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PairwiseIndexedPAFAdapter

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

Also note: this document represents the config API for the current released version of jbrowse. If you are not using the current version, please cross reference the markdown files in our repo of the checked out git tag

Source code

GitHub page

Docs​

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',
        },
      }