how can i generate a seed gam format and give it into GraphAligner ?

[shihjimmy]

I generate sequences using pbsim3 and based on the pbsim3 output, I get the corresponding subgraph from the genome graph

Hence, I have my subgraph's: start id / offset in the graph, and I want to put those info directly to GraphAligner, so that it can skip the seeding step and do alignment only, but I encounter some problem:

By the way, the parameter --seeds-first-full-rows is not valid to use, it tells me this option doesn't exist, why ?

Below is my code for generating gam file , Is there anything wrong ??

def generate_gam_format(seq_name, start_node):

# Create a Position message
alignment_position = vg_pb2.Position(
    node_id=start_node,
    offset=0,
    is_reverse=False,
)

# Create a Mapping message using the Position
alignment_mapping = vg_pb2.Mapping(
    position=alignment_position
)

# Wrap the alignment_mapping in a list as the Path expects an iterable (list)
alignment_path = vg_pb2.Path(
    mapping=[alignment_mapping]  # Pass the mapping as a list
)

# Create the Alignment message
alignment = vg_pb2.Alignment(
    path=alignment_path, 
    name=seq_name,
    query_position=0,
)

return alignment

Here is the result:

the ALIGNMENT message I print out look like this:

Alignment: path {
mapping {
position {
node_id: 3120591
}
}
}
name: "S1_4557"

And Here is the execution result:

Load graph from ./out_trim_10k/chr1_S1_19915.gfa
Build alignment graph
Load seeds from ./out_trim_10k/chr1_S1_19915_gam_file.gam
0 seeds
Seeds from file
Seed cluster size 1
Extend up to 5 seed clusters
Alignment bandwidth 35
Clip alignment ends with identity < 66%
X-drop DP score cutoff 14705
Backtrace from 10 highest scoring local maxima per cluster
write alignments to test.gaf
Align
Alignment finished
Input reads: 1 (15976bp)
Seeds found: 0
Seeds extended: 0
Reads with a seed: 0 (0bp)
Reads with an alignment: 0 (0bp)
Alignments: 0 (0bp)
End-to-end alignments: 0 (0bp)

Could you help me fix this out ?
I really need GraphAligner to do this ,thank you for reading

[adamnovak]

Are you sure your Mapping doesn't need an Edit in it with from_length and to_length set to 1 (or the actual number of matching bases on that node)? And that you don't need a sequence on the Alignment? Without any edits or any sequence, the alignment doesn't actually assert that any read bases match any graph bases.