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Gff3TabixAdapter

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

Source file​

plugins/gff3/src/Gff3TabixAdapter/configSchema.ts

Gff3TabixAdapter - Slots​

slot: gffGzLocation​

gffGzLocation: {
      type: 'fileLocation',
      defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
    }

slot: index.indexType​

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

slot: index.indexType​

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

slot: dontRedispatch​

the Gff3TabixAdapter has to "redispatch" if it fetches a region and features it finds inside that region extend outside the region we requested. you can disable this for certain feature types to avoid fetching e.g. the entire chromosome

dontRedispatch: {
      type: 'stringArray',
      defaultValue: ['chromosome', 'region', 'contig'],
    }