Add a 'flip' tool.

[arq5x]

Like bit flipping, this would flip the strand of every interval.

[brentp]

this and shift seem like a job for awk, no?

[arq5x]

Agree, but harder for BAM files. It's is certainly debatable though.

[arq5x]

Also, for flip, I wanted to have a random strand assignment function which would be (slightly) harder for most folks with awk.

[brentp]

There is a lot of tools in there already.

random assignment is simple with awk:

awk 'BEGIN{FS=OFS="\t"}{ $6 = int(rand() + 0.5) == 0 ? "-" : "+"; print }'

[arq5x]

In general, I agree but: GFF? GTF? BAM? TABIX? BAM in particular requires literal bit flipping.

[arq5x]

As for too many tools, I don't really see that as an issue. It is more about better documentation, which is lagging badly and I am aware of it.