Removed numberOfCores from testing, as evenly spreading the data among cores leads to different testing md5sum values for each core (always the same for each core, but different between cored)
refactoring the print to make it modular
updating allele printing
adjusting print sub to work with refactoring
_createPrintFileHandles now moved to the start of the xml processing sub
Draft refactor complete
SNP printing with refactored code in progress
SNP generation correct
Simplified the SNP table and phylip printing with refactored code
Getting pan-genome printing correct.
Multiple alleles now printed to pan_genome.txt with _a2 etc. appended.
Matches with the contigId for the locus_alleles files
Core snps now only prints values with SNPs, considering a change to this.
Added tests to allow for multiple alleles in pan_genome, and the reduced set of core SNPS (ie. only print SNPs with values, not missing data)