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2.5.2 Call an external program on each block.

The SystemCall filter runs an external program on each block. For each block, the alignment is written to a temporary file, whose name and format can be specified. This input file is then read by the external program. The called program is expected to generate results in the form of an alignment with the same sequence names, so that it can be read by maffilter. In most case, the external program will be a wrapper script.


maf.filter=                                 \
    SystemCall(                             \
        name=myextprog,                     \
        input.file=tmp.fa,                  \
        input.format=Fasta,                 \,                   \
        output.file=output.fa,              \
        output.format=Fasta),               \



A label to use, might be useful in case several tools are called.


A file path where to write the block alignment, to be used as input by the external program.


Alignment format for input file.


A file path where to read the processed block alignment, output by the external program.


Alignment format for output file.


The system call to run external program.