cn_status = '6'
if chr_name not in chr_list:
continue
rows = reader.get_rows( chr_name )
segment_indices = np.logical_and( rows['position'] >= start, rows['position'] <= stop )
segment_rows = rows[segment_indices]
if len( segment_rows ) == 0:
continue
cncnt_file.add_rows( cn_status, chr_name, segment_rows )
reader.close()
cncnt_file.close()
if __name__ == "__main__":
import sys
args = Namespace()
args.jcnt_file_name = sys.argv[1]
args.cncnt_file_name = sys.argv[2]
args.segment_file_name = sys.argv[3]
jcnt_to_cncnt( args )
