RefNameAliasAdapter

Auto-generated from the config schema in the source — 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',
    },
  },
}

Reads refName aliases for an assembly from a UCSC chromAlias file or any other tab-separated table of 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.

Related links#

• Developer guide: RefName aliasing