Adds check that reference sequence names do not contain semicolon, which clashes with XA:Z

If a user's input reference sequences have a semicolon in the name,
this clashes with the use of the semicolon as a delimiter in XA:Z
tags. It may be useful to warn users of this potential issue during
the bwa index step. For example, if users use xa2multi.pl to make
multiple entries from the XA tag and pass to samtools view, samtools
view will only look for the refname prior to the semicolon.