CalcBaseContent #

[[step]]
    action = "CalcBaseContent"
    segment = "read1" # Any of your input segments, or 'All'
    out_label = "at_content"
    bases_to_count = "AT"
    bases_to_ignore = "N"
    relative = true # default

Counts the percentage of bases that match bases_to_count, while removing any bases listed in bases_to_ignore from the denominator (if relative = True).

Both lists are case-insensitive, and accept only ascii letters. When no bases remain after filtering, the step returns 0.

Set relative = false to emit absolute base counts instead of percentages. Absolute mode requires bases_to_ignore to remain unset, otherwise the configuration check fails.

Use this in combination with StoreTagInComment or FilterByNumericTag to surface the computed percentages downstream.