4.1 Overview

All information on the the model of analysis and the data and pedigree files is specified through the parameter file.

The name of the parameter file should have extension ’.par’. By default, WOMBAT expects to find a file wombat.par in the current working directory.
Other filenames can be specified at run time as the last command line option – see 5 for details.

Setting up the parameter file is straightforward, but care and attention to detail are required to get it ‘just right’. The worked examples give ‘templates’ for various types of analyses which are readily adaptable to other problems. Parsing of the lines in the parameter file is fairly elementary, hence it is important to adhere strictly to the format described in the following in painstaking detail.

WOMBAT performs a limited number of consistency checks on the variables and models specified, but these are by no means exhaustive and should not be relied upon !

If WOMBAT does find an obvious error, it will stop with a message like “exit WOMBAT” or, in verbose mode, “Programmed(error) stop for WOMBAT encountered”. Inconsistencies or errors not discovered are likely to wreak havoc in subsequent steps !

HINT: Use the -v option at run time. This will cause WOMBAT to echo each line in the parameter file as it is read (to the screen) – if there is a programmed error stop at this stage, it is easier to find the mistake as you know which is the offending line.