Incorrect AMP filtering

[arichards2564]

https://github.com/mskcc/facets-suite/blob/8a6e3712d8866f1bfb04729247b2f7dca74bd0b9/R/gene-level-changes.R#L111

This line and the next are incorrect. The filters for cf and number of genes on segment are only being applied when the amp is already too big. These are 3 separate filters and should be applied as such: 1) bp size, 2) cf too low, 3) # genes on segment is too large. Also, tcn > 8 is good, now bad so I'm not sure why that's being flagged.

I think it needs to be re-written to look like the previous version. This one tries to separate the types of failing CNAs but because we only need 1 of the 3 factors to "PASS" in order to pass the CNA, it doesn't really work. https://github.com/mskcc/facets-suite/blob/97b1e7e6dc866f502c7ccd21f4e6001e3c3eb625/geneLevel.R#L327-L338