Potential way to screen for inversions automatically

[BiologicalScientist]

Summary of discussion around pseudocode concept for detecting inversions with the output of corekaburra when core gene % is set to less than 100%. - currently a challenge, triplets of core genes works well for 100% presence core genes but fails when you allow < 100% presence of core genes

genome A (reference)
genome B (inverted seq with core genes missing)

genome A list { A, B, C , D, E ,F ,G, H, I, J, K, L, M ,N, O, P } - pangenome order
genome B list { A, B, C , D, E ,F ,G, K, H, L, M ,N, O, P } - pangenome order missing IJ

make list where elements exist in both
genome A list { A, B, C , D, E ,F ,G, H, K, L, M ,N, O, P } - pangenome order
genome B list { A, B, C , D, E ,F ,G, K, H, L, M ,N, O, P } - pangenome order

check where list elements in B do not match to A
genome B list { T, T, T , T, T ,T ,T, F, F ,T, T ,T, T,T }
genome B list { A, B, C , D, E ,F ,G, K, H L, M ,N, O, P }

gives you the core genes that encode an inverted region which can then be investigated in both genomes to pull out the region
Genome A {H,I,J,K}
Genome B {K,H}