updates to calc-median-distribution in sandbox/
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
Bug fix: make-initial-stoptags.py error on missing .ht input file, actual input file is .pt
Merge pull request #391 from RamRS/bugfix-htpt

Bug fix: make-initial-stoptags.py error on missing .ht input file, actual input file is .pt
Update partitioning-big-data.txt

Add in a note about the default parsing behaviour of load-graph.py when there is no recognised file extension.
update MANIFEST.in
add remainder of libz libs
Merge pull request #374 from ged-lab/fix/manifest

fix zlib via MANIFEST.in & setup.py
Remove argparse from the requirements

unless it isn't available. Argparse is bundled with Python 2.7+.
This simplifies the installation instructions. Tested with cpython 2.6
& 2.7 on Ubuntu 13.10.
Merge pull request #401 from ged-lab/fix/argparse-nodep

Remove argparse from the requirements
Merge pull request #400 from ctSkennerton/patch-1

Update partitioning-big-data.txt
Explicit python2 invocation
Merge branch 'master' of github.com:ged-lab/khmer into calc_best_assembly
Adds hash table write error alert.

Writing can silently fail on certain systems (like mine).  I don't know how to prevent it, but here's a few lines to add in error alerts.
Bypass clang error

See http://bruteforce.gr/bypassing-clang-error-unknown-argument.html
Merge pull request #412 from ged-lab/fix/jenkins-osx

Bypass clang error
Merge pull request #404 from ged-lab/fix/python2

Explicit python2 invocation
fixed thread hanging issue khmer#384