Remove negative conservation values from plot.

PhastCons does not have negative values so the negative part of the axis in
the plot is redundant.
Fix PDL integer overflow (long -> longlong)

A multiplication of a perl variable with a `long` slice resulted in a new
slice of type `long`. This is the point where the overflow was happening. Now
before the multiplication the slice is converted to longlong. Hopefully this
will be valid ofr all real world uses.
Minor changes in code formating
Fix division by 0 in R

When all counts were 0 the calculation of density values resulted in a
division by 0 because the sum of counts was 0. To fix it we now always add 1
to the sum.
Remove records_class from the options.

Decided to hide this option because it is to technical to be exposed.
Update tutorial pod documentation.

Add extra information, cleanup and change format.
Delete redundant nucleotide_preference.
New version.