Yan Gao

The above MSA result may look weird, but it is indeed correct given your input. The local alignment in abPOA aligns part of the sequence to the current graph with...

I could not reproduce your above MSA, so I can only guess what is going on there: The Ts were considered aligned for the top sequences, but not the bottom...

One more thing you may want to know is that the local mode is good for consensus calling purposes, as the unaligned part is unlikely to be part of the...

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

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...

Sure, you are very welcome to implement! Here is the code to add [node](https://github.com/yangao07/abPOA/blob/c48d7e9c272bda109f7e3767ae8acc77edfe1a26/src/abpoa_graph.c#L409)/[edge](https://github.com/yangao07/abPOA/blob/c48d7e9c272bda109f7e3767ae8acc77edfe1a26/src/abpoa_graph.c#L418). So to remove node/edge, you need something similar.

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...

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?

Hi, this is quite easy to add for pyabpoa. You can build/install it using the latest source code. Pypi should be available in the next released version.

I see. Thanks! I should use the smooth.bam instead of raw bam for kanpig, right?