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Fusion with frameshift in donor and variant right after accepter breakpoint #786

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zhuchcn opened this issue Aug 2, 2023 · 0 comments · Fixed by #787
Closed

Fusion with frameshift in donor and variant right after accepter breakpoint #786

zhuchcn opened this issue Aug 2, 2023 · 0 comments · Fixed by #787
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priority: now Issue to be fixed immediately

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zhuchcn commented Aug 2, 2023

Fuzz test caught an edge case when there is a frameshift in the donor transcript and a variant right after the accetper breakpoint in the accepter transcript. The DNA graph is like below. The node C in reading frame 2 got skipped so fit_into_codon terminated early leaving nodes not being multiple of three.

                                  |                G
                                  |               / \
0-  ATACAC..TGAGGG-TAGAGGGAAATGGG-ATAGCC..CCAGAT-C-T-TGTCTC..ACATCC
                  \
                   T-------------
                                 \                 G
                                  |               / \
1-  TACACT..TGAGGG-TAGAGGGAAATGGG-ATAGCC..CCAGAT-C-T-TGTCTC..ACATCC

                                    G
                                   / \
2-  ACACTC..TGAGGG-TAGAGG..CCAGAT-C-T-TGTCTC..ACATCC
                  \
                   T------------
                                \
``
@zhuchcn zhuchcn self-assigned this Aug 2, 2023
@zhuchcn zhuchcn added the priority: now Issue to be fixed immediately label Aug 2, 2023
zhuchcn added a commit that referenced this issue Aug 2, 2023
… early when there donor has a frameshift an accepter has a variant right after the breakpoint. #786
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