Bwamem stream

Add the bwamem-stream aligner module which can potentially be a lot faster and use a lot less /tmp space than the bwamem aligner.
I simplified the code a bit. now it does this:

swap stdout/stderr, pipe stderr into tee in order to a) let the warnings pass through unmolested and b) do the checking we want to do with grep -q,

then finally at the end swap stderr/stdout back.