prettified README
changed to markdown
bug fix in plot2dWithMargins; added rudimentary gene annotation for 2d plots
adding a warning
merging
whitespace cleanup, a few informative error messages
bugfix related to minimum depth
fixed subsetting of rows, corrected filtering for adequate depth
plotting 1d clusters fixed
better placement of gene annotations in 2D plot; added error bar option (overlayErrorBars) for 2d plots
merged changes
Don't discard vaf == 0, just depth < minDepth
Don't discard vaf == 0, just depth < minDepth
Bug fixes: setting numClusters and cn's outside of specified regions
Fixed bug with outliers in 2D (but still not plotting outliers); added annotation argument to sciClone to add gene names to output cluster table
bug fix with outliers in sc.plot2d (was assigning to cluster 1)
Shift VAF = 100% (as well as VAF = 0%) by delta; changed delta to be 100 * machine precision
bugfix in cn adding, option change: plot1dHistogram->plotHistogram