FeatureFilter remove parts of the alignment corresponding to certain features.
The features to extract are typically provided via a GFF file. See
in order to keep only the feature parts.
maf.filter= \ [...], FeatureFilter( \ ref_species=species1, \ feature.file=species1.gff3, \ feature.file.compression=none, \ feature.format=GFF, \ feature.type=(mRNA,tRNA), \ file=data.trash_features.maf.gz, \ compression=gzip), \ [...]
The name of the species for which the coordinates of the features are provided.
The file where the features are described.
Compression format for the feature file.
Format for the feature file, currently GFF (v3.0), GTF or BedGraph.
Specifies which type of feature should be extracted from the feature file, if several are available.
An optional file were extracted features will be stored, in the MAF format.
Compression format for output file (if file != none).