The user should be able to assign weights to the 3 score types to produce an overall score that includes: GT ratio of resolution, OR gap score, and DP score. I should probably rename the scores to reflect "ratio of resolution", "gap/separation", and "depth adequacy". Sorting should be based on this score. I would have to also create additional options for the weights and a separate threshold for GT ratio of resolution (apart from -a). I could also add options for how to treat "no data" in the context of GT and DP scores the way I do for OR using the gap-measure (edge or mean). E.g. GT could grow and be filtered based on a hard cutoff of no data or no mixing of calls (even if the union of 1 group differs from the other. And I could (instead of not add samples under the min-depth, add them as long as the average depth of a sample group is above the min depth score.
The user should be able to assign weights to the 3 score types to produce an overall score that includes: GT ratio of resolution, OR gap score, and DP score. I should probably rename the scores to reflect "ratio of resolution", "gap/separation", and "depth adequacy". Sorting should be based on this score. I would have to also create additional options for the weights and a separate threshold for GT ratio of resolution (apart from -a). I could also add options for how to treat "no data" in the context of GT and DP scores the way I do for OR using the gap-measure (edge or mean). E.g. GT could grow and be filtered based on a hard cutoff of no data or no mixing of calls (even if the union of 1 group differs from the other. And I could (instead of not add samples under the min-depth, add them as long as the average depth of a sample group is above the min depth score.