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arq5x / bedtools2

bedtools - the swiss army knife for genome arithmetic
MIT License
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Strand specific behavior is broken #1103

Open Thomas1664 opened 3 months ago

Thomas1664 commented 3 months ago

This problem can be observed for example for shift. The documentation states that the flags -m and -p can be used for strand-specific shifting. The documentation also provides an example but when I try the example with the latest version of bedtools (2.31.1), I get this output instead:

$ bedtools shift -i a.bed -g my.genome -p 2 -m -3
chr1    7       102     +
chr1    802     982     -

It seems like the problem is not limited to shift. The problem also exists for example in the window command.

I also observed this issue with my own data.