{
  "seq_reads_file": "test/samples/ss.subsample005.bam",
  "vector_type": "ss",
  "vector_bed": "test/samples/ss.annotation.bed",
  "vector_fa": "test/samples/ss.construct.fasta",
  "packaging_fa": "test/fasta/packaging.fa",
  "host_fa": "test/fasta/hg38.chr19trunc-chrM.fa",
  "itr_label_1": "ITR",
  "itr_label_2": "ITR",
  "repcap_name": "pRep2Cap9",
  "helper_name": "pHelper",
  "lambda_name": "Lambda",
  "flipflop_name": "AAV2",
  "flipflop_fa": "test/fasta/AAV2.flipflop.fasta",
  "target_gap_threshold": 200,
  "max_allowed_outside_vector": 100,
  "max_allowed_missing_flanking": 100,
  "container_version": ":dev"
}