Wbiesing/3 jan implement ray mutual overlap and long candidates

@anbangx @Nan-Zhang @JavierJia @Elmira88 

Hi all,

This branch pulls in #115 #118, #119, and #120  and then adds the mutual overlap and long-candidate search as I mentioned today.  If you want only the diff of the scaffolding changes, have a look at 8b2d00c.

There might be a few small problems with offsets being exactly right and paired-end reads definitely need looking into.  I'm submitting this PR now so we can all look at the code and I'd be happy to see this branch merged into the main branch-- it supersedes all my other branches and since it includes multiple PR's in it, it probably supersedes some of your own :)

Please make a close examination and let's make sure I didn't make dumb mistakes :stuck_out_tongue: 

Thanks, and Happy New Year!