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RefNameAliasAdapter

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

Example usage

Goes on an ASSEMBLY, under refNameAliases — not on a track. Writing refNameAliases: { uri: '...' } is shorthand for exactly this adapter:

{
  name: 'hg38',
  sequence: {
    type: 'ReferenceSequenceTrack',
    trackId: 'hg38-ReferenceSequenceTrack',
    adapter: {
      type: 'BgzipFastaAdapter',
      uri: 'https://example.com/hg38.fa.gz',
    },
  },
  refNameAliases: {
    adapter: {
      type: 'RefNameAliasAdapter',
      uri: 'https://example.com/hg38.chromAlias.txt',
    },
  },
}

Example: named column

When the primary column — the one whose values match your FASTA — is not the first, name it. refNameColumnHeaderName reads the last #-prefixed line as the header; refNameColumn takes a zero-based index instead.

{
  name: 'hg38',
  sequence: {
    type: 'ReferenceSequenceTrack',
    trackId: 'hg38-ReferenceSequenceTrack',
    adapter: {
      type: 'BgzipFastaAdapter',
      uri: 'https://example.com/hg38.fa.gz',
    },
  },
  refNameAliases: {
    adapter: {
      type: 'RefNameAliasAdapter',
      uri: 'https://example.com/aliases.txt',
      refNameColumnHeaderName: 'ucsc',
    },
  },
}

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

can read "chromAliases" type files from UCSC or any tab separated file of refName aliases

Config slots

These slots go inside the track's adapter: "adapter": { "type": "RefNameAliasAdapter", ... }. 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
location
fileLocation = { uri: '/path/to/my/aliases.txt', locationType: 'UriLocation' }		location of the alias table: a UCSC chromAlias.txt, or any tab-separated file whose rows each list the alternate names of one reference sequence (chr1<TAB>1<TAB>NC_000001.11). It is what lets a 1-named file load against a chr1-named assembly.
refNameColumn
number = 0		by default, the "ref names that match the fasta" are assumed to be in the first column (0), change this variable if needed
advanced
refNameColumnHeaderName
string = ''		refNameColumnHeaderName
advanced