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:Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec, Fall 9 : 9 Dec to 20 Dec
Description
Situation:
When determining the offsets between each level 5 region of the BAI file, the output is the number of bytes/bits. Depending on the size of the BAM file, these numbers can be very large. The data should be scaled for easier viewing in IGB.
In addition, some of the offsets are negative. It is unclear why they are negative, but when we compare the negatives to estimateCoverage from BioVizBase, they are always set to 0.
Task:
Set any negative offsets to 0.
Scale the data by determining either the mean or median for all offsets across the BAI file, then divide the offsets by that number. This should result in most offset values being around 1.
Look at Bai.java
Attachments
Issue Links
- relates to
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IGBF-1920 Visualizing the index
- Closed
Activity
Nowlan Freese
created issue -
Nowlan Freese
made changes -
Field | Original Value | New Value |
---|---|---|
Epic Link |
|
Nowlan Freese
made changes -
Nowlan Freese
made changes -
Description |
Situation:
When determining the offsets between each level 5 region of the BAI file, the output is the number of bytes/bits. Depending on the size of the BAM file, these numbers can be very large. The data should be scaled for easier viewing in IGB. In addition, some of the offsets are negative. It is unclear why they are negative, but when we compare the negatives to estimateCoverage from BioVizBase, they are always set to 0. Task: Set any negative offsets to 0. Scale the data by determining either the mean or median for all offsets across the BAI file, then divide the offsets by that number. This should result in most offset values being around 1. |
Situation:
When determining the offsets between each level 5 region of the BAI file, the output is the number of bytes/bits. Depending on the size of the BAM file, these numbers can be very large. The data should be scaled for easier viewing in IGB. In addition, some of the offsets are negative. It is unclear why they are negative, but when we compare the negatives to estimateCoverage from BioVizBase, they are always set to 0. Task: Set any negative offsets to 0. Scale the data by determining either the mean or median for all offsets across the BAI file, then divide the offsets by that number. This should result in most offset values being around 1. Look at Bai.java |
Ann Loraine
made changes -
Sprint | Fall 6 : 28 Oct to 8 Nov [ 77 ] | Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov [ 77, 78 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov [ 77, 78 ] | Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec [ 77, 78, 79 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Srishti Tiwari (Inactive)
made changes -
Assignee | Srishti Tiwari [ stiwari8 ] |
Srishti Tiwari (Inactive)
made changes -
Assignee | Srishti Tiwari [ stiwari8 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Rank | Ranked lower |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Nowlan Freese
made changes -
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Nowlan Freese
made changes -
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] | Sai Charan Reddy Vallapureddy [ svallapu ] |
Nowlan Freese
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Nowlan Freese
made changes -
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
made changes -
Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Sprint | Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec [ 77, 78, 79 ] | Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec, Fall 9 : 9 Dec to 20 Dec [ 77, 78, 79, 80 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Nowlan Freese
made changes -
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] | Sai Charan Reddy Vallapureddy [ svallapu ] |