Granular control over needleman-wunsch parameters

[Jdbeck66]

Is your feature request related to a problem? Please describe. Not really a problem as much as the desire to have more granular control over the Needle_wunsch alignment parameters to incentivize alignment around multiple nick sites

Describe the solution you'd like I'd like to pass in gap open and extension vectors that match the length of the quantification window.

Describe alternatives you've considered I am currently tweaking the global incentive parameter to see if there is a "sweet spot"

Additional context Add any other context or screenshots about the feature request here.

[kclem]

Hi @Jdbeck66 you can provide NW alignment parameters using the parameters:

• --needleman_wunsch_gap_open: Gap open option for Needleman-Wunsch alignment, default=-20
• --needleman_wunsch_gap_extend: Gap extend option for Needleman-Wunsch alignment, default=-2
• --needleman_wunsch_gap_incentive: Gap incentive value for inserting indels at cut sites, default=1
• --needleman_wunsch_aln_matrix_loc: Location of the matrix specifying substitution scores in the NCBI format (see ftp://ftp.ncbi.nih.gov/blast/matrices/), default='EDNAFULL'

Note that the match/mismatch scores are provided in the aln_matrix.

I hope that helps! Happy analyzing!

[Jdbeck66]

I think I didn't explain what I was looking for very well. I'd like the ability to set those values by position. For example, if I want the incentive value for the four spaces before and after the cut site to be [0 0 3 4 3 2 0 0], that doesn't seem possible given the structure you note above.

I think its just a matter of modifying code here to accept a vector and then allowing the parameters to accept the input of that vector.