Unexpected overlap between adjacent (non-overlapping) features

[GoogleCodeExporter]

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?
I would not expect that the following two features are treated as overlapping 
by intersectBed:
chrF     540124  540124 
chrF     540125  540125

but they are. Why? is this an error?

What version of the product are you using? On what operating system?
I have tried two versions: v2.16.1 and bedtools v2.17.0 on a linux machine.

Please provide any additional information below.

Original issue reported on code.google.com by abascalf...@gmail.com on 3 Feb 2014 at 11:37

[GoogleCodeExporter]

I found the "problem" by myself. Bedtools reports a intersection because I am 
not properly writing the coordinates. They should be:
chrF     540124  540125 
chrF     540125  540126

Then, bedtools is able to recognize that these are two adjacent 
"non-overlapping" features.

Original comment by abascalf...@gmail.com on 3 Feb 2014 at 11:48

[GoogleCodeExporter]

This is because the bed format is zero-based.

Original comment by abascalf...@gmail.com on 3 Feb 2014 at 11:52

[GoogleCodeExporter]

Original comment by aaronqui...@gmail.com on 3 Feb 2014 at 12:31

• Changed state: Invalid