Cohort node - minimum sample count per gene (not per variant)

[davmlaw]

🤖 Written by Claude

Split out of #24 (2020 wishlist), which is now closed.

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Cohort node minimum counts are per-variant: "this variant is het/hom in at least N samples". We also want per-gene: "at least N samples have some qualifying variant in this gene".

That's a different shape of query - it aggregates the node's variants up to gene level, then filters variants back down to the genes that pass.

Where the pieces already are

• AbstractZygosityCountNode.get_zygosity_count_arg_q_dict() (analysis/models/nodes/zygosity_count_node.py) - the current per-variant min/max counts, on CohortNode and AllVariantsNode.
• NodeGenesCountCollection.get_or_create_gene_counts_qs_for_node() (analysis/models/gene_counts.py) - already does node → per-gene counts, and ZygosityNode uses it for compound het (gene_counts_qs.filter(count__gte=2).values('gene_id')). That is the closest existing pattern, though it counts variants per gene rather than samples per gene.

Open questions

• Does a sample count per gene need its own collection/cache, or can NodeGenesCountCollection be extended?
• Which node does this live on - CohortNode's Counts accordion, or its own filter node (cf. Gene based analysis #406 Gene based analysis)?
• Transcript vs gene-level aggregation, given Analysis filters apply across all transcripts (rather than only representative) #297.

Related: #406, #297.