script to calculate best assembly from a list of contig/scaffold files
minor cleanup for khmer protocols
test_normalize_by_median_no_bigcount() now runs in temp dir

tests.test_normalize_by_median_no_bigcount() produced a temp file in
pwd, now modified to run test within temp dir
Changelog formatting, locally ignored file removed from gitignore
extract-partitions test cov 99%, pylint+pep8 on test-script+extr-part
fixed runscript to handle SystemExit; removed unnecessary popenscript fn
clarify Makefile targets; tweak autopep8 to ignore E309
formatting fixes, pylint cleanup
updated ChangeLog with test_scripts/popenscript removal
Merge pull request #332 from ged-lab/fix/test_scripts_popenscript

fixed runscript to handle SystemExit
zlib 1.2.3 -> zlib 1.2.8
Merge pull request #336 from ged-lab/fix/zlib-1.2.8

zlib 1.2.3 -> zlib 1.2.8
Copyright headers corrected for all Python and shell scripts.

Updated copyright headers in all CPP and MATLAB files, added when not
found

sandbox/*.py: chmod u+x; autopep8
1. fix a bug in hashbits.cc of 'Division or modulo by zero' described by  https://github.com/ged-lab/khmer/issues/182
2. add test code for count-overlap.py
3. fix count-overlap.py (a character was removed accidently some time and hashsize was replaced by min_hashsize)
4. count-overlap.py needs hashbits table generated by load-graph.py. This information is added to the "usage:" line.
chmod +x to count-overlap.py
formatting fix
pylint fixes
fix minor PyLint issues
fix -ksize in test_scripts.py about count-overlap
modify ChangeLog