Process eland extended (or multi) read files.

Process eland extended (or multi) read files.

This also updates the report tools to be compatible with 1.0.
For multi reads I mapped 0/1/2 mismatch reads to U0/U1/U2 if the number of
reads equaled 1 (for each category seperatly) and I mapped reads >1 and < 255
to R0/R1/R2.

Unfortunately 1.1rc1 changed the summary file, so this patch is not
compatible with it yet.