This addresses issues #9, #25, and #28. Jury is still out on #29.
Additionally, this removes the expectation for an HLA output in the preprocessing results. Ancedotaly, with one abnormal sample having ~41M host reads (over 55% of the sample), the optityper scheme only recovered 263 HLA reads. For normal stool samples the likelihood of having enough host reads to determine the HLA type is very low.
Because this is removing an output, I'm adding this as a pr for the 0.4.0 release
This addresses issues #9, #25, and #28. Jury is still out on #29.
Additionally, this removes the expectation for an HLA output in the preprocessing results. Ancedotaly, with one abnormal sample having ~41M host reads (over 55% of the sample), the optityper scheme only recovered 263 HLA reads. For normal stool samples the likelihood of having enough host reads to determine the HLA type is very low.
Because this is removing an output, I'm adding this as a pr for the 0.4.0 release