add gmt bwa run-mem

A command to map fastqs to coordinate sorted bam files with bwa mem.
I have very little familiarity with this, but...given it might be helpful to know which part of the pipeline failed, should we consider using $PIPESTATUS here to indicate which chunk failed? http://unix.stackexchange.com/questions/14270/get-exit-status-of-process-thats-piped-to-another/73180#73180