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HtsgetBamAdapter

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 fetch data from Htsget endpoints in BAM format, using the gmod/bam library

HtsgetBamAdapter - Slots​

slot: htsgetBase​

htsgetBase: {
      type: 'string',
      description: 'the base URL to fetch from',
      defaultValue: '',
    }

slot: htsgetTrackId​

htsgetTrackId: {
      type: 'string',
      description: 'the trackId, which is appended to the base URL',
      defaultValue: '',
    }

slot: sequenceAdapter​

sequenceAdapter: {
      type: 'frozen',
      description:
        'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
      defaultValue: null,
    }