Updated metavars
Merge pull request #1 from quattro/patch-1

Updated metavars
Parallel for for Allele Frequency Estimation.
Merge remote-tracking branch 'origin/master'
Aligned fasta as input handling added. Output reads instead of haplotypes.
Documentation extended. Output haplotypes option added.
Documentation extended. Output haplotypes option added.
Initial sequencies handling added. Haplotypes and reads output.
Picard from Maven
Reorganized structure to have separate test folders.
Added initial maxdistancewrapper.