Configuration file

When running retmap, the only required argument is the name of the configuration file, usually called config.in. This contains all the information needed by the application to run, such as the location of the needed files and the expected output.

The configuration file is a plain text file structured as:

KEY_WORD           argument

where KEY_WORD represents the option needed to be edited and argument the respective option. The distance between the two entries should be at least one empty space. In case multiple entries are needed (e.g. when multiple data files should be processed at the same time), the arguments should be added on the same line with at least one space in between them.

KEY_WORD           argument1  argument2  ...  argumentN

In case multiple data files are processed at the same time, the user can choose to use either the same number of arguments for all settings or only one argument. In the later case it is assumed that all the arguments should take the same value.

KEY_WORD1          argument1  argument2  ...  argumentN
KEY_WORD2          argument1 (argument1) ... (argument1) 

There are however a few special keys that do not abide by this rule (e.g. those that denote ranges, prediction parameters, etc.), which will be discussed in their respective parts.

To allow for easy organization of the config.in file, empty lines can be used to separate different settings blocks. Also, if the first word of the line is not in the list of recognized key-words, the line will be ignored. This behaviour allows for comments to be used inside the configuration file, with little limitations. Still, it is recommended that comments start with some sequence of symbols (e.g. //) to ensure that the first word does not match an implemented key-word. This is also good for future proofing, as no key-words starting with symbols are planned to be implemented.

// This is the first block of settings
KEY_WORD1          argument1  argument2  ...  argumentN
KEY_WORD2          argument1

// This is the second block of settings
KEY_WORD3          argument1

Both key-words and arguments are case-sensitive, with the former written in uppercase and the latter in lower case. For the boolean clauses (a.i. those that evaluate for either True or False), yes represents True while any other string represents False. However, it is recommended that no is used for false to future-proof the file.