r427: fixed bugs in backtrack

See comments in ksw_global() for details.
print debugging msg to stdout
debugging code only: print seeds
r428: allow to change the default chain_drop_ratio
fix duplicate PG lines in bwape and bwase
Merge pull request #21 from bpow/fix-duplicate-pg

fix duplicate PG lines in bwape and bwase
r430: fix a bug producing incorrect alignment

Ksw uses two rounds of SSE2-SW to find the boundaries of an alignment. If the
second round gives a different score from the first round, it will fail. The
fix checks if this happens, though I have not dig into an example to understand
why this may happen in the first place.
r431: added the MD tag to bwa-mem
Released bwa-0.7.6-r432
Release bwa-0.7.6a-r433
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
Released bwa-0.7.7-r441
dev-r442: suppress exact full-length matches
Fixed clang compiling warnings