The input bed file validation of the summary wfs could be improved in several aspects; this particular issue requests a check to make sure PAS are reported as single nucleotide, as is required by the APAeval specifications. This could be easily implemented by checking whether start and end differ by 1. For corresponding code see
|
coord_check = participant_data.dtypes[1] == np.int64 and participant_data.dtypes[2] == np.int64 |
The input bed file validation of the summary wfs could be improved in several aspects; this particular issue requests a check to make sure PAS are reported as single nucleotide, as is required by the APAeval specifications. This could be easily implemented by checking whether start and end differ by 1. For corresponding code see
APAeval/summary_workflows/quantification/quantification_dockers/q_validation/validation.py
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