bamCompare --normalizeUsing and --ratio/--method

[dpryan79]

1. --ratio no longer makes much sense as an option, either --method or something like --operation would make more sense.
2. There's still a --normalizeTo1x option (is it used though?). Presumably this should also be move to --normalizeUsing. Additionally, we have the --normalizeUsing methods AND the --scaleFactorsMethod methods. This seems a bit duplicated to me and I'd favour just making them all --normalizeUsing. I think that'd be much clearer.

[fidelram]

Let's change --ratio to --operation. @vivekbhr can you comment on the --normalizeTo1x?

[vivekbhr]

I proposed the above change (#2) in order to make the options more consistent with what they do..

[dpryan79]

Consensus from in office discussion:

1. Just use --operation
2. Remove --normalizeTo1x in bamCompare and move it into --normalizeUsing in bamCoverage. The docs for bamCompare should clarify that "normalization" scales both samples and then does the operation, whereas "scaling" scales one sample (but not both) and then the operation is done. I think I borked this in the documentation update a bit.

[steffenheyne]

3. introduce --effectiveGenomeSize option, this is only used in combination with --normalizeUsing RPGC

or?

[vivekbhr]

Yes, since we need it only for the RPGC

[dpryan79]

This is now merged into develop.