Integer plotting and width definition change

[walaj]

gTrack has typically plotted ranges with a different definition of widths than GRanges. e.g. a range of [4,5] is width 1 in gTrack and width 2 in GRanges. This can cause strange behavior and odd looking plots when looking at small genomes where single base-pairs make a difference.

I have changed the code so that gTrack now defines width the same as GRanges. This means that the x-axis had to be shifted by 0.5 as below, and GRanges-width 1 ranges now plot to "cover" that base:

mdat <- matrix(sample(10, 4, replace=TRUE), ncol=2, nrow=2)
mdat[upper.tri(mdat)] <- mdat[lower.tri(mdat)]
gr <- GRanges(c(1,1), IRanges(c(5,6), width=1), strand=c("+","-"))

gr <- GRanges(1, IRanges(c(5), width=1), strand=c("+"))

Doing some debugging on this fix, will check in soon.