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Reverse complement negative strand reads in fastq output #737
This does slightly differ from Picard.
This then will leave unmapped reads unaltered on output (which seems to be the correct thing to do) but I'm not sure why the aligner would mark it as negative if it was unmapped. I.E. if the aligner reverse complements but then removes the mapping (sets the
Other than a few nits, looks good to me! Thanks @arahuja.
Also, the failing test in Jenkins appears to be