get_formatted_chrm: don't crash after "chrX"

After encountering "x" or similar, chr_string becomes an int and the next test for "y" crashes because ints don't have a "lower" method. Fix: return immediately, don't keep going after "x".
Merge pull request #3 from etal/patch-1

get_formatted_chrm: don't crash after "chrX"
Fixed plotting code to work with X as copy number
Fix test code in plotting, help in RunTHetA and remove extraneous file