2.4.7 Output coordinates of a set of species for each block.

The OutputCoordinates takes as input a list of species and output the coordinates of each of the corresponding sequences in each block. This filter only works if no more than one sequence per species are present, otherwise an error is casted. If some species are missing in some blocks, NA are produced in the output file.

Synopsis:

maf.filter=                                 \
    [...],
    OutputCoordinates(                      \
        file=coordinates.txt.gz,            \
        compression=gzip,                   \
        species=(species1,species2),        \
        output_src_size=yes)                \
    [...]

Arguments:

file={none|{path}}

A file path for the output text file.

compression={none|gzip|zip|bzip2}

Compression format for output file.

species={list of species}

A list of species for which coodinates should be written.

output_src_size={boolean}

Tell if the size of source sequences should be output.