BamAdapter
Note: this document is automatically generated from configuration objects in our source code. See Config guide for more info
Source file
plugins/alignments/src/BamAdapter/configSchema.ts
used to configure BAM adapter
BamAdapter - Slots
slot: bamLocation
bamLocation: {
type: 'fileLocation',
defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
}
slot: index.indexType
indexType: {
model: types.enumeration('IndexType', ['BAI', 'CSI']),
type: 'stringEnum',
defaultValue: 'BAI',
}
slot: index.location
location: {
type: 'fileLocation',
defaultValue: {
uri: '/path/to/my.bam.bai',
locationType: 'UriLocation',
},
}
slot: fetchSizeLimit
fetchSizeLimit: {
type: 'number',
description:
'size to fetch in bytes over which to display a warning to the user that too much data will be fetched',
defaultValue: 5_000_000,
}
slot: sequenceAdapter
generally refers to the reference genome assembly's sequence adapter currently needs to be manually added
sequenceAdapter: {
type: 'frozen',
description:
'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
defaultValue: null,
}