Overlap point segment patch #183

[smitkadvani]

This PR addresses Issue. Overlap operations between point and segment is fixed.

import numpy as np
import bioframe as bf
import pandas as pd
df1 = pd.DataFrame(
        [
            ['chr1', 1, 1]
        ], 
        columns=['chrom','start','end']
    ).astype({"start": pd.Int64Dtype(), "end": pd.Int64Dtype()})

df2 = pd.DataFrame(
    [
        ['chr1', 1, 2]
    ], 
    columns=['chrom','start','end']
).astype({"start": pd.Int64Dtype(), "end": pd.Int64Dtype()})

b = bf.overlap(
    df1,
    df2,
    on=None,
    how="left",
    return_index=True,
    return_input=True,
)
print(b)
b = bf.overlap(
    df2,
    df1,
    on=None,
    how="left",
    return_index=True,
    return_input=True,
)
print(b)

Result :

   index chrom  start  end  index_ chrom_  start_  end_
0      0  chr1      1    1       0   chr1       1     2
   index chrom  start  end  index_ chrom_  start_  end_
0      0  chr1      1    2       0   chr1       1     1

[gfudenberg]

this may break desired behavior of subtract-- let's try to write the subtract tests and see if they pass. If they do not, the place to think about modifying the code may be with the searchsorted for points: https://github.com/open2c/bioframe/blob/424d3a1609f960612591bcf04a2e3a983874d99c/bioframe/core/arrops.py#L333C1-L338C85

[smitkadvani]

this may break desired behavior of subtract-- let's try to write the subtract tests and see if they pass. If they do not, the place to think about modifying the code may be with the searchsorted for points: https://github.com/open2c/bioframe/blob/424d3a1609f960612591bcf04a2e3a983874d99c/bioframe/core/arrops.py#L333C1-L338C85

expected behavior of subtract is contained and extra test cases added for subtraction operation

[golobor]

It seems legit to me! It's a nice solution, hacky but not too much.
There would still be no overlap between ('chr1', 1, 2) and ('chr1, 2, 2), right? (maybe worth adding a small test, since our intervals are explicitly semi-open?)

test added!

[gfudenberg]

functionality added:

• overlap now correctly deals with point intervals (e.g. ['chr1', 1, 1]). This is implemented internally by converting points to pseudo-len1 segments.

tests for overlap added:

• no overlap ['chr1', 1, 2], ['chr1', 2, 2]
• no overlap ['chr1', 2, 2], ['chr1', 1, 2]
• yes overlap ['chr1', 1, 2], ['chr1', 1, 1]
• yes overlap ['chr1', 1, 1], ['chr1', 1, 2]
• no overlap ['chr1', 1, 1], ['chr1', 2, 2]

tests for subtract added:

• subtract( ['chr1', 1, 2], ['chr1', 1, 1]) = ['chr1', 1, 2]
• subtract( ['chr1', 0, 2], ['chr1', 1, 1]) = ['chr1', 0, 1], ['chr1', 0, 2]

closes #183