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CramAdapter

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

Example usage

The uri shorthand auto-resolves the .crai index:

{
  type: 'AlignmentsTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'CramAdapter',
    uri: 'https://example.com/sample.cram',
  },
}

sample.cram infers CramAdapter and AlignmentsTrack on its own, and name defaults to the file name. In a config declaring one assembly, assemblyNames comes from there too — see the shortest track.

{
  trackId: 'my_track',
  uri: 'https://example.com/sample.cram',
  assemblyNames: ['hg38'],
}

Reads CRAM alignments, fetching only the containers overlapping the visible region through the .crai index. Decoding happens against the enclosing assembly's sequence, so it has to be the reference the file was compressed against; a mismatched one isn't rejected, it just decodes into mismatches.

JBrowse fills in sequenceAdapter from the enclosing assembly's sequence track, so a config never specifies it.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "CramAdapter", ... }. 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
fetchSizeLimit
number = 5_000_000		size in bytes over which to display a warning to the user that too much data will be fetched
advanced
useSliceWorkerPool
boolean = true		decode CRAM slices on a pool of workers rather than in the thread that asked
advanced
cramLocation
fileLocation = { uri: '/path/to/my.cram', locationType: 'UriLocation' }		location of the CRAM file
craiLocation
fileLocation = { uri: '/path/to/my.cram.crai', locationType: 'UriLocation' }		location of the CRAM index (.crai). Only needed when it is not named <file>.cram.crai, the name the uri shorthand assumes.

Retired keys

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.

KeyOn load
sequenceAdapterignored