Now DONT_CHECK is not checking any Genotype in the variant for be sure that the tool will return a correct result. Although it is an user misuse of the option, it will be nice to check from time to time if this is correct. It will speed anyway the processing, and including a random check will give more confidence that the results obtained with the tool are reliable.
Two different ways of random checking could be implemented:
Check every x variants. This is the preferred method. All the Genotype will be checked: if they are haploid, they pass the filter; if they have a different ploidy, both alleles should be the same. Otherwise, an UserException should be thrown.
Check a random genotype in each variant. This will speed up the processing only in the case that there are tons of samples, but all the results will be reliable.
Now
DONT_CHECKis not checking anyGenotypein the variant for be sure that the tool will return a correct result. Although it is an user misuse of the option, it will be nice to check from time to time if this is correct. It will speed anyway the processing, and including a random check will give more confidence that the results obtained with the tool are reliable.Two different ways of random checking could be implemented:
Genotypewill be checked: if they are haploid, they pass the filter; if they have a different ploidy, both alleles should be the same. Otherwise, anUserExceptionshould be thrown.