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yangao07 / abPOA

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
MIT License
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abPOA prune graph #71

Open cgroza opened 1 week ago

cgroza commented 1 week ago

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 commented 1 week ago

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

cgroza commented 1 week ago

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

-------- 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?

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yangao07 commented 1 week ago

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 commented 1 week ago

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

-------- 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, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

yangao07 commented 1 week ago

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