Cleaned up module "bam"
https://bitbucket.org/aloraine/alorainefork/branch/IGBF-1699#diff

Purged references to sf.net and igb-picard as this old functionality has been replaced by htsjdk-igb, which is being deployed as an OSGi bundle from https://github.com/lorainelab/htsjdk branch igb-2.16.2 (currently).

Previously Kiran Korey worked on this. I'm not sure why he did not already remove these references – possibly because of a note in the BAM parser module requesting that we retain some old unused code for creating BAM indexes. He may not have wanted to remove that code, which was forcing us to keep the old artifact hanging around.

I got rid of it.

Merged commits into master. Moving to needs to testing.

To test:

• Unpack master branch jar file
• Check that the igb jar file no longer contains the purged dependencies
• Can review commit history to determine which packages are not longer in the project.

Also, some good news from Chaitanya Kintali who found installers from latest master are smaller than 9.0.2 installer. See: https://jira.transvar.org/browse/IGBF-1548

Prof. [~aloraine], I have checked each and every jar under the master jar file for the unneeded dependencies.
I have found that IGB has a dependency on genometry module which again is dependent on net.sf. Also, the shared-lib-wrapper is dependent on net.sf. Could you please confirm if we need to change that or not?
Also, I have searched the codebase just to confirm if there are any references to the unneeded dependencies or not.
I had a few doubts:
1) The build.xml file has a copy tag : <copy file="$

/picard.bnd.jar" todir="temp/bundle" />
Could you please confirm if this is really needed not not?
2) There are some error messges in the BAM and SAM files which has references to picard. Do we need to change them as well?

Is "build.xml" being used? I think it may be obsolete and we can remove it, but I'm not sure. Please investigate – maybe you can try building locally and in bb pipelines to determine if we can safely remove it.

Regarding your question about net.sf: Can you please check which packages and code are being used from these two?

Sure Prof. [~aloraine]. I will investigate on both the things and will provide an update on this soon.

I found out that the build.xml is a part of Luceneindexing folder under tools which is used to create apache lucene indexes on a directory of data files for IGB. I am not sure if it is needed because when I removed the folder from the tools directory in IGB Project then I was able to build the project successfully.
Prof. [~aloraine], please let me know if I need to push these changes in the master.
Regarding the net.sf dependency, the genometry and shared-lib-wrapper module uses image4j package.

Yes please – it is fine to remove lucene indexing code from the repository. It's not being used for anything.