add support to estimate copy number from chromosomal dna

[tiagofilipe12]

Right now copy number estimation is artificial because it only takes into account the self contained database (check here). This will fail if for instance we want to know plasmid copy number in a bacteria. Therefore it would be interesting to allow the user to provide a genome that allows to estimate the copy number for that genome as a standard and then use the same approach for plasmids where the median value for the median multiplicity values would be compared between chromosomal dna and plasmid dna (with chromosomal dna being the default copy number).