Created a gatk walker to do the same thing as the maf2igv.py scrips but work with different type of variant files.
There are currently a number of differences between them.
Added guard to test for the case at the end of the rod.
Added -bam input because it didn't like using -I with a RODWalker.
Added "exit" to the end of the generated script.

Replacing "".format with String.format().
Modifying maf2igv.sh to make it run gatk instead of maf2igv.py.
Deleting python script and renaming run script.
Wrote a very barebones walker to do the same thing as maf2igv.py.
Merge branch 'CreatingWalker'

Conflicts:
	maf2igv.py