help="whether to delete the intermediary hdf5 file. Default: False.")
args = parser.parse_args()
sys.path.insert(0, "/mnt/archgen/users/yilei/tools/hapROH/package")
from hapsburg.PackagesSupport.hapsburg_run import hapCon_chrom_BFGS
conpop = []
if args.conpop == None:
conpop = ['CEU']
else:
conpop = [args.conpop]
hapCon_chrom_BFGS(iid=args.iid,
mpileup=args.mpileup,
bam=args.bam,
q=args.q,
Q=args.Q,
n_ref=2504,
diploid_ref=False,
exclude_pops=["AFR"],
conPop=conpop,
h5_path1000g=args.ref,
meta_path_ref=args.meta,
folder_out="",
c=0.025,
roh_jump=300,
e_rate_ref=1e-3,
logfile=False,
output=False,
cleanup=args.cleanup)
conMLE, lower95, upper95 = hapCon_chrom_BFGS(
iid,
ch='X',
path_targets=f"{outFolder}/data.h5",
h5_path1000g=
'/mnt/archgen/users/yilei/Data/1000G/1000g1240khdf5/all1240/chr',
meta_path_ref=
'/mnt/archgen/users/yilei/Data/1000G/1000g1240khdf5/all1240/meta_df_all.csv',
folder_out=outFolder,
prefix_out="",
e_model="readcount_contam",
p_model="SardHDF5",
post_model="Standard",
save=False,
save_fp=False,
n_ref=2504,
diploid_ref=True,
exclude_pops=["TSI"],
conPop=[],
readcounts=True,
random_allele=False,
c=0.025,
roh_in=1,
roh_out=0,
roh_jump=300,
e_rate=err_rate,
e_rate_ref=e_rate_ref,
cutoff_post=0.999,
max_gap=0,
roh_min_l=0.01,
logfile=False)