shuffle -incl: Fall out of -incl include.bed file

[chenludi]

Dear developer,

I want to replace genomic blocks (A.bed) randomly on blocks of specified genomic regions (include.bed). However, the new genomic coordinates fall out of the "include.bed". human.genome

$cat A.bed
chr1 0 100
chr2 0 1000

$cat include.bed
chr1 200 203
chr1 204 400
chr1 300 325
chr2 2000 4000

$ head human.genome
chr1 240000000
chr2 240000000

$bedtools shuffle -i A.bed -g human.genome -chrom -incl include.bed
chr2 2811 2911
chr2 2666 3666

After shuffling, it exceeds the include.bed and the chromosome number was not kept. Did I misunderstand what the command does? Also, what if there is not enough room in include.bed to place the blocks in A.bed?

Thank you!
Best,
Chenlu

[chenludi]

In addition, I used betools v2.30.0.