search

eth-sri / astarix

AStarix: Fast and Optimal Sequence-to-Graph Aligner
Mozilla Public License 2.0
72 stars 8 forks source link

Segmentation fault #4

Open cjain7 opened 2 years ago

cjain7 commented 2 years ago

Hello,

I wish to test astarix on small test data available in minigraph repository. The graph is in GFA format with zero overlaps.

For this, I ran the following command: 

./astarix align-optimal -g MT.gfa -q MT-human.fa -o $PWD

I get the following output:

$ ./astarix --verbose=2 align-optimal -g MT.gfa -q MT-human.fa -o $PWD
----
Assert() checks:       ON
        verbose:        2
----
Loading reference graph... astarix: ext/GraphAligner/GfaGraph.cpp:172: static GfaGraph GfaGraph::LoadFromFile(std::string): Assertion `overlap >= 0' failed.
Aborted

Can you please check and suggest what may be going wrong? I've pulled the latest code from master branch for this. When I run the code without assert checks, it returns segmentation fault.

Thanks in advance.

cjain7 commented 2 years ago

On looking deeper into the code, it seems that the external code in your GraphAligner folder is not in sync with the latest GraphAligner code. If this can be done, this issue will be resolved.