prefix arg was deprecated and completely removed in samtools sort 1.3, so let's use '-T' option for it (cherry picked from commit c45210d)
prefix arg was deprecated and completely removed in samtools sort 1.3, so let's use '-T' option for it
(cherry picked from commit c45210d)

brentp/bwa-meth,brentp/bwa-meth,brentp/bwa-meth