Fix edge case in indels in repetitive regions

arkal / Transgene

This is a repository to host the transgene tool. Transgene takes a snpeffed vcf and a peptide fasta , and returns 3 peptide fastas containing 9-, 10- and 15-mers harboring the called mutations

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Fix edge case in indels in repetitive regions #51

Closed arkal closed 6 years ago

arkal commented 6 years ago

Normal: AAAAAAAAAAAAAAAAAAAAGGLAAAG
Tumor:  AAAAAAAAAAAAA      AGGLAAAG

will not be discarded since we do not check for mismatch=-1 when looking from the right during trimming.