Adds check that ref sequence names do not contain semicolon during index #16
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…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 the XA:Z tag. 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.
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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 the
XA:Ztag. It may be useful to warn users of this potential issue during the bwa index step. For example, if users usexa2multi.plto make multiple entries from the XA tag and pass to samtools view, samtools view will only look for the refname prior to the semicolon.