modified which library files git should ignore
Annotations are no longer contrained to the data tables Candy gave me. We melt them down now into row,col,value like we should have done originally.
Loci now have a collapse method so we can turn neighbor snps into a larger locus
Overhauled the log object. Its now a class with different levels of logging. Also added some plotting things for terms. WE might want to move these into term class evenutally.
Genes are now always stored as .upper() in the database. Also added refgen methods to import from gff.
Moved a shitload of old cob methods to the expr class.
Added methods to the GEO class which do some gut checks in terms of looking at the sanity of the expression values. If we detect that things are not in log space we do a log2 transform. If samples are being added from different platforms, we throw a warning
Added an effective SNP for terms. There are some transitions going on with the create and __init__ methods. They aren't done yet
added exception control for deleting datasets
Changed default sqlite parameters for opening databases. Also handle init methods slightly different, we are allowed to init things more than once, just throws warnings now
Moved a ton of things to Expr class. added cluster convenience method and a way to get the correlation distance matrix