STL tags are included elsewhere
Changed stdout output in scripts to stderr;
updated changelog
pep8
ignore Doxyfile
Merge pull request #648 from ged-lab/fix/odds-n-ends

Fix/odds n ends
Fixed for pep8
polished for pylint
Merge pull request #626 from b-wyss/fix/scriptstderr

Changed stdout output in three scripts to stderr
Close open file handles in load-into-counting.py

We now use `with open(X) as y:` which automatically handles the closing
of files.
Add a tab-seperated output to load-into-counting

This adds a CLI flag to load-into-counting.py allowing it to output the
FPR, total number of distinct k-mers (cm-sketch occupancy) and input
files in a machine/R/excel readable format to save us from resorting to
regex hacks to pull this info out of out.kh.info etc.

I've also make the info files contain all files used as input.

I've also also added a test of the tsv creation behaviour.

Changes:
	modified:   scripts/load-into-counting.py:
			new cli flag, write all inputs to .info file
	modified:   tests/test_scripts.py:
			add test of the new cli flag
load-into-counting: Fix typo in "total kmers" line

Writing it to the info file had the wrong sentence.
load-into-counting: Less confusing info print line
load-in2-count: Add json/TSV machine readable info

This changes the CLI flag that enables machine readable info so that to
enalbe this behaviour, you give it an argument of either 'json' or
'tsv'. This allows for a user choice of a versioned, dat-friendly json
or something easy to whack into R and plot.
Add format version to load-in2-counting json info

Add a file format version key-val pair
Use argparse's choices param to validate arg

We now use the choices kwarg to parser.add_argument to validate the
---machine-readable-info argument, instead of manually checking it.

Also, updates the tests.

	modified:   scripts/load-into-counting.py
	modified:   tests/test_scripts.py