--s= precedes a list of three comma separated parameters for SMERFS
- the order of parameters is as following:
- 1. window width - an integer and an odd number
- 2. how to allocate window scores to columns, two ways are possible:
- MID_SCORE - gives the window score to the middle column
- MAX_SCORE - gives the column the highest score of all the windows it
- belongs to
- 3. gap percentage cutoff - a float greater than 0 and smaller or equal 1
- EXAMPLE: -s=5,MID_SCORE,0.1
- Optional, default values are 7,MID_SCORE,0.1
-