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BamAdapter

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

Source file​

plugins/alignments/src/BamAdapter/configSchema.ts

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,
    }