GAM surject incompatible with VG

[jiadong324]

Dear developer,

I want to convert the GAM to BAM format via VG surject command, but it failed because of the different attributes between GraphAligner and vg aligner. The differences are shown below:

VG aligner:

GraphAligner:

It looks like vg surject uses node_id for conversion, and this node_id is the one in the GFA graph. Here, GraphAligner assigns a different value to node_id, as a result, the error shows Attempted to get handle for node 2797 not present in graph.

I am wondering if it convenient for you to change the output format, so that it is compatible with VG's GAM.

Best, Jiadong

[maickrau]

Hi, could you share the graph and the read?

[yeeus]

Hi, I also met this issue, have you solved it?

[NourMarzouka]

Any idea how to solve this? I am facing this issue when trying to convert the GAM to BAM format. Any alternative ways? Thanks!