bugfix: fixed calculating average sigma in best_fit_newton, was not
adding back in low_sigma the first time.
bugfix: if 3sigma extends over edge of chromosome, truncate.
feature: can filter waves on height or sigma
bugfix: print height or sigma threshold correctly
bugfix: takes standard deviation of wave into account when determining
if wave is in a .bed file bin. If wave position is within 3SD of bin, is
included.
bugfix: sets sample attribute "hide" to True. This gets changed to False
when sample metadata is added.
bugfix: sets "hide" to False when metadata is added
bugfix: sets "hide" to True or False (boolean)
bugfix: changing samples to query
Merge branch 'master' of
https://github.com/apfejes/epigenetics-software.git

Conflicts:
	Epigenetics/MongoDB/mongoUtilities/MongoEpigeneticsWrapper.py
sbrown: merged
bugfix: Changed batch size from 100000 to 8000, prevent it from locking
tables for too long
feature: update will ensure index on relevant fields for waves and
samples
created: Converts .waves file to .wig file for viewing in genome
browser. Uses wave sigma value threshold to determine which waves to
write to file.
bugfix: normalizes baseline file to sample file before subtraction
(scaling it by a factor equal to the ratio between average probe
intensity for each file). Note: this will only INCREASE the baseline
values to subtract, it will never decrease it.
feature: command line argument to determine if samples should be hidden
or not
Merge branch 'master' of https://github.com/apfejes/epigenetics-software.git
todo: ensure index not working for key pairs. debug this.
addition: added minsigma threshold
Merge branch 'master' of
https://github.com/apfejes/epigenetics-software.git

Conflicts:
	Epigenetics/MongoDB/mongoUtilities/MongoEpigeneticsWrapper.py