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

Source file


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',
'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
defaultValue: null,