feat: use filtered variants in tmb and signatures #470
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ericblanc20
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mbenary
approved these changes
Dec 20, 2023
| config = self.w_config["step_config"]["somatic_variant_signatures"] | ||
| name_pattern = "{mapper}.{caller}" | ||
| if config["is_filtered"]: | ||
| if len(config["filters"]) > 0: |
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tiny detail: in all cases beforehand the if-clause is the other way around starting with if len(config["filters"]) == 0 . Meaning is always the same, so the phrase could also be the same.
| threshold = config.get("ebfilter_threshold", 0) | ||
| elif "eb_filter" in config and "ebfilter_threshold" in config["eb_filter"]: | ||
| threshold = config["eb_filter"].get("ebfilter_threshold", 0) | ||
| elif "ebfilter" in config and "ebfilter_threshold" in config["ebfilter"]: |
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Is it intended to allow "ebfilter" as well as "eb_filter"?
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Nevermind, I believe I understood. It's "eb_filter" vs "one_ebfilter", correct?
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Yes, I think both might be used in the code.
eb_filter vs one_ebfilter: it needed while we keep the old way of filtration (dkfz+eb_filter+oxo_g). one_ebfilter is the new way of filtering.
ericblanc20
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This was referenced Dec 9, 2024
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