Details
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Type:
New Feature
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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 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May
Description
Currently, the BAI file reader is converting the BAI file to a temporary graph file, which is then getting read.
It would be far more efficient to simply read the file directly and create a GraphSym out of it.
For this task, modify the code to create a GraphSym instead of a BedGraph intermediate file. To do this, make a new SymLoader class that will be returned by the FileLoader class.
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Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Rank | Ranked higher |
| Rank | Ranked higher |
Some example bai/bam files that Pawan and I have been using for testing: https://drive.google.com/drive/folders/1Y9krI6VX3vBzTKEcneGy1McnMJEK739m
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Pooja Nikhare [ pooja.nikhare ] |
| Description |
Currently, the BAI file reader is converting the BAI file to a temporary graph file, which is then getting read.
It would be far more efficient to simply read the file directly and create a GraphSym out of it. For this task, modify the code to create a GraphSym instead of a BedGraph intermediate file. |
Currently, the BAI file reader is converting the BAI file to a temporary graph file, which is then getting read.
It would be far more efficient to simply read the file directly and create a GraphSym out of it. For this task, modify the code to create a GraphSym instead of a BedGraph intermediate file. To do this, make a new SymLoader class that will be returned by the FileLoader class |
| Description |
Currently, the BAI file reader is converting the BAI file to a temporary graph file, which is then getting read.
It would be far more efficient to simply read the file directly and create a GraphSym out of it. For this task, modify the code to create a GraphSym instead of a BedGraph intermediate file. To do this, make a new SymLoader class that will be returned by the FileLoader class |
Currently, the BAI file reader is converting the BAI file to a temporary graph file, which is then getting read.
It would be far more efficient to simply read the file directly and create a GraphSym out of it. For this task, modify the code to create a GraphSym instead of a BedGraph intermediate file. To do this, make a new SymLoader class that will be returned by the FileLoader class. |
I have converted the Output after bin comparison of chromosomes to and input stream instead of temp file and then parsing the data to create syms.
Please review the changes :
https://bitbucket.org/pnikhare/integrated-genome-browser/branch/IGBF-2329#diff
Testing Steps:
- Use bai files given in the above comments
Example bai: http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Bam/Bam_HomoSapien.bai - Click on Homo Sapien species and click on open file to select bai file
- View the local files under the data access tab
- Verify the track name has .bai extension
- Click on load data. The parsed data is loaded.
cc : [~aloraine] , Nowlan Freese - I have not yet added changes from pawan's branch. I can do that once tested.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Pooja Nikhare [ pooja.nikhare ] |
Lets test the basic functionality after the meeting.
Depending on how that goes, please make a next draft of BaiSymLoader.java which removes unneeded code:
- The bai format does not have track lines or comments. Remove code for parsing and handling track lines.
- Check for code that is not called or does not override - and remove it.
Refactored BaiSymLoader file. Please review:
https://bitbucket.org/pnikhare/integrated-genome-browser/branch/IGBF-2329#diff
| Sprint | Spring 7 : 13 Apr to 24 Apr [ 92 ] | Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 92, 93 ] |
| Rank | Ranked higher |
This looks fine to me and ready for PR.
Pawan Bole and Nowlan Freese - could you also take a look?
| Sprint | Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 92, 93 ] | Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 92, 93, 94 ] |
| Rank | Ranked higher |
| 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 ] |
| Assignee | Pooja Nikhare [ pooja.nikhare ] |
As of today, Pawan is working on this branch:
https://bitbucket.org/pawanbole/integrated-genome-browser-pawan/branch/IGBF-2221
Review:
esp. Wiggle.java which capture graph loading logic