Here I am working on an re-implementation of seqwish based on interval trees, where matches between sequences and the graph are recorded in range sets. This will dramatically reduce the memory (disk backed) and runtime of seqwish. A previous partial change of the alignment set into this form saved more than 100-fold runtime and memory costs. This also greatly simplifies several steps in the algorithm.
Here I am working on an re-implementation of seqwish based on interval trees, where matches between sequences and the graph are recorded in range sets. This will dramatically reduce the memory (disk backed) and runtime of seqwish. A previous partial change of the alignment set into this form saved more than 100-fold runtime and memory costs. This also greatly simplifies several steps in the algorithm.