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BamAdapter

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

Example usage

The uri shorthand auto-resolves the .bai index (pass csi: true for a .csi index). For a differently-named index, set index explicitly with the full slot form:

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

sample.bam infers BamAdapter 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.bam',
  assemblyNames: ['hg38'],
}

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

used to configure BAM adapter

Note: sequenceAdapter does not need to be specified manually — JBrowse automatically supplies it from the enclosing assembly's sequence track.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "BamAdapter", ... }. It also accepts the shorthand keys uri, baseUri, csi 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
bamLocation
fileLocation = { uri: '/path/to/my.bam', locationType: 'UriLocation' }		location of the BAM file. Per-base mismatches come from the record's MD tag when it has one, and are otherwise computed against the assembly's reference sequence.
index.indexType
stringEnum (BAI, CSI) = 'BAI'		BAI is the usual samtools index output. CSI is required for a reference longer than 512 Mb, which BAI cannot address.
index.location
fileLocation = { uri: '/path/to/my.bam.bai', locationType: 'UriLocation' }		location of the index. Only needed when it is not named <file>.bam.bai (or .bam.csi), which is what the uri shorthand assumes.
fetchSizeLimit
number = 5_000_000		size to fetch in bytes over which to display a warning to the user that too much data will be fetched
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