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Genomicus / bedtools

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Invalid option in windowBed? #160

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. windowBed -a file1.bed -b file2.bed -c f 1.0

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

I expect counts of the number of entries in file B that overlap with file A
and where the entire faction of entry in file A is overlaped by an entry in 
File B

I get instead an error says *ERROR: Unrecognized parameter: -f
This indicated that the file of operation I am trying to achieve is not 
supported... However, if is documented in the usage for the tool under the -c 
Argument:
        -c      For each entry in A, report the number of overlaps with B.
                - Reports 0 for A entries that have no overlap with B.
                - Overlaps restricted by -f.

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

bedtools v2.16.2, Linux Debian

Original issue reported on code.google.com by duartemo...@gmail.com on 17 Sep 2013 at 12:53

GoogleCodeExporter commented 9 years ago 
The issue is also present in the latest version of bedtools

Original comment by duartemo...@gmail.com on 17 Sep 2013 at 1:15