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MultiGenomeIndexedPAFAdapter

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the comparative-adapters plugin. View source.

The tabix-indexed (PIF) form of the MultiGenomePAFAdapter. Run jbrowse make-pif all_vs_all.paf on a multi-genome 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 MultiGenomePAFAdapter: the file may state any set of pairs (a complete all-vs-all or a star against one reference), one-vs-all in a plain LGV, single-pair when the synteny view supplies a targetAssemblyName. When every row targets one assembly, or every row queries from one, the header names it as the star's anchor, and a multi-way display composes its lanes' links through it instead of asking for each pair.

Example usage

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

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "MultiGenomeIndexedPAFAdapter", ... }. 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 (the track labels unlisted mates by their PanSN prefix).
pifGzLocation
fileLocation = 
{ uri: '/path/to/all_vs_all.pif.gz', locationType: 'UriLocation' }
location of the multi-genome 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 a separate 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 tier (uppercase T/Q prefix), whose CIGAR is folded to its large indels. The file has the last word: one with no coarse tier (make-pif --no-coarse) serves the fine tier at every zoom, and a threshold below the --coarse bound its #pif header states is raised to that bound, since below it the coarse tier is served at zooms where the indels it folded away are wide enough to see.
advanced
index
TabixIndex		The tabix index location and its kind. The uri shorthand derives both, so a config using it states neither.
attributeColumns
stringArray = []		PAF tags to offer as color-by fields, by name: ["syri", "color"] offers syri:Z:INV as a field whose labels paint in the color:Z: beside them