First line

It is critical that the first line start with a pound symbol, a space, a number, the word bychromosome, a -filetype token, and the map.inp token as shown below:

# 123456789    bychromosome      -filetype map.inp
 ^          ^                ^            ^
space      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 map.inp tells the QTL Cartographer programs that this is a map.inp formatted file. The bychromosome word is a vestige of an idea that simply needs to hang around.