Changes

* supplementary reads

* supplementary reads

The Deduper will not work if secondary or supplementary reads are not excluded.  It will not properly find the mates since there will be more than 2 reads with the same mate information.

Secondary (0x100) and Supplementary (0x800) reads currently must be excluded.

=== Turn on Verbose Mode (<code>--verbose</code>) ===

=== Turn on Verbose Mode (<code>--verbose</code>) ===