Script that takes a SAM file and removes leading/trailing insertions/deletions from CIGAR string such that samtools tview likes it better.

fix_sam.py

#!/usr/bin/env python

import sys

def splitCigar(cigar):
    result = []
    count = ''
    operation = ''
    for x in cigar:
        if x not in '0123456789':
            operation = x
            if count:
                result.append((int(count), operation))
            operation = ''
            count = ''
        else:
            count = count + x
    return result

def fixLine(line):
    vals = line.split('\t')
    if vals[3] == '*' or vals[5] == '*':
        return line
    pos = int(vals[3])
    cigar = vals[5]
    if cigar != '*':
        cigar = splitCigar(cigar)
        if cigar[0][1] == 'I':
            pos -= cigar[0][0]
            if len(cigar) > 1 and cigar[1][1] == 'M':
                cigar[1] = (cigar[0][0] + cigar[1][0], 'M')
                cigar.pop(0)
            else:
                cigar[0] = (cigar[0][0], 'M')
        elif cigar[0][1] == 'D':
            pos += cigar[0][0]
            cigar.pop(0)
        if cigar[-1][1] == 'I':
            if len(cigar) > 1 and cigar[-2][1] == 'M':
                cigar[-2] = (cigar[-1][0] + cigar[-2][0], 'M')
                cigar.pop()
            else:
                cigar[-1]= (cigar[-1][0], 'M')
        elif cigar[-1][1] == 'D':
            cigar.pop()
            #if len(cigar) > 1 and cigar[-2][1] == 'M':
              #  cigar[-2] = (cigar[-1][0] + cigar[-2][0], 'M')
              #cigar.pop()
              #else:
                #cigar[-1]= (cigar[-1][0], 'M')
        cigar = ''.join(''.join(map(str, list(x))) for x in cigar)
    vals[3] = str(pos)
    vals[5] = cigar
    return '\t'.join(vals)

if __name__ == '__main__':
    for line in sys.stdin:
        if line.startswith('@'):
            print line.strip()
        else:
            print fixLine(line.strip())

Also see https://gist.github.com/holtgrewe/8735877.