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Genomicus / bedtools

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merge bed and intervals in which start=stop #154

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.$ echo -e "chr1\t9\t10\nchr1\t10\t20" | mergeBed -i -
chr1    9       20
$ echo -e "chr1\t9\t9\nchr1\t10\t20" | mergeBed -i -
chr1    8       20
$ echo -e "chr1\t0\t0\nchr1\t10\t20" | mergeBed -i -
Error: malformed BED entry at line 1. Start was greater than end. Exiting.
$ echo -e "chr1\t9\t9" | mergeBed -i -
chr1    8       10
$ echo -e "chr1\t1\t9\nchr1\t9\t9" | mergeBed -i -
chr1    1       10

What is the expected output? What do you see instead?

Seems inconsistent handling of intervals for start=stop, which i guess should 
be either invalid or zero length, since the base referred to by start coord "i" 
is really the "i + 1"th base in the sequence.

What version of the product are you using? On what operating system?
v2.17.0

Please provide any additional information below.
Thanks very much for bedtools, which I have found very useful

Original issue reported on code.google.com by frankcui...@gmail.com on 3 Jul 2013 at 11:14

GoogleCodeExporter commented 9 years ago 
bedtools v2.18.2 still have the same problem.
IMHO an empty interval should intersect nothing and be simply ignored in the 
output.

Original comment by balwi...@gmail.com on 6 Mar 2014 at 7:09