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Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
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Bug in parse_blast.pl script causes max length deletion to be incorrectly reported in rare cases #68

Closed nawrockie closed 1 year ago

nawrockie commented 1 year ago

If a blast alignment query gap (deletion) ends with a position that is a residue in the query and a gap in the subject, the maximum length deletion is not properly updated in parse_blast.pl.

Simple example:

Query  4    TTKPTNKPPTKTTNK-------------------RDPKTLAKTPKKETTINPTKKPTPKT  126
            TT PT KP  KTT +
Sbjct  226  TTDPTKKPTPKTTERDTSTPQSTVLDTTTSKHTE--------------------------  259

Subject: KU950619.1:4663..5604:+/4688..5629:+ Query: OK078774.1 Using rsv models: vadr-rsv-models-1.5-2

nawrockie commented 1 year ago

Fixed and test files added (iss68-blastmaxde) with commits ecc8936, 2ee8be0, b5e288a .