SamAdapter

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

Example usage#

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

sample.sam infers SamAdapter 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.sam',
  assemblyNames: ['hg38'],
}

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

plain-text SAM, either a file or an inline string

There is no index, so the whole file is loaded and held in memory — this is for small files (a BLAT result, a handful of assembled contigs, a test case). Use BAM or CRAM for anything sequencing-scale.

Note: sequenceAdapter does not need to be specified manually — JBrowse automatically supplies it from the enclosing assembly's sequence track. It is what per-base mismatches are computed against for records with no MD tag.

Related links#

• Track: AlignmentsTrack
• Display: LinearAlignmentsDisplay
• Guide: Supported file types

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "SamAdapter", ... }. 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.