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2.1 Command syntax

Most of the MORGAN programs need at least two input files in order to run: one parameter file and one pedigree data file.

The general syntax to run a MORGAN program is:

 
progname parfile [filetype filename]...

Here progname is the name of one of several MORGAN main programs. The parfile is the name of the parameter file which must be present. Square-brackets indicate optional arguments. All other files can be specified either in the parameter file or in the command line through pairs of file type specifiers and file names.

Possible filetype options include (see File identification statements for more information):

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.



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