start = int( row[1] )
stop = int( row[2] )
if chr_name != old_chr_name:
# Close old chromosome out.
out_row = [old_chr_name, old_stop + 1, int( 1e10 ), unknown_class_id]
writer.writerow( out_row )
# Open new chromosome
if start != 0:
out_row = [chr_name, 0, start - 1, unknown_class_id]
writer.writerow( out_row )
# Fill gap in middle of chromosome
if old_stop != start:
out_row = [chr_name, old_stop + 1, start - 1, unknown_class_id]
writer.writerow( out_row )
writer.writerow( row )
if __name__ == "__main__":
import sys
from argparse import Namespace
args = Namespace()
args.seg_file = sys.argv[1]
args.out_file = sys.argv[2]
main( args )
