Informally, for a base in a DNA sequence, a side is either the 5'-end or the 3'-end of the base. Each base has two sides. When we join sides in a set of sequences with edges, we get a side graph. A side graph is (implicitly) bidirected, encoding both strands of DNA sequences. It is equivalent to a generic bidirected/string graph with a coordinate system invariable to the addition of new sequences.
This repo explores the storage and exchange of side graphs. For now, it only has one functionality "reformat": read a side graph into RAM and write the graph out. It takes a format like the following:
S R1 100 # reference R1
J R1:20:3 R1:23:5 # a deletion
S R2 120
J R2:30:5 R1:50:3 # translocation
S A 2 # an MNP n R1
J A:0:5 R1:10:3
J A:1:3 R1:12:5
S B 2
J B:0:5 A:1:3
J B:1:3 R1:14:5
where a "Sequence" line gives the sequence name and length and a "Join" line gives the two sides that are joined together. In the input, a "J" line may use a sequence that has not been defined on an "S" line. In the output, a "J" line never uses sequences that have not appeared on "S" lines before.
The reformat tool optionally takes a graph in the "insert" representation like:
S R1 100
S R2 120
J R1:50:3 R2:30:5
J R1:20:3 R1:23:5
I A 2 R1:10:3 R1:12:5
I B 2 A:1:3 R1:14:5
The reformat of this graph is the same as the first example.
So far, the reformat tool has only been tested on toy examples. It probably has bugs that may show up on other graphs. Nonetheless, the underlying implementation is very efficient and should work with huge real-world graphs in principle.