Use system htslib; a couple minor tweaks

[julianhess]

The htslib submodule was getting stale; I think it's better if we use whatever system htslib is already included.

Also implemented a more efficient way of getting the number of softclipped bases, and provided a function for getting the current region index.

[julianhess]

BTW, it looks like we have to update the test suite VM to include an installation of htslib.

[walaj]

I think this makes sense, thanks for the updates. I'd like to see it pass the test suite first. Can you add the following to travis-before-install.sh? That should work. I made a branch jhess with this, but can't figure out how to get Travis CI to build this branch.

    ## install htslib
    mkdir htslib
    wget --no-verbose --output-document=- https://github.com/samtools/htslib/releases/download/1.12/htslib-1.12.tar.bz2 | tar xfj - --strip-components=1 -C htslib
    cd htslib && ./configure
    sudo make
    sudo make install