This adds the code that prints the features used by qtip (paper: https://doi.org/10.1186/s13059-017-1290-3) to predict mapping qualities. They are printed in an extra flag called ZT:Z. To date I'd only made the changes available as a patch in the qtip repo (https://github.com/BenLangmead/qtip/blob/master/software/bwa/bwa_conc_flags_0.7.15.patch), but I wanted to also turn them into a more convenient pull request in case this is something others might use.