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

I think you should bring this up with the maintainers of the third party software. The GenomicRanges package has proper support for strand, and they should be using it.