Thousand genomes allele count not applied for SVs

[holtgrewe]

Describe the bug
The allele count for SVs appears to be not applied for SVs.

To Reproduce
Steps to reproduce the behavior:

1. Filter a case with a limit of SVs, e.g., of 10
2. See that variants with higher G1K counts are in the result

Expected behavior
Such variants should be removed by the filter.

Screenshots
N/A

Additional context
N/A

[holtgrewe]

Root Cause Analysis

• The threshold is not incorporated into the query.
• Root cause is that the form field is called g1k_max_alleles and not g1k_max_carriers. This is not properly reflected in ExtendQueryPartsPublicDatabaseFrequencyJoinAndFilter.

[holtgrewe]

Resolution Proposal
Simply fix the problem in svs.queries.

Affected Components
VarFish Server

Affected Modules/Files
svs.queries

Required Architectural Changes
None

Required Database Changes
None

Backport Possible?
Not desired (SV filtration not officially supported in anthenea)

Resolution Sketch

diff --git a/svs/queries.py b/svs/queries.py
index 95e5bb2..a966291 100644
--- a/svs/queries.py
+++ b/svs/queries.py
@@ -385,6 +385,7 @@ class ExtendQueryPartsPublicDatabaseFrequencyJoinAndFilter(ExtendQueryPartsBase)
     def extend_conditions(self, _query_parts):
         result = []
         for token, _, _ in self.TOKEN_MODEL_FIELD:
+            entity = "alleles" if token == "g1k" else "carriers"
             if (
                 self.kwargs.get("%s_enabled" % token, False)
                 and ("%s_overlap_count" % token) in self.fields
@@ -392,7 +393,7 @@ class ExtendQueryPartsPublicDatabaseFrequencyJoinAndFilter(ExtendQueryPartsBase)
             ):
                 result.append(
                     self.fields["%s_overlap_count" % token]
-                    <= self.kwargs["%s_max_carriers" % token]
+                    <= self.kwargs["%s_max_%s" % (token, entity)]
                 )
         return result