First line

it is critical that the first line start with a pound symbol, a space, a number, a -filetype token, and the cross.inp filetype:

# 123456789    -filetype   cross.inp
 ^          ^            ^             
space      space       space

The spaces are necessary, because the input is token based. The program will read the second token in the file as a long integer and use it as an identifier for the file. Thus, each file should have a unique identifier following the pound symbol.

The -filetype cross.inp tells the QTL Cartographer programs that this is a cross.inp formatted file.