin, write code to identify if there is a readable bam file. The bam file should be located in the same directory as the bai file and should have the same name as the bai file, but with a .bam extension. Note that the bai itself may have .bam in front of the .bai extension (EXAMPLE.bam.bai). If a bam file is present, use the appropriate Samtools method to retrieve the bam header.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 1 : 25 Dec to 17 Jan [ 84 ] | Spring 1 : 25 Dec to 17 Jan, Spring 2 : 20 Jan to 31 Jan [ 84, 85 ] |
| Rank | Ranked higher |
| Sprint | Spring 1 : 25 Dec to 17 Jan, Spring 2 : 20 Jan to 31 Jan [ 84, 85 ] | Spring 1 : 25 Dec to 17 Jan, Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb [ 84, 85, 86 ] |
| Rank | Ranked higher |
| Assignee | Nowlan Freese [ nfreese ] | Pawan Bole [ pbole ] |
| Description | When a user loads a bai file, need to check if there is a bam header so that we can determine the order of the chromosomes. If the bam header is available, order the chromosomes for the bai graph in IGB in the same order as the bam header. |
Situation: Because the bai file does not include the chromosome information, we have been assuming that the order of the bai file chromosomes are the same as that in IGB. However, many bai files are not ordered exactly the same as IGB. The only way to know for sure the order of the bai file is to look at the header of the bam file. However, because we allow the user to load a bai file directly, there may not be a readable bam file.
Task: Within the BAI index visualization handler plugin, write code to identify if there is a readable bam file. The bam file should be located in the same directory as the bai file and should have the same name as the bai file, but with a .bam extension. Note that the bai itself may have .bam in front of the .bai extension (EXAMPLE.bam.bai). If a bam file is present, use the appropriate Samtools method to retrieve the bam header. |
| Story Points | 5 | 2 |
| Sprint | Spring 1 : 25 Dec to 17 Jan, Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb [ 84, 85, 86 ] | Spring 1 : 25 Dec to 17 Jan, Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 21 Feb [ 84, 85, 86, 87 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| 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 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Able to read bam file header.
Closing issue.