genemetrics maybe have bugs in 0.9.7

[diushiguzhi]

Hi,
when I use genemetrics with cnvkit 0.9.7 , the variants are disappeared, which can be detected with cnvkit 0.9.6.

Then I check the scripts, the differents as follows :
a. The function "as_dataframe" in skgenome/gary.py is different between 0.9.7 and 0.9.6
b. In 0.9.6 the dataframe index is reset，which is not reset by default in 0.9.7
c. So the script of function "by_gene" in cnary.py "yield gene, subgary.as_dataframe(subgary.data.iloc[start_idx:end_idx])" return the none

[eriktoo]

Hi Diushiguzhi,

Take a look at my comments, especially the latest one, on the issue linked below. I think I found a bug in the way by_gene() handles arrays which was in my case yielding None type arrays. I include a fix that seems to work for me.

#576

Thanks,
Erik