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)the URL to the GFF3 file
the config string generated by assembly
a character vector of stringified FeatureTrack JSON configuration
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/
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\" } }}}"