config.yaml

read_cut_padding: 1000

region_file: "resources/conflict_regions.txt"
alternative_haplotype_vcf: "resources/alternative_haplotypes.vcf.gz"

liftover_root: "resources/references/liftover/"

# Settings for the pairwise alignment
pw_alignment:
  match: 2
  gap: -1
  mismatch: -1

clustering:
  eps: 0.6 # float, the higher the bigger the clusters can be

samples: ['17_08']

# display names and file names of the used references
# the reference files have to be in resources/references/
ref_dict:
  hg38: 'hg38.fna'
  t2t: 't2t.fa'

main_ref_name: 'hg38'