Clean up temporary files in reference_free_variant_caller.pl
Remove temporary files in map_snp_call.pl
Add error message to dodgy temporary files
Fix scope of tmp file variables
Use file to track tmp files instead of array - fixes previous commit
Use file to track tmp files instead of array - fixes previous commit
Merge branch 'testing' of https://github.com/johnlees/bioinformatics into testing

Conflicts:
	assembly_scripts/assembly_common.pm
Remove temp files works now
Merge branch 'testing'

Adds functionality to remove temporary files