NaN likelihood and custom code section

[shen1025]

Hello,

I tried to construct a BCR light chain model by modifying the C++ code in “run_demo” section. The modified code passed compiler but failed in running inference. (I use IMGT germline gene and 1000 mouse kappa chain as test input). It always shows -nan value for likehoods, and all values in final_marginal files are 0. I had modified “ probability threshold” as suggested, but it doesn’t help. There are some parameter need to be set when calling the C++API, is there a detail document for C++ API?

Thanks,
Brian

[qmarcou]

Hello @shen1025 ,
In general you should not be modifying the code directly inside the run_demo section but rather append your code in the custom section section of the main.cpp file line 2002:

	else{
		//Write your custom procedure here

}

This section of the code is reached using the -run_custom flag instead of -run_demo. But this is just a comment on style and changing code in the demo section should not create any bug. Also, unlike what is done in the demo section you could also use the environment variables obtained via command lines if you want to be able to play with parameters without having to recompile everytime.

As for your problem with 0 NaN likelihood I would suggest you to read my replies to the following issues: #28 , #31 and #32 . Reading these 3 posts should give you the answers you seek. If not, please don't hesitate to reply here and attach your logs/alignments/main.cpp files for a dummy example with just a few sequences.

Hope this helps,
Best regards

[qmarcou]

Hi,
I just realized I did not answer to your last question: there is indeed a Doxygen generated documentation for the C++ API called docs/IGoR_CPP_manual.pdf.

Best,