2.1 Command syntax

The parameter file name must be passed to MORGAN on the command line when calling the program. Other file names can be passed to MORGAN on the command line or in the parameter file. The minimum syntax to call a MORGAN program is:

./progname parfile

In the statement above, progname is the name of one of several MORGAN main programs, such as genedrop or lm_lods. The parfile is the name of the parameter file which must be present. For example, to run genedrop using a parameter file named `genedrop.par', the command is:

./genedrop genedrop.par

Note that if the current directory is in your PATH, you may say

progname parfile

but the form ./progname is more universal, and used throughout this tutorial.

Additional file names can be passed to MORGAN on the command line, but these file names must be accompanied by a file type to identify them. The syntax is:

./progname parfile [filetype filename]...

Square brackets indicate optional arguments. Possible filetype options include:

ped

Input pedigree file

mark

Input marker data file (Note that only Autozyg programs use marker data)

oped

Output pedigree file

seed

Input seeds for random number generator

oseed

Output random seeds

oscor

Output score file

If the name for a particular file type is given both in the command line and in a parameter statement, the name in the command line takes precedence.

The programs put informational messages to stdout and error messages to stderr which default to the screen. It is possible to redirect either or both to a named file.