diCal2 Code

Version update into readme.

Added an option to ignore double entries in the vcf.

Going back to storing fwd/bwd tables as doubles, because the loss of precision apparently breaks some cases.

hidden parameters now handled correctly

Apparently, latex needs some convincing to display the correct quotation marks in the verbatim environment.

Cosmetic changes for reading in vcfs. If no segregating sites left after filtering, an error is thrown. Minor bugfixes.

fwd & bwd table now TwoDimFloatArray instead of ArrayList(ArrayList(double[]))
-- Should save even more memories.

(You'll float too!)

fwd & bwd table now TwoDimDoubleArray instead of ArrayList(ArrayList(double[]))
-- Should save loads of memories.

HmmStepHandler implements the missing sites more memory efficient

reading vcf more memory efficent (not yet fully tested)