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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
match: 2
gap: -1
mismatch: -1
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/
hg38: 'hg38.fna'
t2t: 't2t.fa'
main_ref_name: 'hg38'