Metheor input and --pairs flag

[cgeisenberger]

Dear Dr. Lee,

thank you very much for your great software, it has already helped me a lot. I think it would be helpful if your README would include a note that sorted BAM files should be supplied as input. I got suspicious when running metheor on my (unsorted) data I got barely any output. In addition, the -p, --pairs flag for metheor lpmd could benefit from further clarification. When I supply just the flag without any value I get an error.