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AllVsAllPAFAdapter

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: 'AllVsAllPAFAdapter',
    uri: 'all_vs_all.paf.gz',
    assemblyNames: ['grape', 'peach', 'cacao'],
  },
}

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

Loads a single "all-vs-all" PAF (e.g. minimap2 all.fa all.fa, or the PGGB mapping step) where every sequence name is PanSN-prefixed with its assembly (sample#haplotype#contig). Because such a file contains every pairwise alignment, one file (and one track) backs every synteny band of a multi-way view: the synteny view tells the adapter which pair a given band draws, and the adapter keeps only those records, stripping the PanSN prefix to recover each assembly's own refName. In a plain LGV (LGVSyntenyDisplay) there is no band to isolate, so the track draws its assembly against every OTHER sample in the file — "one vs all" — including samples not listed in assemblyNames (those mates are labelled by their PanSN prefix). assemblyNames therefore only needs to list the assemblies you actually load into JBrowse and want the track to appear on.

A reference-anchored alignment is not this — HPRC publishes 465 haplotypes against GRCh38 alongside its complete all-vs-all — and read as all-vs-all it draws an empty band for every pair not involving that reference. Order the synteny rows so the reference sits between the others, use a complete all-vs-all if the project publishes one, or view a larger cohort as a multiple alignment (MAF) rather than a stack of pairwise bands.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "AllVsAllPAFAdapter", ... }. It also accepts the shorthand keys uri, baseUri 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).
pafLocation
fileLocation = { uri: '/path/to/file.paf', locationType: 'UriLocation' }		can be optionally gzipped
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.