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RefNameAliasAdapter

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

Source file

plugins/config/src/RefNameAliasAdapter/configSchema.ts

can read "chromAliases" type files from UCSC or any tab separated file of refName aliases

RefNameAliasAdapter - Slots

slot: location

location: {
type: 'fileLocation',
defaultValue: {
uri: '/path/to/my/aliases.txt',
locationType: 'UriLocation',
},
}

slot: refNameColumn

by default, the "ref names that match the fasta" are assumed to be in the first column (0), change this variable if needed

refNameColumn: {
type: 'number',
defaultValue: 0,
}