Added more generic function to calculate percentage overlap with bins. Eg when bed file are not readily available.
Added function to calculate continuous coordinates to ease plotting.
Optimized code to calculate overlap of bins with an arbitrary list of segments.
Added documentation to describe DGV black listing
Modified segment function to take in a function for data transformation. Currently log2 (default) and sqrt transformation are implemented.
Modified calculation of continous linear coordinates.
Added option to disable plotting of segments and calls even if they are present in the object.

Added option to specify pointpch and pointcex.
Added generic function to highlight datapoints.
Moved toConlin function to plot-methods.R
Added toConlin function to calculate linear continuous positions
Added function to zoom in on selected region.
Modified plot function:
- Plots empty regions when data starts with filtered bins. Only omits when chromosome contains no data.
- Utilized toConlin function to calculate cooridnates
- Fixed plotting of labels when subselection of a chromosome is plotted.
Scaled plot incorrectly displayed chromosome labels. Fixed.
Modified the zoom function to also support non scaled plots. Also, recursive zoom is now possible.
Prevent ylim from being changed of calls are ommited from plotting.
Fixed calculation of the expected variance for all samples in line for plotting
Added first version of clonality test based on correlation and log likelihood ratio