Added a single script 'do-partition.py' that does partitioning mostly in memory.

This script combines the basic functionality of load-graph, partition-graph,
merge-partitions, and annotate-partitions into one script.
Merge branch 'master' of github.com:ctb/khmer

Conflicts:
	tests/test_scripts.py
updated docs with do-partition.py
Finish ripping out the old FASTA and FASTQ parsers.
Merge 'spartanem:mt-reader' into 'ged-lab:bleeding-edge'.
Rip out all the ReadMask stuff everywhere.
Fix small memory leak: delete parser states in parser destructor.
Fix huge memory leak: delete parser object created by 'consume_fasta' compatibility wrapper method for hashtables.
sweep out the reads with multiple query files/ht
Apply standard changes from 'autopep8'.
Manually fix long lines horked by 'autopep8'. (Still need to fix lines in sandbox scripts.)
Merge 'ged-lab:bleeding-edge' into 'spartanem:pep8ify'.
Manually fix long lines in sandbox scripts.
Ignore reads with length < K size when sweeping out reads

Modified sweep-reads3.py to compute the estimated mem usage as #hts * ht size, instead of just estimated size of 1 ht
Reduce line length and mark the end of user-servicable parts in top-level Makefile.
Bug Fix: Use hash table after it has been initialized. (Caught by Pylint.)
Identify the second read of a pair using a regex search.
(Note: Still need to test in multithreaded operation.)
Create test data set with new Illumina read name format.
Support Python for..in iteration on ReadParser objects.
Create C++ exception for signalling when no more reads are available.
Create script to convert from old FAST{A,Q} name format to new one (as of Casava 1.8).