first commit
Accidentally added unit tests instead of the actual GATK framework. I removed the unit tests and added the framework.
Added README.
Forgot to 'git add'. Now I've added the GATK Framework code.
Removed all GATK code, added jar dependencies, and wrote a good beginning of the code. It is not functional yet, but should give enough to become comfortable.
Delete VCFReader.java

Not part of the code. Was just practice using an example I found on the web (http://plindenbaum.blogspot.fr/2012/11/readingwriting-vcf-file-with-gatk-api.html).
Added more logic to SetOperator for argument parsing and intersecting. Also fixed several bugs.
Merge branch 'master' of github.com:mebbert/NewProject2
Delete tmp1.vcf
Delete tmp1.vcf.idx
Improved intersect logic and updated various methods in VariantPool and other data structures.
Merge branch 'master' of github.com:mebbert/NewProject2
Updated Intersect logic.
Added UtilityBelt and beginnings of VarStats. Also began union logic for SetOperator.
Updated Union logic. Also added command line option to include/exclude 'chr' in chromosome
Added VarStats.java
The latest version of VarStats.
this is a test commit
Latest changes to Varstats and Varstatsengine
Merge branch 'master' of https://github.com/mebbert/NewProject2.git