diCal2 Code

minor bug in coordinateOrder fixed

optimized M-steps (memoiziation)

I think that I did not break anything, but the previous version was probably safer.

ODE Core does not work properly with admixutre pulses yet.

Added some failsafe checks so that it is never used

Should now be able to read haploid vcf files as well.

before starting to implement haploid vcf reading

finished deleting old sequence format

removed old sequence format from examples

just some restructuring

The default behaviour is now to not accept unphased genotypes. If they should be accepted, you have to explicitly specify a flag.

if a vcf file is read, we now explicitly print out how many segregating sites have at least one missing allele. and warn about them being ignored in the analysis