refactored LOG* calls especially for MPI Gathered log entries
refactored algorithm to run large contig files in batches
added option max-contigs-per-batch to DNA
fixed some build and test problems on hopper
.
added todo comments
refactored ReadSetStream and applied to DistributedKmerSpectrum and MeraculousCounter
bugfix in fastq quality score calibration when using ReadSetStream
minor performance fixes
checkpoint in BucketExposedMap refactor
checkpoint in BucketExposedMap refactor
checkpoint in BucketExposedMap refactor
refactored KmerArray to KmerArrayPair
more refactoring.  moved Iterators into BucketExposedMap template
more refactoring.  moved PurgeMinCount and merge functions
changed tempalting parameters of KmerSpectrum
more refactoring... still not compatible with STL
more progress
another checkpoint. refactor is close now.
checkpoint. compiles again.