Code crashes on Grch38 reference

[mmterpstra]

Code crashes on Grch38 reference available in the GATK bundle. this is due to the fact this contains 'chr' style chromosomes and 'HLA-' type contigs

Ideally the code below should just read the header to an hash and validate each line of input to that hash. and if not the line/linenumber and maybe the chromosomes matched against.

https://github.com/duartemolha/CoNVaDING_reload/blob/master/CoNVaDING.pl#L2845-L2914

Lazy fix:
https://github.com/duartemolha/CoNVaDING_reload/blob/master/CoNVaDING.pl#L2874 change to if ($chr =~ m/^chr.+|^HLA-.+/gs) { and test.