Merge/Collapse regions within a certain distance

Question

[Adrian Pelin]

Hello, I am sure this has been asked before but I can't find it. Basically:

scaffold_1 100 200
scaffold_1 300 400
scaffold_1 1000 2100

merge features at a minimum proximity of 200bp and:

scaffold_1 100 400
scaffold_1 1000 2100

Is this possible? Thanks, Adrian

Answer 1

[Pierre Lindenbaum]

bedtools merge with option -d

-d  Maximum distance between features allowed for features
    to be merged.

[Adrian Pelin]

Did not realize that would work for only one file. Thanks!

[Adrian Pelin]

Actually it seems like it takes only one file as input. This makes things complicated in certain cases. Is there any way to only merge features from file A to those of file B, but not merge features within file A or within B?