r434: added the missing bwasw/aln commands!
r435: bugfix - base not complemented on the rev
r436: fix rare MD/NM-CIGAR inconsistencies
r437: print timing for each batch of reads
r438: still an issue in MD

It occurs when the global alignment disagrees with the local alignment.
r439: expose mem_opt_t::max_matesw
r440: a condition not work due to a typo