Move Sequenom gtcheck tests into separate subroutine, to run with both iRODS and non-iRODS input
Add tests for input from local (non-iRODS) filesystem
Add chromosomes and manifest options; if no VCF output path, store VCF as string instead of writing to tempfile; make compatible with changes to VCFConverter and VCFGtcheck
Allow output to STDOUT, or return of VCF as a string
Input as either a VCF string or file path given as arguments to run()
Update function arguments; add test of output written to STDOUT