r370: suppress "D" at the end of a cigar

This is caused by seeds in tandem repeats, in which case, bwa-mem may not
extend the true seed. The change in this commit is only a temporary cure.
r371: extend overlapping seeds

to avoid misalignment in tandem repeats
fixed an issue caused by a Mac/Darwin bug

On Mac/Darwin, it is not possible to read >2GB data with one fread().
r373: optionally distable mate rescue
r374: fix - clipping penalty not always working

This only happens to gaps where mem underestimates the bandwidth without
considering the clipping penalty.
r375: fixed compiling errors by the last change
Merge branch 'master' into master_fixes.  Merged up to master r375.

Conflicts:
	bwt.c