Add make stitch operation

[dkhofer]

Add "make stitch" operation.

cargo run -- init
cargo run -- import --fasta fixtures/simple.fa
# Create two example integration points
cargo run -- update --fasta fixtures/aa.fa --start 3 --end 5 --region-name m123 --new-sample test1
cargo run -- update --fasta fixtures/aa.fa --start 15 --end 20 --region-name m123 --sample test1 --new-sample test2
# Derive chunks with breakpoints in between the edits
cargo run -- derive-chunks --new-sample splits --region m123 --breakpoints 1,8,25 --sample test2
# View one of the new chunks
cargo run -- view -s splits m123.2
# Stitch two chunks together
cargo run -- make-stitch --sample splits --new-sample stitched --regions m123.2,m123.3 --new-region m123.2-3

[dkhofer]

This seemed like the easiest solution. From talking with Bob about it today, one problem is propagating annotations. If nodes change from one sample to a child sample, but represent the same part of a sequence, it's harder to pass annotations along. I'm open to other ideas for what to do

[Chris7]

what are the challenges hit when reusing nodes?

[Chris7]

Can you leave this comment here for future-me?

TODO: Annotation support. We do not reuse node ids because nodes control the graph topology. If we duplicated nodes via these operations, it would leave to unintentional cycles. A node cannot exist in 2 places. This will be non-intuitive for annotation propagation and needs to be handled.

[dkhofer]

Yep, done

[Chris7]

can you use the Node::is_start_node/etc. methods?

[dkhofer]

Oops, yep, done

[Chris7]

since we're adding +1 here, it seems like we're trying to get the first unused chromosome_index. If this is true, shouldn't this by max_by?

[dkhofer]

🤦 No idea why I had min_by there, fixed

[Chris7]

Thanks for the info on reusing node ids. non-blocking comments added.