1.2 How to run the program

MafFilter is a program written in C++ with the Bio++ libraries. It is a command line program (that is, without graphical user interface) which uses the Bio++ Options (BppO) syntax. This syntax is of type ‘keys’=‘values’, which can be passed directly as arguments of the maffilter program

maffilter option1=value1 option2=value2 ... optionN=valueN

or more conveniently, stored in an “options” file (specified with param=option_file), or a combination of both:

maffilter param=option_file
maffilter param=option_file option1=value1 option2=value2

See the Bio++ Program Suite (BppSuite) manual for more information.

MafFilter typically takes as input a MAF file and a series of commands which determine the output file(s) that will be written and where. Additional input files might be specified, such as gene annotation files (typically in GFF/GTF format). Here is the structure of a minimal option file:

DATA=example.file //A user-defined variable, representing the input maf file, without extension
input.file=$(DATA).maf.gz  //Input maf file, gzipped
input.file.compression=gzip
output.log=$(DATA).maffilter.log //Output log file
maf.filter= //A coma separated list of filters, here empty (the programs only read the input file and exits).

The list of filters can be split on multiple lines for convenience, providing each line is escaped by a ’\’ at the end to indicate that the next line is a continuation of the current one:

maf.filter=Filter1,\
           Filter2,\
           Filter3

Please refer to the Bio++ Program Suite manual for more details, including the use of variables, priority of option values, etc.