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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,
    }