Add calcHistogram and drawHist
Add fittingMixture
Fix a bug when computing likelihood
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 branch 'genomix/fullstack_genomix' into anbangx/fitting-mixture-model
Separate two option to set LowCoverage: 1. default; 2. set by fitting mixture
add setMinScaffoldingSeedLength
Set cutoff length of scaffolding seed pass test
Add command option to specify if automatically generate minScaffoldingSeedLength
set cutoff length of scaffolding seed pass test

Conflicts:

	genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
Add command option to specify if automatically generate minScaffoldingSeedLength

Conflicts:

	genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/config/GenomixJobConf.java
	genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
add sorter for counters
Remove -setMinScaffoldLength
Copy array to arraylist rather than reassignment
Some tweaks
Add sortedCouner.clear before add obj
Merge pull request #107 from uci-cbcl/anbangx/findStartSeedMinLength

Anbangx/find start seed min length