Speed up read compression and reduce disk load

[fungs]

Hi,

I see that you have already incorporated pigz, if available. You might also consider compressing reads while they are calculated using a pipe. That will also save you disk space and double disk I/O (saving plain reads, reading plain reads, saving compressed reads).

Best,
Johannes

[fungs]

Basically all final is uncompressed as well. For light intermediate compression which does not cost CPU but saves disk I/O you can, for instance, use LZ4.