[BioC] A problem about trimLRPatterns

[wang peter]

i have found a problem
if we allow edit distance as 1, with indel=1
subject aaaaaaATCGACTG
pattern                TCGACTG
and i found some reads were trimmed ATCGACTG
not TCGACTG

that is ok for RNA-seq
but not ok for microRNA, if we want to keep the whole microRNA sequences

-- 
shan gao
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Boyce Thompson Institute
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