From Genome Analysis Wiki
* ReadName/Fragment combo is in one file, but not in the other file within the window set by recPoolSize & posDiff
* ReadName/Fragment combo is in both files, but at least one of the specified fields to diff is different
The first line of the difference output is just the read name.
The 2nd line is the flag followed by the diff'd fields from one of the records.
If <code>onlyDiffs</code> is specified, only the
diff'd fields that are different are printed in lines 2 & 3.
If <code>onlyDiffs </ code> is NOT specified, all the fields that are diff'd (per the parameter settings) are printed in lines 2 & 3.
The diff'd lines are tab separated:
== readReference ==