in_format='bigwig',
cstyle=args.cstyle)
elif command == 'vcf':
chain_file = args.chain
in_file = args.in_vcf
genome_file = args.in_refgenome
out_file = args.out_vcf
if args.no_comp_alleles is None:
args.no_comp_alleles = False
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file)
crossmap_vcf_file(mapping=mapTree,
infile=in_file,
outfile=out_file,
liftoverfile=chain_file,
refgenome=genome_file,
noCompAllele=args.no_comp_alleles,
compress=args.compression,
cstyle=args.cstyle)
elif command == 'gvcf':
chain_file = args.chain
in_file = args.in_gvcf
genome_file = args.in_refgenome
out_file = args.out_gvcf
if args.no_comp_alleles is None:
args.no_comp_alleles = False
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file)
crossmap_gvcf_file(mapping=mapTree,
infile=in_file,
IS_std=options.insert_size_stdev,
fold=options.insert_size_fold,
addtag=False)
else:
parser.print_help()
elif sys.argv[1].lower() == 'vcf':
if len(sys.argv) == 6:
chain_file = sys.argv[2]
in_file = sys.argv[3]
genome_file = sys.argv[4]
out_file = sys.argv[5]
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file)
crossmap_vcf_file(mapping=mapTree,
infile=in_file,
outfile=out_file,
liftoverfile=sys.argv[2],
refgenome=genome_file)
else:
vcf_help()
sys.exit(0)
elif sys.argv[1].lower() == 'gvcf':
if len(sys.argv) == 6:
chain_file = sys.argv[2]
in_file = sys.argv[3]
genome_file = sys.argv[4]
out_file = sys.argv[5]
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file)
crossmap_gvcf_file(mapping=mapTree,