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:5
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Epic Link:
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Sprint:Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar
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: If a bam header was retrieved successfully, use the chromosome order from the bam header instead of the genome.txt order to assign chromosome values to the bai data. For example, if the order in the bam header is chr3, chr1, chr2, then this is the order that the data will be retrieved from the bai file. You do not need to sort the data.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| 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. |
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: If a bam header was retrieved successfully, use the chromosome order from the bam header instead of the genome.txt order to assign chromosome values to the bai data. For example, if the order in the bam header is chr3, chr1, chr2, then this is the order that the data will be retrieved from the bai file. You do not need to sort the data. |
| Sprint | Spring 3 : 3 Feb to 14 Feb [ 86 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 21 Feb [ 86, 87 ] |
| Rank | Ranked higher |
| Attachment | galaxy_outOfOrder.bam [ 14656 ] | |
| Attachment | galaxy_outOfOrder.bam.bai [ 14657 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb [ 86, 87 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 86, 87, 89 ] |
| Rank | Ranked higher |
| Attachment | sorted.bam [ 14664 ] | |
| Attachment | sorted.bam.bai [ 14665 ] | |
| Attachment | sorted.sam [ 14666 ] | |
| Attachment | unsorted.bam [ 14667 ] | |
| Attachment | unsorted.bam.bai [ 14668 ] | |
| Attachment | unsorted.sam [ 14669 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Pawan Bole [ pbole ] | Nowlan Freese [ nfreese ] |
| Story Points | 3 | 5 |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Attachment | sorted.bam [ 14664 ] |
| Attachment | sorted.bam.bai [ 14665 ] |
| Attachment | sorted.sam [ 14666 ] |
| Attachment | unsorted.bam [ 14667 ] |
| Attachment | unsorted.bam.bai [ 14668 ] |
| Attachment | unsorted.sam [ 14669 ] |
| Attachment | galaxy_outOfOrder.bam [ 14656 ] |
| Attachment | galaxy_outOfOrder.bam.bai [ 14657 ] |
| Assignee | Nowlan Freese [ nfreese ] | Pawan Bole [ pbole ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 86, 87, 89 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 86, 87, 89, 90 ] |
| Rank | Ranked higher |
| Assignee | Pawan Bole [ pbole ] | Nowlan Freese [ nfreese ] |
| 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 ] |
| Assignee | Nowlan Freese [ nfreese ] | Pawan Bole [ pbole ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Pawan Bole [ pbole ] | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| 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 ] |