add window parameter to surjection
add window parameter to surjection

Makes this configurable for testing. Most surjection time is spent aligning,
and if we can decrease the size of the alignment target, we can go much faster.

ekg/vg,dnanexus-rnd/vg,abeconnelly/vg,dnanexus-rnd/vg,ekg/vg,abeconnelly/vg,ekg/vg