config.yaml

manifest: manifest.tab
# Size of the methylation windows to average over
window_size: 5000
# Slide size of the methylation windows of the target region
slide: 5000
# Minimum size of CDR to report
report_threshold: 25000
# Size of ALR repeat stretches to include in search of CDR
alr_threshold: 100000
# Distance to search on the edge of CDRs to ensure that methylation reaches max around
edge_search: 50000
# Threshold for mean percent methylation to clear in order for standard calling, 
## if below, it is assumed that this is the low end of the distribution and the windows will be taken based on what is 1/2 a standard deviation above the mean 
low_threshold: 39