<config data_dir="/Users/alastairm/Documents/Work/ScaleHDTests/Data/debug/" forward_reference="/Users/alastairm/Documents/Work/Huntington/TypicalRefs/4k-HD-INTER.fas" reverse_reference="/Users/alastairm/Documents/Work/Huntington/AtypicalRefs/Reverse/RV_CAG-1-1-CCG-2.fasta">
  <instance_flags quality_control="True" sequence_alignment="True" atypical_realignment="True" genotype_prediction="True"/>
  <trim_flags trim_type="Adapter" quality_threshold="5" adapter_flag="-a" forward_adapter="GATCGGAAGAGCACACGTCTGAACTCCAGTCAC" reverse_adapter="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" error_tolerance="0.39"/>
  <alignment_flags min_seed_length="19" band_width="100" seed_length_extension="1.5" skip_seed_with_occurrence="500" chain_drop="0.50" seeded_chain_drop="0" seq_match_score="1" mismatch_penalty="4" indel_penalty="6,6" gap_extend_penalty="4,4" prime_clipping_penalty="5,5" unpaired_pairing_penalty="17"/>
  <prediction_flags plot_graphs="True"/>
</config>