link .bai when linking .bam
Changes due to processing new data set
xsq2cn changed to use ngCGH
Change xsq2cn to use ngCGH
fix bug in handling bam file names
Draw density plot (per segment, per gene) for xsq2cn
Changes due to processing new data set
Changes due to processing new data sets
Added lists of blood bam files as pooled normal for xsq2cn
Changes due to processing new data set
Produce evolution tree for paired samples using CNA results
Computes 'retSig' values