Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Critical
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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:1
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Epic Link:
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Sprint:Fall 2
Description
Situation: We've recently added support for the CRAM file format to IGB.
Task: Update the File Formats page of the IGB Release Documentation to include a test case for the CRAM file format.
Attachments
Activity
Field | Original Value | New Value |
---|---|---|
Epic Link | IGBF-1531 [ 17617 ] |
Rank | Ranked higher |
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Attachment | NB72462M_HomoSapien.cram [ 18502 ] |
Attachment | NB72462M_HomoSapien.cram.crai [ 18503 ] |
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Assignee | Paige Kulzer [ pkulzer ] | Nowlan Freese [ nfreese ] |
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Assignee | Nowlan Freese [ nfreese ] | Paige Kulzer [ pkulzer ] |
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 ] |
I've added a CRAM section to the File Formats page which includes the name of the file to be added from the Smoke Testing Quickload, the chromosome and region to zoom to, and a picture of what IGB should look like at that region.
Next steps: Add the CRAM file and its index to the Smoke Testing Quickload. Since the original CRAM file is quite large, I've subsetted it to only include a small region of chromosome 2 using samtools:
I then checked the header to confirm that only the specified region was included (which it was):