[Samtools-help] CIGAR string with indels

[Wes B. <wes...@cs...>]

I have a sam file that originated from 454 sequencing.  Processing
this file for SNPs using SAMtools pileup, samtools.pl varFilter, etc,
yields very few SNPs because the CIGAR string contains mostly single
insertion/deletion pairs surrounded by matches.  For example, I see
many CIGAR strings containing patterns like this:

50M1D1I12M

I've written a perl program to convert instances such as this to:

63M

This allows SAMtools to properly identify these variations and call
SNPs.  My question is: "Is there a preferred method for handling
situations like this?"  Is there a CIGAR string "fixer" of some sort
available?
-- 
Wes Barris