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Error in bedtools pairtopair output

Open Rseq opened this issue 4 years ago • 0 comments

Hi,

First, thank you for developing bedtools and even more for keeping it updated. I'm opening here what I understand as an error in bedtools pairtopair

If

wc -l Afile.bedpe
4591 Afile.bedpe

If

bedtools pairtopair -is -type either -a Afile.bedpe -b Bfile.bedpe | wc -l
2216

how?

bedtools pairtopair -is -type neither -a Afile.bedpe -b Bfile.bedpe | wc -l
3475

Why is it not 2375? 4591-2216 = 2375

Meaning either + neither != total Afile.bedpe

-type both and noboth gives me the expected result

bedtools pairtopair -is -type both -a Afile.bedpe -b Bfile.bedpe | wc -l
32
bedtools pairtopair -is -type noboth -a Afile.bedpe -b Bfile.bedpe | wc -l
4559

both + noboth = total Afile.bedpe

Any input on this would be highly appreciated!

Thank you very much in advance

EDIT: grammar error

Rseq avatar Apr 28 '21 15:04 Rseq