Uploaded microarray data (generated from read_data.R script) from 3
projects and probe annotation for testing
Initial commit of two modules and unittest used by mongoAPI.py
Removed the microarray: I realized github thought I coded 2 million
lines.
Merge branch 'master' of
http://apfejes@github.com/apfejes/epigenetics-software.git

Conflicts:
	Epigenetics/Utilities/WigFileThread.py
Wave File writer now has same mechanism as Dan proposed for use with the
wig file writer.
Rename MapDecompingThread to MapDecomposingThread
adding gitignore *.pyc
Removing pyc files.
First unit test for MapDecomposingThread
Mostly working code, removing some bugs in the decomposition. Some
formatting cleanup after discovering how badly conventions were being
abused.
Modified read_data.R to set directories correctly
Cleaned up mongoAPI code and modularized in a cleaner manner.
Updated gitignore file.
Updated an R script
Merge branch 'master' of
https://github.com/apfejes/epigenetics-software.git

Conflicts:
	Epigenetics/.gitignore
Chip-Seq Tool now works, generates correct results and operates as a
multi-process (multi-cpu) code with passing queues for information.
Fixed bugs in decomposing and includes read model upgrades.
Bugfix: closing queues before queues are empty.
untested end_process flag for mapdecomposingthread
Cleaning up the MapDecomposingThread, removing debugging code.
Cleanup of ChipSeq main.
minor change to ConnectToMongo - StaticMethod
Cleanup to MapDecomposingThread and replacement of deepcopy() with
list()
Changing close operations on threads/queues.
Bugfix on pet readahead iterator - removing calls to removed parameters.
Bugfix typo in wave file header.
Merge branch 'master' of https://github.com/apfejes/epigenetics-software.git
Now numbering waves, so you can tell which is the primary peak, and
which are sub-peaks.
Maximum read length now enforced for PET reads. 
Code now terminates correctly
Minor tweaks in code, nothing major.