2.2 Parameter file

A MORGAN parameter file contains a series of statements. Many statements are common to all MORGAN programs, particularly those that define the format of the pedigree file and identify other files to be used for program input or output. Many statements are optional, with some default behavior. If statements irrelevant to the MORGAN program called by the user are included in the parameter file, those statements are ignored and a warning message is issued.

Each statement must begin on a new line and begins with one of the MORGAN statement keywords. A statement consists of any number of lines. Case is not significant for the keywords. Only the first four letters of the keywords are significant; the remainder of the word is ignored. The order of the statements does not matter. If the same statement is repeated, the last one overrides previous ones and a warning is given in the output file. A # starts a comment so that the rest of the line is ignored. Either single or double quotation marks (' or ") can be used to delimit strings such as file names. Look at the warnings issued by MORGAN to make sure the parameters are as you intended.

The most common statements are for identifying input and output files (counterparts of the command line options) and for describing the input pedigree file format.

Below is a simple parameter file, `check.par', from the examples included with the MORGAN software under the subdirectory `MORGAN_Examples/Pedcheck'.

input pedigree file `check.ped' input pedigree size 30 input pedigree record gender absent input pedigree record observed present assign gender output pedigree chronological output pedigree file `check.oped'

A brief description of the most commonly used parameter file statements follows in the next section. For a complete and more detailed description of MORGAN statements, please see the sections of this tutorial relevant to specific MORGAN programs and the documentation that comes with MORGAN in the files `README_userdoc' in the various program subdirectories.