The input is token based. A token is any string of non-whitespace surrounded by whitespace. Each time a token begins with a -, it is read to determine what follows it. The next token is then read and processed. The program will ignore any token that it doesn't recognize.
Case is important.
An integer value for this must be given. If there is some portion of the data file that you don't want read, just put in a '-skip' token. Everything will be ignored until an '-unskip' token. Between the start token and the end token, you should have a repeating sequence of a Chromosome token, then markers ordered, with their names followed by the appropriate distances. This example has the markers followed by their positions in centiMorgans.