StrandOps is setup to handle alleles coded as ATCG or actg but cannot handle matching an upper-cased allele to a lower-cased allele. Both a 'T' and a 't' would be considered valid alleles but not treated as the same allele. This means when determining strand config, an A/G and a/g SNP are not recognized as a match. This issue can be seen when running a gene score pipeline with a .meta file that contains lower-case alleles and study data with upper-case alleles. Error messages such as Alleles in study (T/G) do not match source alleles (t/g) for 3:158126327 appear.
StrandOps is setup to handle alleles coded as ATCG or actg but cannot handle matching an upper-cased allele to a lower-cased allele. Both a 'T' and a 't' would be considered valid alleles but not treated as the same allele. This means when determining strand config, an A/G and a/g SNP are not recognized as a match. This issue can be seen when running a gene score pipeline with a .meta file that contains lower-case alleles and study data with upper-case alleles. Error messages such as Alleles in study (T/G) do not match source alleles (t/g) for 3:158126327 appear.