untergasser
commented
2 years ago Thank you for your contribution and the great tests. This was a tricky feature.
Please be not discouraged by my following implementation, which has the following differences:
- I prefer the overhang on the right primer as attached to the 5' end.
- We do not store primer sequences (as there can be many) only their features and calculate the sequence at need.
- Performance improvements if no overhang is specified.
- As overhang is only used for dpal and thal, the limit can be 60 bp for primer + overhang, the 36bp limit only applies to Tm calculations.
- Some tiny cleanups on the way.
Best,
Andreas
Implements #14 by adding two new input fields. SEQUENCE_OVERHANG_LEFT is added to the 5' end of the fwd primer while the reverse complement of SEQUENCE_OVERHANG_RIGHT is added to the 5' end of the rev primer, such that SEQUENCE_OVERHANG_LEFT and SEQUENCE_OVERHANG_RIGHT are both supplied in the same orientation. The overhang sequences are utlized in calculating SELF_ANY, SELF_ANY_STRUCT, SELF_END, SELF_END_STRUCT, HAIRPIN, HAIRPIN_STRUCT, COMPL_ANY, COMPL_END, plus the _TH versions of those outputs, and PRODUCT_SIZE. The TM and GC_PERCENT calculations have not been modified, so they will only be based on the 3' portion of the oligo that binds to the template. Total oligo length remains limited to 36 bp, therefore long overhangs will limit the length of the primer section of the oligo.