lh3/bwa — pull request #16 by vsbuffalo (2013-05-20 21:33:59+00:00)
Title: Adds check that ref sequence names do not contain semicolon during index

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.