Issue:
Currently IBDMap always outputs that the number of excluded individuals in an analysis is 0 even if there are NAs in the phenotype file. The example string below is from running IBDMap in a large cohort of 13,000 individuals.
Phenotype counts --> cases: 74, controls: 12273, excluded: 0
Explanation of why this is happening:
I think this is happening because the excluded individuals are skipped at lines 33-34 in the parse function within phenotypes.cpp. These rows never get added to the phenotypes vector. Later when the create_indexer function is called it never enters the default case of the switch because those values values were never added tot he phenotypes vector. This doesn't seem to affect the math or performance of IBDMap but just affects the message to the user.
Issue:
Currently IBDMap always outputs that the number of excluded individuals in an analysis is 0 even if there are NAs in the phenotype file. The example string below is from running IBDMap in a large cohort of 13,000 individuals.
Phenotype counts --> cases: 74, controls: 12273, excluded: 0Explanation of why this is happening:
I think this is happening because the excluded individuals are skipped at lines 33-34 in the parse function within phenotypes.cpp. These rows never get added to the phenotypes vector. Later when the create_indexer function is called it never enters the default case of the switch because those values values were never added tot he phenotypes vector. This doesn't seem to affect the math or performance of IBDMap but just affects the message to the user.