Hail backend - In-silico filter #3530
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…oadinstitute/seqr into hail-backend-in-silico-filter
…oadinstitute/seqr into hail-backend-in-silico-filter
…l-backend-in-silico-filter
…nstitute/seqr into hail-backend-in-silico-filter
hail_search/hail_search_query.py
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| require_score = in_silico_filters.get('requireScore', False) | ||
| in_silico_filters = { | ||
| k: v for k, v in in_silico_filters.items() | ||
| if k in self.PREDICTION_FIELDS_CONFIG and v is not None and len(v) != 0 |
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Is the v is not None and len(v) != 0 equivalent to v?
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yeah, this was copy-pasted from elasticsearch code, but it does not seem to be neccessary
| @@ -411,6 +419,44 @@ def _filter_by_frequency(self, frequencies): | |||
| pop_filter &= pf | |||
| self._ht = self._ht.filter(hl.is_missing(pop_expr) | pop_filter) | |||
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| def _filter_by_in_silico(self, in_silico_filters): | |||
| in_silico_filters = in_silico_filters or {} | |||
| require_score = in_silico_filters.get('requireScore', False) | |||
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Using includes_missing_score for the requireScore is more understandable.
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but this is passed from the ui so its not something we can change. I think its clearer to name the variable what its called in the UI code and what its passed in the json as rather than to rename it to something else that means the same thing
…nstitute/seqr into hail-backend-in-silico-filter
…l-backend-in-silico-filter
hail_search/hail_search_query.py
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| missing_q &= q | ||
| in_silico_qs.append(missing_q) | ||
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| in_silico_q = in_silico_qs[0] |
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Can this block be replaced by hl.any(in_silico_qs)?
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I feel like I was frustrated that there was no easy way to do this in hail, and now I'm like "oh duh, of course there is"
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