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The per_base_error_rate function in pipeline.py is not properly parsing VCF files. This appears to be in part due to improperly walking through the VCF, and in part because incomplete VCF files are being written by nanopolish.
The
per_base_error_ratefunction inpipeline.pyis not properly parsing VCF files. This appears to be in part due to improperly walking through the VCF, and in part because incomplete VCF files are being written by nanopolish.