`getData` method of `tools.r` fails when the VCF has only a single record

[archmageirvine]

For an input VCF containing a single variant and multiple samples, the getData method in tools.r fails with the error message below. I encounter this problem when trying to carry out step5 of the pipeline_1000G_AIMs_noAMR.r script applied to a reduced set of variants.

Error in rownames<-(x, value) : attempt to set 'rownames' on an object with no dimensions Calls: getData -> row.names<- -> row.names<-.default -> rownames<- Execution halted