Allow Redundant Paths to Consider Indels #19
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Before the redundant path purger could only remove SNPs, this allows it to call paths like A -> B -> F / A->C->D->E->F as redundant, simplifying the graph quite a bit. Changes include: * Make PathWithOrientation class to be internal to the assembly * Remove redundant null check on pass graph * Allow paths to converge if they have different lengths but wind up at same end node * Verified that the paths not only end on the same node, but also approach it from the same direction The checking for loops needs to be much faster than it is.
e.g. A->B->C->D overlaps with E->F->G->C->D so C should be preserved even if not part of the best path as it may be part of other paths.
With the new pruning techniques several tests are expected to fail. The tests are a complicated construction, so for now I am just going to write new ones, rather than modify the old ones to work at present.
Not working yet, but this needs to eventually pass.
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Before the redundant path purger could only remove SNPs, this allows
it to call paths like A -> B -> F / A->C->D->E->F as redundant,
simplifying the graph
quite a bit.
Changes include:
same end node
approach it from the same direction
The checking for loops needs to be much faster than it is.