Reduce use of shift in subroutine arguments; instance variables for X,Y chromosome names
Add instance variable for column header titles
Make snpset and chromosome lengths into arguments for converter
Removed unnecessary comments
Tidy up snpset irods path
Remove manifest and plex_coll options from command line script
Tidy up logging initialization
Add test of script with non-iRODS input
Initial commit
Move hard-coded filenames to start of script
Whitespace fix
Add option to cancel normalization of SNP names in VCF body
Move logic to identify/normalize the call, SNP and sample into AssayResult classes
Rename snp/sample/call access methods
Merge branch 'vcf_devel' into devel