abPOA prune graph

[cgroza]

Hi,

Is it possible to delete nodes from a graph, then remap reads to it?

If so, could I have small snippet showing how?
It's not clear to me which fields I need to update when I delete a node.

[yangao07]

Hi, do you have an example case where specific nodes need to be deleted?

[cgroza]

In error correction of long reads with variation graphs. As in VeChat https://www.biorxiv.org/content/10.1101/2022.01.30.478352v1

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-------- Original Message --------

On 6/24/24 3:04 PM, Yan Gao wrote: Hi, do you have an example case where specific nodes need to be deleted? — Reply to this email directly, [view it on GitHub](#71 (comment)), or [unsubscribe](https://github.com/notifications/unsubscribe-auth/AAE4SC37273JHL4AZOUO7DTZJBUTBAVCNFSM6AAAAABJ2JWZIOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBXGIZDAOJVHE). You are receiving this because you authored the thread.Message ID: ***@***.***>

[yangao07]

Thanks! The overall idea of this paper looks interesting.
abPOA does not support APIs for deleting nodes right now.

For diploid input reads, it is indeed a promising scenario for abPOA.
We may implement something specific for it, including deleting nodes.

[cgroza]

That's great. In the meantime, any pointers in how I could implement this myself?

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-------- Original Message --------

On 6/24/24 4:39 PM, Yan Gao wrote: Thanks! The overall idea of this paper looks interesting. abPOA does not support APIs for deleting nodes right now. For diploid input reads, it is indeed a promising scenario for abPOA. We may implement something specific for it, including deleting nodes. — Reply to this email directly, [view it on GitHub](#71 (comment)), or [unsubscribe](https://github.com/notifications/unsubscribe-auth/AAE4SC4BXBENZECCQAHVZX3ZJB7ZFAVCNFSM6AAAAABJ2JWZIOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBXGM3DINRQGI). You are receiving this because you authored the thread.Message ID: ***@***.***>

[yangao07]

Sure, you are very welcome to implement!
Here is the code to add node/edge.
So to remove node/edge, you need something similar.

[cgroza]

Hi
Thank you for the pointers.

I did manage to remove nodes and edges and the GFA output shows that the graph looks good.
I tried to align reads to the pruned graph and this also works fine in most cases.

However, sometimes I prune the graph and then run the topological sort, I get the error:
"Failed to set node index".

I tried to read the source code but no obvious cause presents to me.
Am I forgetting to update some fields?

[yangao07]

In abPOA, graph updating includes adding edges, adding nodes, and adding aligned nodes (for mismatch bases).
So, to remove, you may also remove everything about the node, including edges and aligned nodes.
I am not 100% sure, but did you remove the aligned_node_id for those nodes?

[cgroza]

I did not remove anything about aligned node id. I don't understand that part of the data structure. How would I identify the aligned node IDs to be removed, given a node id.

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-------- Original Message --------

On 7/17/24 4:44 PM, Yan Gao wrote: In abPOA, graph updating includes adding edges, adding nodes, and adding aligned nodes (for mismatch bases). So, to remove, you may also remove everything about the node, including edges and aligned nodes. I am not 100% sure, but did you remove the aligned_node_id for those nodes? — Reply to this email directly, [view it on GitHub](#71 (comment)), or [unsubscribe](https://github.com/notifications/unsubscribe-auth/AAE4SC6QYOWHPVEALT257S3ZM3JSPAVCNFSM6AAAAABJ2JWZIOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZUGI2DOOJXGA). You are receiving this because you authored the thread.Message ID: ***@***.***>

[yangao07]

Actually, I think the aligned nodes may not be the issue.
Did you clean the out_edge_n/out_id/in_edge_n/in_id for nodes around the deleted nodes?