samerrors.py is the original version.  It takes names of samfiles on the command line and you have to
specify the readlen.  I think this as well as the other versions handle MD field in variable position.

samerrors2.py reads sam file contents from the command line instead.  Determines readlen automatically 
from the data.

Fri Mar  9 12:52:41 PST 2012
samerrors3.py is the same as samerrors2.py except it can handle input files where the read length
varies, like ION Torrent data.  I hope to maintain just this version going forward. 

bamerrors_cutoff.py is for postprocessing samerrors runs to find cells above a certain cutoff value.

bamerrors.py takes a list of bamfiles.  Creates and submits a pbs job array that converts each
file to .sam format and runs samerrors3.py on it.  It also creates but doesn't submit a script
to run bamerrors_cutoff.py.