file=sys.stderr)
print("Number of stdev from the mean = %f" %
(args.insert_size_fold),
file=sys.stderr)
if args.add_tags:
print("Add tags to each alignment = %s" % (args.add_tags),
file=sys.stderr)
else:
print("Add tags to each alignment = False", file=sys.stderr)
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file)
crossmap_bam_file(mapping=mapTree,
chainfile=chain_file,
infile=in_file,
outfile_prefix=out_file,
chrom_size=targetChromSizes,
IS_size=args.insert_size,
IS_std=args.insert_size_stdev,
fold=args.insert_size_fold,
addtag=args.add_tags,
cstyle=args.cstyle)
elif command == 'gff':
chain_file = args.chain
in_file = args.in_gff
out_file = args.out_gff
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file)
crossmap_gff_file(mapTree, in_file, out_file, cstyle=args.cstyle)
elif command == 'wig':
chain_file = args.chain
print("Insert size stdev = %f" % (options.insert_size_stdev), file=sys.stderr)
print("Number of stdev from the mean = %f" % (options.insert_size_fold), file=sys.stderr)
if options.add_tags:
print("Add tags to each alignment = %s" % ( options.add_tags), file=sys.stderr)
else:
print("Add tags to each alignment = %s" % ( False), file=sys.stderr)
chain_file = args[1]
in_file = args[2]
out_file = args[3] if len(args) >= 4 else None
(mapTree, targetChromSizes, sourceChromSizes) = read_chain_file(chain_file)
if out_file in ["STDOUT","-"]:
out_file = None
if options.add_tags:
crossmap_bam_file(mapping = mapTree, chainfile = chain_file, infile = in_file, outfile_prefix = out_file,
chrom_size = targetChromSizes, IS_size=options.insert_size, IS_std=options.insert_size_stdev,
fold=options.insert_size_fold,addtag=True)
else:
crossmap_bam_file(mapping = mapTree, chainfile = chain_file, infile = in_file, outfile_prefix = out_file,
chrom_size = targetChromSizes, IS_size=options.insert_size, IS_std=options.insert_size_stdev,
fold=options.insert_size_fold,addtag=False)
else:
parser.print_help()
elif sys.argv[1].lower() == 'vcf':
usage=("\nCrossMap.py vcf <chain_file> <input.vcf> <refGenome.fa> <output_file> [options]\n\nExamples:\n"
"CrossMap.py vcf hg19ToHg18.over.chain.gz test.hg19.vcf hg18.fa test.hg18.vcf #comparing ref_allele to alt_allele to make sure they are different.\n"
"CrossMap.py vcf hg19ToHg18.over.chain.gz test.hg19.vcf hg18.fa test.hg18.vcf --no-comp-alleles #do NOT compare ref_allele to alt_allele.")
parser = optparse.OptionParser(usage, add_help_option=False)
parser.add_option("--no-comp-alleles", action="store_true",dest="no_comp_alleles", help=
"If set, CrossMap does NOT check if the reference allele is different from the alternate allele.")