feat: inhouse freqs useable in seqvars query (#232)

.gitattributes

@@ -2,8 +2,10 @@ tests/db/compile/** filter=lfs diff=lfs merge=lfs -text
 tests/db/hpo/** filter=lfs diff=lfs merge=lfs -text
 tests/seqvars/ingest/db/grch37/** filter=lfs diff=lfs merge=lfs -text
 tests/seqvars/ingest/db/grch38/** filter=lfs diff=lfs merge=lfs -text
+tests/seqvars/query/db-dynamic/** filter=lfs diff=lfs merge=lfs -text
 tests/strucvars/query/*.vcf filter=lfs diff=lfs merge=lfs -text
 tests/strucvars/query/grch37/** filter=lfs diff=lfs merge=lfs -text
 tests/strucvars/query/noref/** filter=lfs diff=lfs merge=lfs -text
 tests/strucvars/query/db/** filter=lfs diff=lfs merge=lfs -text
+tests/strucvars/query/db-dynamic/** filter=lfs diff=lfs merge=lfs -text
 src/strucvars/query/snapshots/*smoke_test*.snap filter=lfs diff=lfs merge=lfs -text

src/seqvars/aggregate/mod.rs

@@ -396,6 +396,11 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
         tracing::info!("  writing meta information");
         let cf_meta = db.cf_handle("meta").unwrap();
         db.put_cf(&cf_meta, "varfish-worker-version", common::worker_version())?;
+        db.put_cf(
+            &cf_meta,
+            "genome-release",
+            args.genomebuild.name().to_lowercase(),
+        )?;
         db.put_cf(&cf_meta, "db-name", "seqvars-aggregation")?;
         tracing::info!("... done opening RocksDB");
 

src/seqvars/query/interpreter/frequency.rs

@@ -45,6 +45,23 @@ pub fn passes(query: &CaseQuery, s: &VariantRecord) -> Result<bool, anyhow::Erro
             );
             return Ok(false);
         }
+        // Note that allele frequency cannot be calculated from inhouse data as of yet
+        // as we cannot differentiate between "no coverage" and "hom. ref." yet.
+        if frequency.inhouse.enabled
+            && (frequency.inhouse.max_het.is_some()
+                && s.population_frequencies.inhouse.het
+                    > frequency.inhouse.max_het.expect("tested before")
+                || frequency.inhouse.max_hom.is_some()
+                    && s.population_frequencies.inhouse.hom
+                        > frequency.inhouse.max_hom.expect("tested before"))
+        {
+            tracing::trace!(
+                "variant {:?} fails in-house frequency filter {:?}",
+                s,
+                &frequency.inhouse
+            );
+            return Ok(false);
+        }
     } else {
         if frequency.gnomad_exomes.enabled
             && (frequency.gnomad_exomes.max_af.is_some()
@@ -88,6 +105,26 @@ pub fn passes(query: &CaseQuery, s: &VariantRecord) -> Result<bool, anyhow::Erro
             );
             return Ok(false);
         }
+        // Note that allele frequency cannot be calculated from inhouse data as of yet
+        // as we cannot differentiate between "no coverage" and "hom. ref." yet.
+        if frequency.inhouse.enabled
+            && (frequency.inhouse.max_het.is_some()
+                && s.population_frequencies.inhouse.het
+                    > frequency.inhouse.max_het.expect("tested before")
+                || frequency.inhouse.max_hom.is_some()
+                    && s.population_frequencies.inhouse.hom
+                        > frequency.inhouse.max_hom.expect("tested before")
+                || frequency.inhouse.max_hemi.is_some()
+                    && s.population_frequencies.inhouse.hemi
+                        > frequency.inhouse.max_hemi.expect("tested before"))
+        {
+            tracing::trace!(
+                "variant {:?} fails in-house frequency filter {:?}",
+                s,
+                &frequency.inhouse
+            );
+            return Ok(false);
+        }
     }
 
     Ok(true)