Skip to main content

HtsgetBamAdapter

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

Source file​

plugins/alignments/src/HtsgetBamAdapter/configSchema.ts

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,
    }