def processhapmap():
print "parsing hapmap genotypes chrom files"
parsegenotypes.parsehapmap()
print "now filtering SNPs"
b = parsegenotypes.filterSNPs('../genotypes/hapmap')
print "{0} SNPs filtered out".format(len(b))
[flips, errors] = parsegenotypes.checkRef('../genotypes/hapmap')
print "{0} flips and {1} errors".format(len(flips),len(errors))
#flips = glob.json('../genotypes/hapmapflips')
#errors = glob.json('../genotypes/hapmaperrors')
parsegenotypes.flipGeno('hapmapGeno', flips, errors)
def processgenotypes():
"""parse genotype files and flip them around according to hg19
"""
for i, n in enumerate(homedirnames):
parsegenotypes.parse1KGvcf(vcffiles[i], names1KG[i])
b = parsegenotypes.filterSNPs(names1KG[i])
print "{0} SNPs filtered out".format(len(b))
c = parsegenotypes.checkRef(n)
print "{0} errors and {1} flipped".format(len(c[1]),len(c[0]))
#parsegenotypes.corrRef(c[0], n)
parsegenotypes.flipGeno(n+'Geno', c[0], c[1])
