Reference paths sometimes extend one node further than haplotypes

[adamnovak]

When I look up a node by ID and draw so many nodes downstream of it, sometimes I will get this situation, where the reference path (top) extends one node further than the haplotypes (bottom). The haplotypes do extend into that next node in reality, but they are getting cut off one node before the reference path is by the chunking.

This is probably some kind of bug in the vg chunk code. @yoheirosen?

[yoheirosen]

Don't think this got resolved. This is because the haplotype tracing proceeds a set number of nodes, counted on a per haplotype basis. If a haplotype includes a deletion then it will extend out one node further than those which do not

For 1000 genomes or other near-linear DAG graphs the solution to this would be to extend all haplotypes to the same node by keeping score of which extends the longest or gets cut off the soonest

But that wouldn't work for general graphs. I think we would need a site based way of defining subgraphs on which to extract haplotypes then you extend haplotypes as far as possible within the subgraphs. For large enough chunks of graph then snarls are sufficient for this.

On Feb 6, 2018 4:20 PM, "Adam Novak" [email protected] wrote:

[image: image] https://user-images.githubusercontent.com/5062495/35891473-59d806b0-0b59-11e8-873a-f631bc2da530.png

When I look up a node by ID and draw so many nodes downstream of it, sometimes I will get this situation, where the reference path (top) extends one node further than the haplotypes (bottom). The haplotypes do extend into that next node in reality, but they are getting cut off one node before the reference path is by the chunking.

This is probably some kind of bug in the vg chunk code. @yoheirosen https://github.com/yoheirosen?

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