There is a bug in subtract() function.

[Luobiny]

I have two dataframes and the first dataframe df1 has all the regions in the second dataframe df2. However, when I run bioframe.subtract(df1, df2), the output contains many regions on chromosome 9. Interestingly when I extract all the regions on chromsome 9 from both dataframes and then run bioframe.subtract(df1_chrom9, df2_chrom9), the output shows no regions, which is correct.

[gfudenberg]

hi @Luobiny -- how large are these dataframes? can you upload? Without more information it is challenging to reproduce the issue you report.
Thanks!