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2.3 File identification statements

File names can be specified through command line options (see filetype options) or in the parameter file.

When naming files in parameter statements, delimit the names with single or double quotation marks (' or "). For example, for file `pedchk_ped', the parameter statement is one of:

 
input pedigree file "pedchk_ped"
input pedigree file 'pedchk_ped'

The most commonly used statements for file identification are:

input pedigree file filename

The input pedigree file is required for most programs and must be specified either in the parameter file or through command line options.

output pedigree file filename

The output pedigree file is required by genedrop. Other programs also check for errors in the pedigree. If there are errors which the program is able to correct or if there are requested changes to the format, the new pedigree data is written to this file.

input marker data file filename

This statement names the marker data file which is used when the marker data is not included in the parameter file. The marker file contains the `set marker data' statements. Marker data is used by Autozyg programs. See Autozyg computational parameters.

input seed file filename

This file contains statements to set random seeds for the Monte Carlo based programs. The seed file may contain multiple lines (as in the case when the input seed file is also used for the output seed file). If so, the seeds in the last line override previous ones (with warnings issued). If no seed file is named on the command line or in a parameter statement and there are no statements to set random seeds in the parameter file, default seeds (12345, 1073 (hexadecimal 0x3039, 0x431)) are used.

output seed file filename

The final random seeds are saved if an output seed file is named. This file could be the same as the input seed file. New entries are appended to the old file.


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