Added functionality for PacBio CCS/HiFi reads

[jelber2]

Thanks for developing this great tool! I just wanted to add the functionality to be able to use PacBio CCS/HiFi reads. I haven't really tested if this is an improvement or not.

[jelber2]

Hmmm. I didn't notice a difference in the assembly results between

 minipolish --pacbio clr --threads 75 $read_overlaps $unpolished_assembly

and

minipolish --pacbio ccs --threads 75 $read_overlaps $unpolished_assembly

So, I wonder if I correctly implemented the --pacbio option in the python code.

[jelber2]

Okay, I think I fixed this. So now --pacbio clr --pacbio ccs or --pacbio no options work. Also changed the README.md and simple running script.

[jelber2]

I also added the functionality of using winnowmap or minimap2 for aligning long reads to the miniasm and polished assemblies. The commits have not been exhaustively tested for errors/bugs.