Skip to main content

AllVsAllIndexedPAFAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the comparative-adapters plugin. View source.

Example usage

{
  type: 'SyntenyTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['grape', 'peach', 'cacao'],
  adapter: {
    type: 'AllVsAllIndexedPAFAdapter',
    uri: 'all_vs_all.pif.gz',
    assemblyNames: ['grape', 'peach', 'cacao'],
  },
}

See the Config slots section below for all available configuration fields.

The tabix-indexed (PIF) form of the AllVsAllPAFAdapter. Run jbrowse make-pif all_vs_all.paf on an all-vs-all PAF whose sequence names are PanSN-prefixed (sample#haplotype#contig) and point this adapter at the resulting .pif.gz. Because PIF double-emits each record keyed on both of its PanSN sequence names, a region query resolves to a tabix range lookup on the anchor's PanSN seqid(s) instead of scanning the whole file — so it scales to whole-genome pangenome alignments that do not fit in memory. Semantics match AllVsAllPAFAdapter: one-vs-all in a plain LGV, single-pair when the synteny view supplies a targetAssemblyName.

A reference-anchored alignment read as all-vs-all draws an empty band for every pair not involving the reference; see AllVsAllPAFAdapter for what to do about that.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "AllVsAllIndexedPAFAdapter", ... }. It also accepts the shorthand keys uri, baseUri, csi in place of writing a location slot out. 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.

SlotDescription
assemblyNames
stringArray = []		The assemblies this track appears on and can back synteny bands for — list the assemblies you load into JBrowse. Each entry must resolve to a PanSN sample (grape) or haplotype (grape#1) prefix present in the file. In a plain LGV the track still draws its assembly against every other sample in the file, so mates need not be listed here (unlisted mates are labelled by their PanSN prefix).
pifGzLocation
fileLocation = 
{ uri: '/path/to/all_vs_all.pif.gz', locationType: 'UriLocation' }
location of the all-vs-all tabix indexed PAF (pif)
assemblyNameToPanSN
frozen = {}		Maps a JBrowse assembly name to its PanSN prefix in the PAF, for when they differ (e.g. assembly grape stored as Vitis_vinifera#1#chr1 would need { grape: 'Vitis_vinifera' }). The prefix may name a sample (grape, matching all of its haplotypes) or one haplotype (grape#1), so a haplotype-resolved pangenome that loads each haplotype as its own assembly maps { grape_hap1: 'grape#1', grape_hap2: 'grape#2' }. Defaults to identity: the assembly name is assumed to be the PanSN sample name.
coarseBpPerPxThreshold
number = 10000		bpPerPx threshold at which a view on "Level of detail: automatic" switches from the per-row CIGAR tier (lowercase t/q prefix) to the coarse no-CIGAR tier (uppercase T/Q prefix), when make-pif was run with a coarse tier. No coarse tier present in the file = always uses the fine tier. Should be at least make-pif's --coarse gap: below it, coarse ribbons are drawn straight across indels wide enough to see.
advanced
index.indexType
stringEnum (TBI, CSI) = 'TBI'		TBI is the usual tabix output. CSI is required for a reference longer than 512 Mb, which TBI cannot address.
index.location
fileLocation = { uri: '/path/to/my.gz.tbi', locationType: 'UriLocation' }		location of the tabix index. Only needed when it is not named <file>.tbi (or .csi), which is what the uri shorthand assumes.