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BamAdapter

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​

used to configure BAM adapter

BamAdapter - Slots​

slot: bamLocation​

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

slot: index.indexType​

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

slot: index.location​

location: {
        type: 'fileLocation',
        defaultValue: {
          uri: '/path/to/my.bam.bai',
          locationType: 'UriLocation',
        },
      }

slot: fetchSizeLimit​

fetchSizeLimit: {
      type: 'number',
      description:
        'size to fetch in bytes over which to display a warning to the user that too much data will be fetched',
      defaultValue: 5_000_000,
    }

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, used to calculate SNPs when BAM reads lacking MD tags',
      defaultValue: null,
    }