Possible updates

[FerriolCalvet]

• Profile computation using alternate reads as opposed to mutation counts
• Implement an alternative dN/dS computation using the trinucleotide & profile adjusted mutation density
• Add option to generate needle plots using ALT_DEPTH instead of simple mutations count. in this scenario each mutation should contribute a maximum of N times, to avoid a mutation in a single sample to take over most of the signal (maybe N should be 5 at max.)