Hi all,

I feel like I'm missing some obvious function, but is there a simple way to
output a table of matching start and end positions between the subject and
pattern in a pairwiseAlignment result (say from a global-local alignment)?
For example:

  s.pos1 s.pos2 p.pos1 p.pos2
 [1,]    354    359      1      6
 [2,]    360    364      9     19

where s.pos1 and s.pos2 are the start and end of a section of the subject
that corresponds to the start and end (p.pos1 and p.pos2)  of the pattern,
taking into account insertions and deletions. I know the insertion and
deletion information is easily available, but I haven't found a function in
the literature that that summarizes them into a mummer like output of
corresponding start and end positions.

-- 
Brian Herb, Ph.D.
Johns Hopkins School of Medicine
Dr. Andrew Feinberg Laboratory
Rangos 580
855 N. Wolfe St.
Baltimore, MD 21205
Phone:410-614-3478
Fax: 410-614-9819

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