added options for labeling, changed sweep script name, updated tests to reflect changes

fixed syntax error in consume output
changed output freq for consume
groups mode in sweep now splits input file as well
added label counts output
outdir option
suppressed warning when read len less than kmer len
suppressed warning message when read length less than k-mer length
added help strings to more arguments for docs
fixed error in printed output of number reads labeled
new test for sweep
added html target for coverage
stripped out unused write_seq function
fixed error handling for IOError when flushing individual buffer
fixed test_sweep_reads_2 to cover all cases of buffer flush, added extra test to cover label-by-group
removed extraneous del statement
checked in new test file for sweep_test_3
silence pylint noise, switch to new-style objects
Merge pull request #345 from ged-lab/sweep_opts

v1.0 fixes for sweep script
don't implicitly downcast tagset_size()

Changes fileformat version for saved tagsets
lib/counting.{cc,hh},khmer/_khmermodule.cc: many downcasts removed
formatting only; astyle -A10 lib/counting.{cc,hh}
more downcast removal; scope reduction; prefix oper
labelhash downcast, no\!
this doesn't work, use git diff -w 96b2164f3e931f4bec20dc26ba7db6509c9db7f1 to review
Check types of PyLists members. Make obj conv sane

The fact that PyLong_AsLongLong worked for all data types was a
confusing fluke.