min_length min_unit ?

[PYB-SU]

Hello,

thanks for the tool.

It does not seem that the min_length and min_unit are taken into account in the output?

Could you detail the options for suppressing the output of repeats of single letter repeats?

Thank you

[DanielOlson]

Thanks for reaching out! Some clarifying questions: Are you finding that there are some labeled tandem repeats that are only a single letter? Or are you trying to exclude period 1 repeats from being annotated?

[PYB-SU]

Well I am interested in getting, let's say, only patterns where 3 or 4 bases are repeated. I thought that I could get by with min_length and min_unit.

Anyway I ended up changing cli.hpp to suit my purposes with 2 options min_rep and max_rep corresponding to the length of the repeated motif and only printing those in the desired range.

[traviswheeler]

It sounds like you'd like to report only repeats with period 3 or 4. Have you tried using the --period flag? -p,--period UINT [100] Maximum detectable repeat period

For example, -p 4 should constrain ULTRA such that it doesn't report repeat regions with period >4.