Bugfix: closing queues before queues are empty.
untested end_process flag for mapdecomposingthread
Cleaning up the MapDecomposingThread, removing debugging code.
Cleanup of ChipSeq main.
minor change to ConnectToMongo - StaticMethod
Cleanup to MapDecomposingThread and replacement of deepcopy() with
list()
Changing close operations on threads/queues.
Bugfix on pet readahead iterator - removing calls to removed parameters.
Bugfix typo in wave file header.
Now numbering waves, so you can tell which is the primary peak, and
which are sub-peaks.
Maximum read length now enforced for PET reads. 
Code now terminates correctly