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I accidentally created a bug in IBDReduce at line 184-187 of the ibdreduce_v3.py.
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Issue:
I accidentally introduced a bug in the parse_pheno function. This bug accidentally always set the phenotype column index to 1 no matter what. This bug was causing the phenotype counts to be off. It only affected trying to run IBDReduce with a phenotype matrix. This did not affect running IBDReduce with a two column phenotype file.
Fix:
I moved the phenotype_indx reassignment into the i==0 if statement so that it would only happen when reading the header line. You could also assign phenotype_indx to 1 before the with statement that opens the file but I think the if/else might be more clear in the future what is happening