Removed old classes
LD calculator works again
Variant annotation
Allele contains function
Not a SNP exception extents genotype data  exception
Test if supplied reference allele is one of the supplied alleles
Move ref allele to first of supplied alleles
Alleles better contains
Improved test VCF
Merge pull request #21 from PatrickDeelen/master

Remove old, more tests, improve variant
Removed get SNP ref allele
Work in progress modifiable genotype data
Merge pull request #22 from PatrickDeelen/master

Removed getSnpRefAllele()  and work in progres modifiable
Removed TODO that was already done
Added sampleVariantProvider cache size
Added sampleVariantProvider cache size 2
Fixed test
ModifiableGenoTypeData work in progress
Merge pull request #23 from PatrickDeelen/master

Added cache size property for variant providers and work on modifiable genotype data
Added impute2