Maybe a typo in the source code, abs(left.startGP.position) < abs(left.startGP.position)?

[Crispy13]

In indexer.cpp:347

...
        // or smaller positive if contig is the same
        if(left.startGP.contig == right.startGP.contig && abs(left.startGP.position) < abs(left.startGP.position))
            return true;
        else
            return false;
...

Your intention was abs(left.startGP.position) < abs("right".startGP.position), wasn't it?