Hi,
I am using a third party software that uses IRanges package for variant calling. I have a BAM file and there are over 30M reads that are on negative strand and that means End < Start and this leads to an error by IRanges:
"Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
solving row 2: negative widths are not allowed
Calls: IRanges -> solveUserSEW0 -> .Call2 -> .Call
"
I know that for IRanges End should be always greater than Start position. I tried going through this website, Stack overflow and other websites and some people suggested flipping the start & end. But I don't think its sensible to do this with 30M reads. Does anyone know if there is any other solution to this and how I can fix it.
Thank you.
abolia
Okay, sure. Thanks.