Regarding line 37 of get_flag_primerPair.py in the Kariton repository https://github.com/mbl-bdmu/kariton/blob/main/bin/get_flag_primerPair.py:
c = primers[(primers[1] < i) & (primers[2] > i)]
It's a comparison with the coordinates in the bed file https://github.com/mbl-bdmu/kariton/blob/main/bin/primer_v4.1.bed
(1.) Are the coordinates in the .bed file part of the coordinates of the primer pairs, so the comparison using exclusive (> and <) rather than inclusive (>= and <=) should be used? Checking the original bed file https://github.com/artic-network/primer-schemes/blob/master/nCoV-2019/V4/SARS-CoV-2.primer.bed, it seems like the start & end coordinates of the amplicon (not the primers) are the contents of our new bed file, so should we use inclusive instead?
(2.) Then in the script https://github.com/mbl-bdmu/kariton/blob/main/bin/fa-mask.py, the input is the .bed file, and it masks only the amplicon between the primer pairs, right, excluding the coordinates that are part of the primer pairs?
This is the relevant line in the fa-mask.py script, showing how it uses the input bed file. Will it work as expected given the coordinates in the primer_v4.1.bed file?
Regarding line 37 of get_flag_primerPair.py in the Kariton repository https://github.com/mbl-bdmu/kariton/blob/main/bin/get_flag_primerPair.py:
c = primers[(primers[1] < i) & (primers[2] > i)]
It's a comparison with the coordinates in the bed file https://github.com/mbl-bdmu/kariton/blob/main/bin/primer_v4.1.bed
(1.) Are the coordinates in the .bed file part of the coordinates of the primer pairs, so the comparison using exclusive (> and <) rather than inclusive (>= and <=) should be used? Checking the original bed file https://github.com/artic-network/primer-schemes/blob/master/nCoV-2019/V4/SARS-CoV-2.primer.bed, it seems like the start & end coordinates of the amplicon (not the primers) are the contents of our new bed file, so should we use inclusive instead?
(2.) Then in the script https://github.com/mbl-bdmu/kariton/blob/main/bin/fa-mask.py, the input is the .bed file, and it masks only the amplicon between the primer pairs, right, excluding the coordinates that are part of the primer pairs?
This is the relevant line in the fa-mask.py script, showing how it uses the input bed file. Will it work as expected given the coordinates in the primer_v4.1.bed file?
