zhaoming159753 / bedtools

Automatically exported from code.google.com/p/bedtools
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wrong strand considered by intersect #173

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago
What steps will reproduce the problem?

1. given the following two bed files:

==> a.bed <==
chr1    14500   15004   g1  0   +

==> b.bed <==
chr1    14935   14980   FUS 1   +

2. bedtools intersect -c -s -a a.bed -b c.bed | cut -f7

What is the expected output? What do you see instead?
expected: 1
obtained: 0

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

Please provide any additional information below.
when given the opposite strand with the -S option, the result is 1.
curiously enough, when I add three fields to b.bed making it a bed9, the 
problem is solved.

Original issue reported on code.google.com by martino....@gmail.com on 2 Jul 2015 at 9:01

GoogleCodeExporter commented 9 years ago
sorry I forgot the operating system: OS X 10.9.5

Original comment by martino....@gmail.com on 2 Jul 2015 at 12:05