Add option for single copy chromosome calls

[stschiff]

It has been suggested to me that in cases where diploid and haploid chromosomes are present, calling should ideally differentiate between the two.

So for example, for human genomes, we should allow to use --randomHaploid for all autosomes, and --majorityCall for Y chromosomes and mitochondria, and even for X chromosomes in case of male samples.

I envision an interface for this which is optional. So we need the following two additional options:

--haploidCh: This can be used multiple times, such as --haploidChr X --haploidChr Y --haploidChr MT. This informs the software about which chromosomes are single copy

--haploidCalling: This option then sets a calling mode for the given haploid chromosomes, independent on the general calling mode. So --randomHaploid --haploidCalling=MajorityCall would specify that only for the chromosomes denoted as haploid, we should use the MajorityCall mode, while for all other chromosomes, we should use the mode set with --randomHaploid.