Hi, I need to get 5'-end position of each read in SAM file. For reads aligned in forward direction it's provided in SAM file (POS). But for reads aligned onto reverse strand the one has to figure it out from the cigar string. You cannot simple add length of the read to left-most position, as reads may be soft-clipped or some indel may occure.

I have written simple python function in order to find right most position of aligned read. Could you have a look and comment on that as I'm not sure if it's correct?

import re

#should nicely separate CIGAR entries
cigar_pat = re.compile(r"\d+[MIDNSHP=X]{1}")

def cigar2end( left,cigar ):
  """Return right-most position of aligned read."""
  #store info about each CIGAR category
  counts={ "M":0, #M 0 alignment match (can be a sequence match or mismatch)
           "I":0, #I 1 insertion to the reference
           "D":0, #D 2 deletion from the reference
           "N":0, #N 3 skipped region from the reference
           "S":0, #S 4 soft clipping (clipped sequences present in SEQ)
           "H":0, #H 5 hard clipping (clipped sequences NOT present in SEQ)
           "P":0, #P 6 padding (silent deletion from padded reference)
           "=":0, #= 7 sequence match
           "X":0, #X 8 sequence mismatch
        }
  #split cigar entries
  for centry in cigar_pat.findall(cigar):
    ccount  = int(centry[:-1])
    csymbol = centry[-1]
    counts[csymbol] = ccount
  #get number of aligned 'reference' bases
  aligned = counts["M"] + counts["D"] + counts["N"] #+ counts["="] + counts["X"]
  right   = left + aligned
  return right