Node merging and Edge Collapsing

[ardakdemir]

We have to implement functions for merging nodes and collapsing edges on a simple path on a DeBruijnGraph type graph.

To do this following steps are important:

• We have to decide on the design concepts on how to represent the merged kmers.
• We have to decide how to update the edges accordingly.
• We have to find an efficient way of finding the simple paths, efficient way of traversing the graph.

[ardakdemir]

I pushed an updated version which includes a simple path finder on dbg. Next step is to collapse the edges on the path.

Things to do :

• Fix the links on the dbg (remove all intermediate links and assign the old links of the extremeties to the new single node)

• Change the edge labels

• Remove the old nodes (number of nodes will be reduced so the old method of indexing to access the nodes and links will not work!! We have to update them accordingly)

[ardakdemir]

I updated the dbg design so that the nodes and links are represented using dictionary data structure. This allows us to easily remove/add links/nodes without having to update index informations.