silhouette score for clustering, bugfix

This release has a variety of changes including:
• Pass the argument --silhouette to DeCiFer to have it automatically determine the best number of clusters using the silhouette score, this is in contrast to the current default method of using the elbow criteria which, in practice, requires adjusting the sensitivity via the --elbow parameter for different samples in order to get good results
• bug fixes that enhance clustering and enable more accurate assignment of genotype trees to SNVs
• when analyzing multiple samples per patient, DeCiFer creates a cluster for SNVs that are truncal in all samples (cluster 1) in addition to one cluster per sample to capture sample-specific SNVs (clusters 2 through n, where n is the number of samples). However, these sample-specific clusters are disabled when analyzing just a single sample from a tumor.