{
  "artifacts": [
    "offset_scan.tsv",
    "audit/",
    "collision_graph.tsv",
    "correction_safety.tsv",
    "demuxed/",
    "summary.json",
    "assignments.tsv",
    "ambiguous.fastq",
    "unmatched.fastq",
    "top_unmatched.tsv",
    "sample_qc.tsv",
    "barcode_counts.tsv",
    "findings.tsv",
    "provenance.json",
    "multiqc_dotmatch_barcode_mqc.yaml"
  ],
  "barcodes": "examples/barcode_demux/data/barcodes.tsv",
  "commands": [
    {
      "argv": [
        "dotmatch",
        "audit",
        "--targets",
        "examples/barcode_demux/data/barcodes.tsv",
        "--k",
        "1",
        "--audit-mode",
        "auto",
        "--out-dir",
        "examples/barcode_autopsy/results/audit"
      ],
      "exit_code": 0,
      "stderr": ""
    },
    {
      "argv": [
        "dotmatch",
        "demux",
        "--barcodes",
        "examples/barcode_demux/data/barcodes.tsv",
        "--reads",
        "examples/barcode_demux/data/SRR391079.subsample100000.fastq.gz",
        "--barcode-start",
        "0",
        "--barcode-length",
        "auto",
        "--k",
        "1",
        "--metric",
        "hamming",
        "--out-dir",
        "examples/barcode_autopsy/results/demuxed",
        "--summary",
        "examples/barcode_autopsy/results/summary.json",
        "--assignments",
        "examples/barcode_autopsy/results/assignments.tsv",
        "--ambiguous-out",
        "examples/barcode_autopsy/results/ambiguous.fastq",
        "--unmatched-out",
        "examples/barcode_autopsy/results/unmatched.fastq"
      ],
      "exit_code": 0,
      "stderr": ""
    },
    {
      "argv": [
        "dotmatch",
        "inspect-unmatched",
        "--targets",
        "examples/barcode_demux/data/barcodes.tsv",
        "--reads",
        "examples/barcode_demux/data/SRR391079.subsample100000.fastq.gz",
        "--target-start",
        "0",
        "--target-length",
        "4",
        "--k",
        "1",
        "--top",
        "100",
        "--out",
        "examples/barcode_autopsy/results/top_unmatched.tsv"
      ],
      "exit_code": 0,
      "stderr": ""
    }
  ],
  "inference": {
    "ambiguous_rate": 0.0,
    "assignment_rate": 0.11283,
    "candidate_count": 65,
    "command": "barcode infer",
    "invalid_rate": 0.0,
    "k": 0,
    "metric": "hamming",
    "no_match_rate": 0.88717,
    "recommended_length": 4,
    "recommended_start": 0,
    "schema_version": 1,
    "score": 0.11283,
    "separation_from_second_best": 0.05402,
    "status": "review",
    "warnings": [
      "best scanned window has a low exact assignment rate; review the barcode sheet, read orientation, and window before treating the offset as ready"
    ]
  },
  "k_values": [
    0,
    1
  ],
  "reads": "examples/barcode_demux/data/SRR391079.subsample100000.fastq.gz",
  "recommended_length": 4,
  "recommended_start": 0,
  "schema_version": 1,
  "workflow": "barcode_autopsy"
}