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
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| 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 |
| 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 ] |
| Rank | Ranked higher |
| 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 ] |
| Rank | Ranked higher |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
| Rank | Ranked lower |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Nowlan Freese
Branch: https://bitbucket.org/svallapu/charan_igb/branch/IGBF-2100-New
Tasks:
1. Removed Negative values. It scaled the bed graph.
2. Last chuck is now handled.
Note: Logic for generating graph is changed. (More lines are added and removed for the same)
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] | Nowlan Freese [ nfreese ] |
Data is scaled correctly and negative values are now set at 0. In addition, the final chunk of each chromosome is showing correctly.
Ready for pull request.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Nowlan Freese [ nfreese ] | Sai Charan Reddy Vallapureddy [ svallapu ] |
Pull request submitted.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] | Ann Loraine [ aloraine ] |
Merged to master.
Sai Charan Reddy Vallapureddy and Nowlan Freese - please note I am about to increment master branch to 9.1.2. You may wish to wait until those for testing.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| 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 ] |
| Rank | Ranked higher |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Data are scaled with no negative values. Last chunk is present.
Closing issue.
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Nowlan Freese [ nfreese ] | Sai Charan Reddy Vallapureddy [ svallapu ] |
Bai.java has been renamed to BaiToBedgraphConverter.java