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CramAdapter

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

Source file​

plugins/alignments/src/CramAdapter/configSchema.ts

used to configure CRAM adapter

CramAdapter - Slots​

slot: fetchSizeLimit​

fetchSizeLimit: {
      type: 'number',
      description:
        'size in bytes over which to display a warning to the user that too much data will be fetched',
      defaultValue: 3_000_000,
    }

slot: cramLocation​

cramLocation: {
      type: 'fileLocation',
      defaultValue: {
        uri: '/path/to/my.cram',
        locationType: 'UriLocation',
      },
    }

slot: craiLocation​

craiLocation: {
      type: 'fileLocation',
      defaultValue: {
        uri: '/path/to/my.cram.crai',
        locationType: 'UriLocation',
      },
    }

slot: sequenceAdapter​

generally refers to the reference genome assembly's sequence adapter currently needs to be manually added

sequenceAdapter: {
      type: 'frozen',
      description: 'sequence data adapter',
      defaultValue: null,
    }