continue
elif line.startswith('chrX') or line.startswith('chr23'):
thisMarker = ChrXMarker()
else: #TODO: more thorough check for validity of data format, like chr numbers??
thisMarker = AutosomalMarker()
#get vcf columns
vcfValues = line.strip().split('\t')
#assert that all genotype values are numeric #TODO: verify that this assert works
assert(all(v.isdigit() or v=="NA" for v in vcfValues[1:])) #1st column is variant id, 2nd onwards are sample genotypes
#set this marker object's sample values
thisMarker.markerID = vcfValues[0]
thisMarker.getSampleGenotypes(vcfValues[1:],pedMemberIndices)
#Note: thought of checking if chrX marker has heterozygous males, but it's not possible since the feature matrix comes in with encoded genotypes.
#So all you can check is whether autosomal chrs have any genotypes other than 0/1/2/NA and chrX has any genotypes other that 0/1/NA for males, 0/1/2/NA for females
#for chrX
#TODO: verify that hasValidGenotypes() works
if isinstance(thisMarker,ChrXMarker) and not thisMarker.hasValidGenotypes(pedNBGender,pedMemberType):
print 'Invalid genotype found at ',thisMarker.markerID,'. This marker will not be tested.'
continue
#for autosomal chromosomes
elif not isinstance(thisMarker,ChrXMarker) and not thisMarker.hasValidGenotypes():
print 'Invalid genotype found at ',thisMarker.markerID,'. This marker will not be tested.'
continue
#COMPUTE ALLELE FREQUENCY
#compute regardless of whether 'mi' has been selected or not, because allele frequency will be reported in the output
