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Note: this document is automatically generated from configuration objects in our source code. See Config guide for more info

Source file


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',
'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',
'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
defaultValue: null,