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rankboost's Issues

fix T/N bug

T/N is considering T>N as good but it should be the opposite

Fix bug in collapsing

'ENST1231.1_S123K,ENST1211.1_S143K_K146S' raises error instead of returning S>K+2X+K>S

collapsing IARs leads to dupes

Collapsing IAR range by filtered neoepitopes can lead to duplicate shortened IARs from the same gene but different transcripts
E.G.

>neoepitope_X
MEGAALLKVSVLCIWMS
>neoepitope_Y
MEGAALLKVSVLCIWVQ

If the above IARs only has interesting neoepitopes ending before CIW, we will see this in the rankboost output

GENE   R>K     neoepitope_X   GAALLKVSVLCIW   0.9     4       2       2       0       4.14    6       2       HLA-B*15:01,HLA-C*03:03
GENE   R>K     neoepitope_Y   GAALLKVSVLCIW   0.9     4       2       2       0       1.51    7       3       HLA-B*15:01,HLA-C*03:03

Obviously, those 2 should be collapsed into one call.

GENE   R>K     neoepitope_X,neoepitope_Y   GAALLKVSVLCIW   0.9     4       2       2       0       ZZZ    6       2       HLA-B*15:01,HLA-C*03:03

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