the question from pairToBed output

[g781]

Hi everyone,

I was testing the pairToBed with version 2.17.0, but I was confused with the output.

-- CASE 1 --
Here is the input A in bedpe:

chrBB	100	230	chrBB	330	400	paired-read-1	60	+	-

Here is the input B in bed6:

chrBB	200	250	gene1	1	+
chrBB	300	350	gene1	1	+

Here is the command for running pairToBed:

pairToBed -a A.bedpe -b B.bed6 -bedpe -type both

Here is the outputs:

chrBB   100     230     chrBB   330     400     paired-read-1   60      +       -       chrBB   200     250     gene1   1       +
chrBB   100     230     chrBB   330     400     paired-read-1   60      +       -       chrBB   300     350     gene1   1       +

-- CASE 2 --
Here is the input A in bedpe:

chrBB	100	230	chrBB	330	400	paired-read-1	60	+	-

Here is the input B in bed6:

chrBB	200	350	gene1	1	+

Here is the command for running pairToBed:

pairToBed -a A.bedpe -b B.bed6 -bedpe -type both

Here is the outputs:

chrBB   100     230     chrBB   330     400     paired-read-1   60      +       -       chrBB   200     250     gene1   1       +
chrBB   200     350     chrBB   330     400     paired-read-1   60      +       -       chrBB   200     350     gene1   1       +

I would expect just one record. But both case seem to me, pairToBed would show the two records for each read in PE-read. Is that correct?

Thanks.