Meanings of commands

The file in Figure 6.1 also has commands embedded into it. Rmap recognizes any token that begins with a minus sign (-) as an embedded command. Some commands require that the following token be a number or piece of information. The following table gives a list of tokens that the program recognizes, their purpose and what the next token should be.

Commands	Followed by	Means
-type	positions	Marker positions are given
-type	intervals	Marker intervals are given
-function	integer 1-8	Code for the map function: Details in manual
-param	real number	Extra parameter needed for some map functions
-Units	cM, M or r	Units are in centiMorgans (cM), Morgans (M)
		or recombination frequencies (r)
-chromosomes	integer $> 0$	Haploid number of chromosomes
-maximum	integer $> 0$	Maximum number of markers on any chromosome.
		Needed for array allocation.
-named	yes or no	Says whether markers will have names.
-skip		Tells Rmap to skip everything until an
-unskip		which is the end of the -skip. These
		cannot be within a -start to -stop block
-start		Start of a map block
-stop		End of a map block
-end		End of the file
-Chromosome	integer, string	Gives the number of the chromosome (if integer)
		or the name (if a string)