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
r376: reduce wasteful seed extension

mainly for contig alignment