lh3/bwa — pull request #36 by EReckase (2014-11-12 20:53:20+00:00)
Title: -q option to put seq/qual strings in secondary alignments

Users should have the option to put the seq/qual strings in the secondary alignments (if -a is specified)...for example, I am doing a batch set of alignments where I have many similar reference sequences, so I expect multiple alignments, but one in particular (which may not be the primary alignment) needs further processing.