Don't display r if coverage is better explained by a contaminating species than by target species.

[Phelimb]

E.g. RH12000540-156-1

We have

                    "Staphylococcus aureus": "159",
                    "Coagulase-Negative Staphylococcus": "5"

and

            "blaZ" :{
                    "per_cov": "100",
                    "median_cov": "10",
                    "conf": "31",
            "induced_resistance": "Penicillin"
            },
            "ermA" :{
                    "per_cov": "100",
                    "median_cov": "18",
                    "conf": "62",
            "induced_resistance": "Erythromycin"
            },
            "mecA" :{
                    "per_cov": "95",
                    "median_cov": "3",
                    "conf": "3",
            "indu

These calls are better explained by the genes existing in the contaminate rather than the aureus. It would be nice if we didn't report r in these cases but report S instead.

[iqbal-lab]

I think this is fixed on your branch Phelim, so will be fixed by when we pull that in

[Phelimb]

Nope. Not fixed on my branch yet.

On Wed, Jul 8, 2015 at 7:51 AM Zamin Iqbal notifications@github.com wrote:

I think this is fixed on your branch Phelim, so will be fixed by when we pull that in

— Reply to this email directly or view it on GitHub https://github.com/iqbal-lab/Mykrobe-predictor/issues/74#issuecomment-119610381 .

[iqbal-lab]

really? I'm sure you've shown me examples

[Phelimb]

I think I showed you an example where it would be good if this is what did happen but pretty sure it's not implemented.

On Wed, 8 Jul 2015 08:25 Zamin Iqbal notifications@github.com wrote:

really? I'm sure you've shown me examples

— Reply to this email directly or view it on GitHub https://github.com/iqbal-lab/Mykrobe-predictor/issues/74#issuecomment-119624475 .

[Phelimb]

Closed by https://github.com/iqbal-lab/Mykrobe-predictor/commit/013a0183b8582c58315704e75a39b952476001cb