TabixIndex
Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Built into JBrowse core. View source.
The index every tabix-indexed adapter hangs off itself: where the index is,
and which of the two kinds it is. indexType is derived from the index file's
own name where the config names a .csi and leaves it unset, so the usual
config states neither — the uri shorthand derives both, and csi: true
beside it switches the pair together. Spell location out for an index that
does not sit beside its data file; a .csi named there is read as a CSI
without indexType as well.
Config slots
These slots go inside the track's adapter: "adapter": { "type": "TabixIndex", ... }. This adapter has no uri shorthand — give it the location slots below. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.
| Slot | Description |
|---|---|
indexTypestringEnum (TBI, CSI) = 'TBI' | TBI is the usual tabix output. CSI is required for a reference longer than 512 Mb, which TBI cannot address. Derived from the index file name where the config names a .csi and leaves this unset. |
locationfileLocation = { uri: '/path/to/my.gz.tbi', locationType: 'UriLocation' } | location of the tabix index. Only needed when it is not named <file>.tbi, which is what the uri shorthand assumes — a .csi beside the file is reached with csi: true rather than by spelling this out. |