Regenie rejects valid pvar files

[Wainberg]

regenie/src/Geno.cpp

Lines 791 to 796 in 51968de

	if( (tmp_str_vec.size() < 5) ||
	(tmp_str_vec[1] != "POS") ||
	(tmp_str_vec[2] != "ID") ||
	(tmp_str_vec[3] != "REF") ||
	(tmp_str_vec[4] != "ALT") )
	throw "header of pvar file does not have correct format.";

and

regenie/src/Geno.cpp

Lines 888 to 893 in 51968de

	if( (tmp_str_vec.size() < 5) ||
	(tmp_str_vec[1] != "POS") ||
	(tmp_str_vec[2] != "ID") ||
	(tmp_str_vec[3] != "REF") ||
	(tmp_str_vec[4] != "ALT") )
	throw "header of pvar file does not have correct format.";

reject pvar files if the columns aren't in the usual order - but the pvar specification allows optional columns and doesn't require the columns to be in any particular order if a header is specified. It would be good for regenie to support all valid pvar files.

[joellembatchou]

Hi,

Thank you for the feedback. This is now handled in v3.4.1.

Cheers,
Joelle