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PairwiseIndexedPAFAdapter

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

Source file​

plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts

PairwiseIndexedPAFAdapter - Slots​

slot: assemblyNames​

assemblyNames: {
      type: 'stringArray',
      defaultValue: [],
      description:
        'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
    }

slot: targetAssembly​

targetAssembly: {
      type: 'string',
      defaultValue: '',
      description: 'Alternative to assemblyNames: the target assembly name',
    }

slot: queryAssembly​

queryAssembly: {
      type: 'string',
      defaultValue: '',
      description: 'Alternative to assemblyNames: the query assembly name',
    }

slot: pifGzLocation​

pifGzLocation: {
      type: 'fileLocation',
      description: 'location of pairwise tabix indexed PAF (pif)',
      defaultValue: {
        uri: '/path/to/data/file.pif.gz',
        locationType: 'UriLocation',
      },
    }

slot: index​

index: ConfigurationSchema('TabixIndex', {
  indexType: {
    model: types.enumeration('IndexType', ['TBI', 'CSI']),
    type: 'stringEnum',
    defaultValue: 'TBI',
  },

  location: {
    type: 'fileLocation',
    defaultValue: {
      uri: '/path/to/my.paf.gz.tbi',
      locationType: 'UriLocation',
    },
  },
})

slot: index.indexType​

indexType: {
        model: types.enumeration('IndexType', ['TBI', 'CSI']),
        type: 'stringEnum',
        defaultValue: 'TBI',
      }

slot: index.location​

location: {
        type: 'fileLocation',
        defaultValue: {
          uri: '/path/to/my.paf.gz.tbi',
          locationType: 'UriLocation',
        },
      }