Alignments track configuration

Example AlignmentsTrack config:

{
  "trackId": "my_alignments_track",
  "name": "My Alignments",
  "assemblyNames": ["hg19"],
  "type": "AlignmentsTrack",
  "adapter": {
    "type": "BamAdapter",
    "bamLocation": {
      "uri": "http://yourhost/file.bam"
    },
    "index": {
      "location": {
        "uri": "http://yourhost/file.bam.bai"
      }
    }
  }
}

BamAdapter configuration options#

• bamLocation - a 'file location' for the BAM
• index - a subconfiguration schema containing
  • indexType: options BAI or CSI. default: BAI
  • location: a 'file location' of the index

Example BamAdapter config:

{
  "type": "BamAdapter",
  "bamLocation": {
    "uri": "http://yourhost/file.bam"
  },
  "index": {
    "location": {
      "uri": "http://yourhost/file.bam.bai"
    }
  }
}

A reduced form is also accepted; the index is inferred as yourfile.bam.bai:

{ "type": "BamAdapter", "uri": "http://yourhost/file.bam" }

CramAdapter configuration options#

• cramLocation - a 'file location' for the CRAM
• craiLocation - a 'file location' for the CRAI
• sequenceAdapter - a subadapter describing the location of the reference assembly (e.g. an IndexedFastaAdapter)

Example CramAdapter config:

{
  "type": "CramAdapter",
  "cramLocation": {
    "uri": "http://yourhost/file.cram"
  },
  "craiLocation": {
    "uri": "http://yourhost/file.cram.crai"
  },
  "sequenceAdapter": {
    "type": "IndexedFastaAdapter",
    "fastaLocation": {
      "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa",
      "locationType": "UriLocation"
    },
    "faiLocation": {
      "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.fai",
      "locationType": "UriLocation"
    }
  }
}

A reduced form is also accepted; the index is inferred as yourfile.cram.crai:

{ "type": "CramAdapter", "uri": "http://yourhost/file.cram" }