As of today, Pawan is working on this branch:
https://bitbucket.org/pawanbole/integrated-genome-browser-pawan/branch/IGBF-2221

Review:

• com.affymetrix.genometry.symloader

esp. Wiggle.java which capture graph loading logic

Example bedgraph: http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/BedGraph/BedGraph_HomoSapien.bedGraph

Example bai: http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Bam/Bam_HomoSapien.bai

Some example bai/bam files that Pawan and I have been using for testing: https://drive.google.com/drive/folders/1Y9krI6VX3vBzTKEcneGy1McnMJEK739m

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.

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

This looks fine to me and ready for PR.
Pawan Bole and Nowlan Freese - could you also take a look?