Add calcHistogram and drawHist
Add fittingMixture
Fix a bug when computing likelihood
refactor ray to work with a partially merged graph
simplify RayMessageType using ordinals & values
Merge remote-tracking branch 'origin/genomix/fullstack_genomix' into wbiesing/ray-works-on-partially-merged-graph

Conflicts:
	genomix/genomix-
data/src/main/java/edu/uci/ics/genomix/data/types/ReadHeadInfo.java
Add -setCutoffCoverage command line option
add RandomWalk Testcase
Merge branch 'genomix/fullstack_genomix' into anbangx/fitting-mixture-model
Add maven dependence on org.apache.commons-math3
Merge remote-tracking branch 'origin/genomix/fullstack_genomix' into wbiesing/ray-works-on-partially-merged-graph
Merge branch 'genomix/fullstack_genomix' into anbangx/fitting-mixture-model
Separate two option to set LowCoverage: 1. default; 2. set by fitting mixture
add configure(conf) to pregelix API, called once per iteration
Merge branch 'wbiesing/add-configure-to-pregelix-api' into wbiesing/ray-works-on-partially-merged-graph
add setMinScaffoldingSeedLength
Set cutoff length of scaffolding seed pass test
Add command option to specify if automatically generate minScaffoldingSeedLength
get readLengths and distances from the cmdline
get MIN and MAX read lengths and outer distances from the conf