[BioC] a problem of trimLRPatterns still confused me

[Wang Peter]

dear Harris
thank you so much for your kindly explanation
i am so ashamed to disturb u again.

my understanding is

when they low-level function to caculate the distance between S and P

S= CAAGATC     AAG
P=     AGATCGGAAG


it will try
CAAGATCAAG
AAGATCAAG
AGATCAAG
GATCAAG
...
G

and get all the edit distance
but 2 is the smallest one

so it will take 2 as the distance between S and P
S'= AGATC     AAG
P= AGATCGGAAG

and then trim the whole S, rather than S'


-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
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