Builds a loose track spec — list(uri = url) plus whatever you pass — that
the view expands into a full track config when it loads, inferring the track
type and adapter from the file extension with JBrowse's own format plugins
(the same inference the "Add track" flow uses). No extension table lives in
R, so every format a bundled plugin recognizes works: .bam/.cram
(alignments), .vcf (variants), .gff/.gff3/.gtf/.bed (features),
.bb/.bigBed (features), .bw/.bigWig (quantitative), .hic (Hi-C), and
more. A bgzipped file (.gff.gz, …) resolves to its indexed tabix adapter, a
plain one to the whole-file adapter. JBrowse derives index locations
(.bai/.crai/.tbi) and, for CRAM, the reference from the assembly, so
only the data URL is required.
track(
url,
name = NULL,
track_id = NULL,
assembly_names = NULL,
index = NULL,
...
)URL to the track data.
Track display name. Left NULL, the view derives it from the
file's base name.
A unique id for the track. Left NULL, the view derives one.
Assembly name(s) the track belongs to. Usually left
NULL — JBrowseR() backfills it from the loaded assembly.
URL of the index file when it isn't the conventional sibling of
url (.bai/.crai/.tbi). A .csi index is detected by extension.
Extra config merged onto the track, overriding the inferred
defaults (e.g. category = list("Genes"), or a type = "AlignmentsTrack"
override).
a loose track spec list
track("https://jbrowse.org/genomes/hg19/gencode.v19.sorted.gff.gz", name = "Genes")
#> $uri
#> [1] "https://jbrowse.org/genomes/hg19/gencode.v19.sorted.gff.gz"
#>
#> $name
#> [1] "Genes"
#>