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
Merge branch 'genomix/fullstack_genomix' into anbangx/fitting-mixture-model

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