Removed net.sf.samtools library, the changes are in the branch mentioned below.
https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1098-sam-so

Ready for first level review.

The branch mentioned above (https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1098-sam-so) has been replaced by this branch:
https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1371-library
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My comments:

The commit for removing the net.sf.samtools is clearly just that.
And the formatting fixes are very simple and clearly just that.
So the code-review and the git review are good. : )

These changes are minor and only affect the pom file. We have already removed all of the import statements for the samtools library.
To make sure IGB is able to build without the net.sf.sam-exec library, I removed it from my .m2, and I cleared IGB's bundle directory, and I ran $mvn clean install.
IGB was able to build with tests, without errors, and run. The net.sf.sam-exec was not re-downloaded to .m2, so it looks like IGB is completely free of the dependency.
That's the only functional review I can think of for this, and it looks good. : )

I'm reassigning this to Kiran and moving it to ready for pull request.

----Because this changes the same files as the IGBF-1366 fix, you may want to put all changes on one branch. Otherwise you will need to do a rebase between the pull requests (maybe ask Ann).

I have made all the changes for 1366 and 1371 in a single branch.

https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1371-library

Please do take a look at it once.

This looks good.
comments are in issue IGBF-1366

Moving this issue to pull request submitted.
Will close IGBF-1366 once the case study document is ready.

Possible problem:

• sam-ext library references are gone, but samVersion is still defined in parent POM (top-level pom.xml)

Check to see if samVersion variable is still needed now that sam-ext library is purged. If not, remove it from parent POM and instances of it being used in child POMs.

I have changed the sam-ext version to htsjdkVersion.
Also, there is a newer version of the library which is available, do you want me to change the version to the newer version.

Tested on master for the functional testing case mentioned by Ivory.
Works fine!
Moving it to done column!