Good morning,
I have found an error using bedtools and now I am trying to make sense of it: Using some scripts I wrote I created a .bed-file, but now when I try to use this file with bedtools it shows me the error:
Error: Invalid record in file genes.bed. Record is chr1 214785930 -2147107995
However, there is no line with this start and end position, and there is no minus sign in the whole file.
I tried it with differen systems, locally I am using bedtools v2.25.0
I uploaded a part of my .bed-file as a gist:
https://gist.github.com/menzel/a497d22f8bdba8e73d635ac998e38e1c
Maybe you can check if you see the same error, right now I tend to think there is some issue with this version of bedtools. The error occurs with merge and intersect, so you can try:
bedtools merge -i genes.bed
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written
by
menzel •
1 answer
the bad record is
$ wget -q -O - "https://gist.githubusercontent.com/menzel/a497d22f8bdba8e73d635ac998e38e1c/raw/6199ba8939299520658dadc519422865baeec166/genes.bed" | grep 21478593
chr1 214785930 2147859301
2147859301 ? not 214785931 ?
anyway 2147859301 is greater than C-INT_MAX : 2147483647 so any operation on this kind of number might lead to strange results. see https://stackoverflow.com/questions/19376682/
INT_MAX + 1
this operation invokes undefined behavior. Signed integer overflow is undefined behavior in C.
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