BamIndex
Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Built into JBrowse core. View source.
Where a BAM's 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 BAM; 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": "BamIndex", ... }. 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 (BAI, CSI) = 'BAI' | BAI is the usual samtools index output. CSI is required for a reference longer than 512 Mb, which BAI cannot address. Derived from the index file name where the config names a .csi and leaves this unset. |
locationfileLocation = { uri: '/path/to/my.bam.bai', locationType: 'UriLocation' } | location of the index. Only needed when it is not named <file>.bam.bai (or .bam.csi), the names the uri shorthand assumes. |