Excluding variants with maf of 0
Imports and comments
Organize Imports
changed main to varargs.
updated help
Test data
Bug fix in Allele class
improvment reader class
Error handeling complement function
Fix in VCF info column reader
removed test that is no longer relevant
added constructor for bineary plink
improved ped map reader
Full test of aligner using hapmap3 data and 1000G data + some minor improvements
Merge pull request #66 from PatrickDeelen/master

Full test of genotype aligner using hapmap3 and 1000G as test + some minor bug fixes and improvements