Adding Summary Statistics Output for Collate

[harrismia]

It would be great if the collate function could chararacterize the collection of samples by generating a file with summary statistics for each column or variant over the collection of samples. For example it would have total number of sequences analyzed, count and % for each lineage and sublineage, count and % for Spoligotype, and summary statistics for DR variants and drugs. For example: 1000 isolates were analyzed, 250 25% lineage 2, 500 50% lineage 4, 250 25% lineage 3. And similar summary for DR variants and drug. For example 340 ,34% have the rpoB p.Ser450Leu mutation.