adding line in procSnps() to ensure required field order#194
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agorelick wants to merge 1 commit intomskcc:masterfrom
Open
adding line in procSnps() to ensure required field order#194agorelick wants to merge 1 commit intomskcc:masterfrom
agorelick wants to merge 1 commit intomskcc:masterfrom
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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.