summarize the softclips in a SAM/BAM file

cigar_summarize.py

#!/usr/bin/python

import sys; 

import pysam

bamFile    = sys.argv[1];

bamFP = pysam.Samfile(bamFile, "rb");

for read in bamFP:
    if( not( read.is_unmapped ) ):   #if it's mapped
        cigarLine=read.cigar;
        for (cigarType,cigarLength) in cigarLine:
            try:
                if cigarType == 4:
                    print cigarLength
            except:
                print "Problem";