Is there any tool that will find whether a position fall into a certain region other than awk or bedtools intersect? That is, lets's assume i have a range with position
and i have a list of positions
chr1 100 1 2 3 chr1 12000 1 2 3 chr1 15000 1 2 3 chr1 25000 1 2 3
So that it will catch chr1 12000 1 2 3 and chr1 15000 1 2 3
I am trying this with awk but it is too slow considering i have lots of positions and ranges. I thought about bedtools intersect but then again, i have some extra information that i dont know how to keep that extra information if i convert the single positions into bed format.
Is there any tools that does this faster than awk?