Improve support for PAR / X chromosome

[apriha]

• HapMap includes data for PAR regions, so use that data when possible
• Revisit doubling of alleles on X chromosome for males

[apriha]

Ancestry's chromosome 25 seems to consist of PAR SNPs from both the X and Y chromosomes... Therefore, those SNPs can't be easily merged into chromosome X or Y without looking up the SNP in dbSNP and identifying the proper chromosome with the SNP's position.

[apriha]

For males, 23andMe reports two alleles for PAR regions, and one allele for the non-PAR region. Ancestry and FTDNA report two alleles for both the PAR and non-PAR regions. Therefore, for now, double all single X chromosome alleles.

In the future, perhaps the PAR regions can be identified, and for males, doubled X chromosome alleles in the non-PAR region can be converted to single alleles. This would mean males could theoretically have two chromosome matches on the X chromosome (in the PAR regions)...

[apriha]

Two chromosome matches on the X chromosome in the PAR regions for males is now handled; see d6b69313f79d9061f0a9e2023db199bcd03f4bf8.

[apriha]

PAR SNPs are now assigned to the X and Y chromosomes based on position; see 1313da4a1ec291288287113f91027b356b8766fb.