your.genome must be tab-delimited.

Here's a one-liner that should work:

$ bedops --complement <( sort-bed A.bed ) <( awk -v OFS="\t" '{ print $1, "0", $2 }' my.genome | sort-bed - )  > answer.bed

This part is called a process substitution in the bash shell:

... <( awk -v OFS="\t" '{ print $1, "0", $2 }' my.genome | sort-bed - ) ...

It uses awk to turn the file my.genome into a sorted BED file, on which you can do set operations with bedops. Basically, everything within <( ... ) returns operational intervals that are fed to the bedops process as a standard input stream.

Here's what the one-liner looks like when broken down into separate commands:

$ sort-bed A.bed > A.sorted.bed
$ awk -v OFS="\t" '{ print $1, "0", $2 }' my.genome | sort-bed - > my.genome.sorted.bed
$ bedops --complement A.sorted.bed my.genome.sorted.bed > answer.bed
$ rm A.sorted.bed my.genome.sorted.bed

Process substitutions might look a little odd, at first, but they help avoid creating intermediate files, which slow down operations on whole-genome scale work. Intermediate files also require disk space and need cleaning up. It's useful to avoid intermediate files, when possible.