script to calculate best assembly from a list of contig/scaffold files
minor cleanup for khmer protocols
initial stab at exception handling around file operations
support using system z,bz2 libraries
update cppcheck's include paths
force remove old zlib Makefile
remove the unused KTable object

Rename ktable.{cc,hh} to kmer_hash.{cc,hh}, purge remaining references
Fix syntax error in preprocessing
Merge pull request #337 from ged-lab/fix/remove_KTable_class

remove the unused KTable object
Merge pull request #346 from ged-lab/feature/system-libs

support using system z,bz2 libraries
update cppcheck command
Merge pull request #342 from ged-lab/feature/cppcheck

update cppcheck command
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
initial CITATION file
work around for build_ext config #352

Distribution.reinitialize_command implies that you get the same command
that get_command_obj() but fails to set options that were supplied in
config files or on the command line like Distribution.get_command_obj()
does.

This includes a monkeypatch to fix this issue.
Merge pull request #353 from ged-lab/fix/build_ext-cfg-workaround

work around for build_ext config #352
set fill_id to zero at initialization; Coverity CID 1054789 redux
docs: fork/tag policy, formatting fixes
new khmer/file module

check_file_status(file_path), check_space(in_files),
check_space_for_hashtable(hash_size), check_valid_file_exists(in_files)

Squash support added & import and usage of file have been updated in all scripts under
scripts/