Previous: QualFilter, Up: Cleaning [Contents]
The FeatureFilter remove parts of the alignment corresponding to certain features.
The features to extract are typically provided via a GFF file. See ExtractFeature
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), \
[...]
|
ref_species={string}The name of the species for which the coordinates of the features are provided.
feature.file={path}The file where the features are described.
feature.file.compression={none|gzip|zip|bzip2}Compression format for the feature file.
feature.format={GFF|GTF|BedGraph}Format for the feature file, currently GFF (v3.0), GTF or BedGraph.
feature.type={all|(list)}Specifies which type of feature should be extracted from the feature file, if several are available.
file={none|{path}}An optional file were extracted features will be stored, in the MAF format.
compression={none|gzip|zip|bzip2}Compression format for output file (if file != none).