arq5x/bedtools2

bedtools 2.30.0 intersect with 0-length intervals

ddrichel opened this issue · 0 comments

bedtools intersect (v.2.30.0) seems to not handle 0-length intervals correctly.
Example for length 1 and 2:

$ cat a.bed
1 1 10000
cat b1.bed
1 5 6
$ bedtools2/bin/bedtools intersect -a a.bed -b b1.bed
1 5 6
$ cat b2.bed
1 4 6
$ bedtools2/bin/bedtools intersect -a a.bed -b b2.bed
1 4 6

So far, makes sense.
But for length 0:

$ cat b0.bed
1 5 5
$ bedtools2/bin/bedtools intersect -a a.bed -b b0.bed
1 4 6

Expected output is:
1 5 5

Kind regards

Dmitriy