Creates the necessary configuration string for an indexed GFF3 file so that it can be used in a JBrowse custom linear genome view.

track_feature(track_data, assembly)

Arguments

track_data

the URL to the GFF3 file

assembly

the config string generated by assembly

Value

a character vector of stringified FeatureTrack JSON configuration

Details

It is important to note that while only the GFF3 file is passed as an argument, tracks_variant assumes that a GFF3 index of the same name is located with the file

For example:

track_feature("data/features.gff")

Assumes that data/features.gff.tbi also exists.

This is a JBrowse 2 convention, and the default naming output of tabix

For more information on creating an index with tabix, visit https://www.htslib.org/

Examples

assembly <- assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE) track_feature("features.gff", assembly)
#> [1] "{ \"type\": \"FeatureTrack\", \"name\": \"features\", \"assemblyNames\": [\"hg19\"], \"trackId\": \"hg19_features\", \"adapter\": { \"type\": \"Gff3TabixAdapter\", \"gffGzLocation\": { \"uri\": \"features.gff\" }, \"index\": { \"location\": { \"uri\": \"features.gff.tbi\" } }}}"