Condition List File Format

[skresearcher]

Hi!

I'm trying to run conditional gene-based testing using a list of significant SNPs from my GWAS, but I'm getting the following error when I try to run REMETA:

terminate called after throwing an instance of 'std::runtime_error'
  what():  called seek with invalid contig
Aborted (core dumped)

Based on the error message and after looking through REMETA's source code a bit, it seems like --condition-list is expecting a bgzipped file that has the variants indexed by chromosome/position:

remeta/src/run_htp.cpp

Line 216 in 2810877

util::get_htp_variants(condition_list_file, condition_htp_files, chr);

remeta/src/util.cpp

Line 56 in 2810877

BgzReader var_reader(variant_file);

But in both the documentation and the example data files, the condition list is a simple text file with variants separated by new lines (which makes more sense since it seems like it would be redundant to store both the variant ID and the chromosome/position):
https://github.com/rgcgithub/remeta/blob/main/example/example.condition_list

Would it be possible to update REMETA so that the condition list can be a simple text file like in the documentation?