On the road to re-implementing core classes in Java
Still on the way, lots of mess
Refactoring of input file parsers
Minor addition to metadata classes
Replaced groovy-based Sample and Clonotype classes with java-based versions. Continuing refactoring
Continued sample collection refactoring
Sample output support
Joint sample to replace "TimeCourse"
Minor refactoring
Diversity estimates update
Minor fixes
Set Java to v1.7
Testing/fixes
Important fix to support multiple read-in for same sample
Removed redundant call to sample collection
Fixed variance -> std for chao1
Fixed diversity stats
Merge