PairHMM test case compiles
adding test case that triggers bug in soot
adding soot-rb with pair_hmm bug fixed. adding new failing test
removing Rootbeer.jar from examples
adding support for Rootbeer.setThreadConfig
starting work on gtc2013 MatrixApp with shared mem
deleting temp file
adding ChangeThreadTest
Merge branch 'develop' of github.com:pcpratts/rootbeer1 into develop
Merge branch 'master' into develop

Conflicts:
	src/edu/syr/pcpratts/rootbeer/test/Main.java
Merge branch 'develop' of github.com:pcpratts/rootbeer1 into develop
working on gtc2013 Matrix fast
gtc2013 Matrix Fast CPU compiles and runs
Merge branch 'master' into develop

Conflicts:
	src/edu/syr/pcpratts/rootbeer/runtime2/cuda/CudaRuntime2.java
Merge branch 'develop' of github.com:pcpratts/rootbeer1 into develop
gtc2013 matrix fast. kernel serialization is too slow