In procSnps(), the rcmat data.frame must have columns in a specific order before its fields are renamed. My SNP matrix from snp-pileup did not match this order, causing depth data to be interpreted as vaf data, resulting in 0 het-SNPs being identified. I added a line to procSnps() to make sure the fields are in the correct order before they are renamed, so that the function can accept input data with arbitrary field order.
In procSnps(), the rcmat data.frame must have columns in a specific order before its fields are renamed. My SNP matrix from snp-pileup did not match this order, causing depth data to be interpreted as vaf data, resulting in 0 het-SNPs being identified. I added a line to procSnps() to make sure the fields are in the correct order before they are renamed, so that the function can accept input data with arbitrary field order.