G.split_size = CONVERTER_SPLIT_SIZE
G.VCF2hdf5(args.out)
else:
raise ValueError(
'Genotype data should be in PLINK/MINIMAC/VCF format and alone in folder'
)
check_converter(args.out, args.study_name[0])
print('Time to convert all data: {} sec'.format(t.secs))
################################### ENCODING ##############################
elif args.mode == 'encoding':
#ARG_CHECKER.check(args,mode='encoding')
mapper = Mapper()
mapper.genotype_names = args.study_name
mapper.chunk_size = MAPPER_CHUNK_SIZE
mapper.reference_name = args.ref_name
mapper.load_flip(args.mapper)
mapper.load(args.mapper)
phen = Reader('phenotype')
phen.start(args.phenotype[0])
gen = Reader('genotype')
gen.start(args.genotype[0],
hdf5=args.hdf5,
study_name=args.study_name[0],
ID=False)
