• "seed" option in test_association does not work. Not sure why but although "seed"is set for permutation tests I still get random results each time the program executes. Will have to figure it out.
• Keyboard interruption exception. Need to make sure the C++ library quits when the main process is interrupted. Currently the main process and C++ threads do not halt simultaneously.
• handling GSL / other unknown C++ level issues. This is related to #1. I have written python interface for C++ std exceptions but not yet for GSL exceptions. For pure C++ implementation the errors will be rendered to stderr on screen but for my Python binding the program will hang. This is a long standing issue with writing Python interfaces. Will have to figure something out. In the mean time the only way to debug is to fall back to pure C++ interface (will have to write it up separately).

This command fails

eqtlbma_bf --geno list_genotypes.txt --scoord snp_coords.bed.gz --exp list_phenotypes.txt --gcoord gene_coords.bed.gz --cis 1000 --out obs_bf --outw --analys join --bfs customized   --error hybrid --gridL grid_phi2_oma2_general.txt.gz --gridS grid_phi2_oma2_with-configs.txt.gz   --priorM "prior-matrix*.txt.gz"   --gridM matrix-scalars.txt.gz -v 1 --wrtsize 3 

Test data is under /home/gaow/GIT/omics-bma/src/unit-tests/data. Apparently this is a GSL exception that eqtlbma_bf failed to handle.

If --cis 5 then there is no issue. This bug should also be fixed at eqtlbma repo

I should contact gtexportal.org site admin asking what it will take to release mash results -- file format, at least, to get the analysis going with mash and we will release the data when mash is published.

Meeting with Matthew.

Tentative schedule

1. A glance at current status of OmicsBMA from its data flow.
2. Next steps:
   • Generate prior matrices
   • Combine Bayes Factors before fitting the mixture
   • Data analysis: GTEx V7 or log transformed GTEx V6/V7? I do not need summary statistics from eqtlbma because OmicsBMA computes it.
   • Write up the model and double-check the math / codes