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 remote-tracking branch 'origin/genomix/fullstack_genomix' into nanzhang/test-merge-readoffset

* origin/genomix/fullstack_genomix:
  Add sortedCouner.clear before add obj
  Some tweaks
  Copy array to arraylist rather than reassignment
  Remove -setMinScaffoldLength
  add sorter for counters
  Add command option to specify if automatically generate minScaffoldingSeedLength
  set cutoff length of scaffolding seed pass test