feat: provide ClinVar SVs for rule sin Sections 4 (#8)

src/strucvars/eval/mod.rs

@@ -9,7 +9,9 @@ use std::{path::Path, sync::Arc};
 
 use annonars::common::spdi;
 use annonars::functional::cli::query::IntervalTrees as FunctionalIntervalTrees;
+use annonars::clinvar_sv::cli::query::IntervalTrees as ClinvarSvIntervalTrees;
 use annonars::pbs::annonars::clinvar::v1::minimal::Record as ClinvarRecord;
+use annonars::pbs::annonars::clinvar::v1::sv::Record as ClinvarSvRecord;
 use annonars::pbs::annonars::functional::v1::refseq::Record as FunctionalRecord;
 use hgvs::data::interface::Provider;
 use itertools::Itertools as _;
@@ -44,7 +46,9 @@ pub struct Evaluator {
 
     /// The ClinVar minimal database.
     clinvar_db: Arc<rocksdb::DBWithThreadMode<rocksdb::MultiThreaded>>,
-    /// The functional elements database.
+    /// The ClinVar SV database wrapped/indexed by `IntervalTrees`.
+    clinvar_sv: ClinvarSvIntervalTrees,
+    /// The functional elements database wrapped/indexed by `IntervalTrees`.
     functional: FunctionalIntervalTrees,
 }
 
@@ -69,7 +73,7 @@ impl Evaluator {
     ///
     /// If anything goes wrong, it returns a generic `anyhow::Error`.
     #[allow(clippy::too_many_arguments)]
-    pub fn new<P1, P2, P3, P4, P5, P6, P7, P8>(
+    pub fn new<P1, P2, P3, P4, P5, P6, P7, P8, P9>(
         assembly: biocommons_bioutils::assemblies::Assembly,
         path_tx_db: P1,
         path_hgnc: P2,
@@ -79,6 +83,7 @@ impl Evaluator {
         path_gnomad_constraints: P6,
         path_clinvar_minimal: P7,
         path_functional: P8,
+        path_clinvar_sv: P9,
     ) -> Result<Self, anyhow::Error>
     where
         P1: AsRef<Path>,
@@ -89,6 +94,7 @@ impl Evaluator {
         P6: AsRef<Path>,
         P7: AsRef<Path>,
         P8: AsRef<Path>,
+        P9: AsRef<Path>,
     {
         let provider = Self::load_provider(assembly, path_tx_db.as_ref())
             .map_err(|e| anyhow::anyhow!("failed to load transcript database: {}", e))?;
@@ -113,6 +119,16 @@ impl Evaluator {
             "clinvar_by_accession",
         )
         .map_err(|e| anyhow::anyhow!("failed to open 'minimal' ClinVar RocksDB: {}", e))?;
+
+        let (clinvar_sv_db, clinvar_sv_meta) = annonars::clinvar_sv::cli::query::open_rocksdb(
+            path_clinvar_sv.as_ref(),
+            "clinvar_sv",
+            "meta",
+            "clinvar_sv_by_rcv",
+        ).map_err(|e| anyhow::anyhow!("failed to open clinvar_sv RocksDB: {}", e))?;
+        let clinvar_sv = ClinvarSvIntervalTrees::with_db(clinvar_sv_db, "clinvar_sv", clinvar_sv_meta)
+            .map_err(|e| anyhow::anyhow!("failed to load ClinVar SV data: {}", e))?;
+
         let (functional_db, functional_meta) = annonars::functional::cli::query::open_rocksdb(
             path_functional.as_ref(),
             "functional",
@@ -132,6 +148,7 @@ impl Evaluator {
             decipher_hi_data,
             gnomad_constraint_data,
             clinvar_db,
+            clinvar_sv,
             functional,
         })
     }
@@ -418,6 +435,27 @@ impl Evaluator {
             .query(&spdi::Range::new(chrom.replace("chr", ""), start, stop))
             .map_err(|e| anyhow::anyhow!("failed to query functional elements: {}", e))
     }
+
+    /// Query ClinVar SV records by overlap.
+    pub fn clinvar_sv_overlaps(
+        &self,
+        chrom: &str,
+        start: u32,
+        stop: u32,
+    ) -> Result<Vec<ClinvarSvRecord>, anyhow::Error> {
+        tracing::trace!(
+            "starting ClinVar SV query {}:{}-{}",
+            &chrom,
+            start,
+            stop
+        );
+        let start = start as i32;
+        let stop = stop as i32;
+
+        self.clinvar_sv
+            .query(&spdi::Range::new(chrom.replace("chr", ""), start, stop))
+            .map_err(|e| anyhow::anyhow!("failed to query ClinVar SV db: {}", e))
+    }
 }
 
 #[cfg(test)]
@@ -438,6 +476,7 @@ pub mod test {
             "tests/data/strucvars/gnomad_constraints.tsv",
             "tests/data/strucvars/hi_ts/clinvar/rocksdb",
             "tests/data/strucvars/hi_ts/functional/rocksdb",
+            "tests/data/strucvars/hi_ts/clinvar-sv/rocksdb",
         )
         .expect("could not initialize global evaluator")
     }
@@ -496,6 +535,26 @@ pub mod test {
         Ok(())
     }
 
+    /// Test internal working of `clinvar_sv_overlaps`.
+    #[tracing_test::traced_test]
+    #[rstest::rstest]
+    #[case("1", 8_018_845, 8_044_954, "VCV000007063")]
+    #[case("21", 1, 1, "almost-empty")]
+    fn clinvar_sv_overlaps(
+        #[case] chrom: &str,
+        #[case] start: u32,
+        #[case] stop: u32,
+        #[case] label: &str,
+        global_evaluator_37: &Evaluator,
+    ) -> Result<(), anyhow::Error> {
+        mehari::common::set_snapshot_suffix!("{}", label);
+
+        let result = global_evaluator_37.clinvar_sv_overlaps(chrom, start, stop)?;
+        insta::assert_yaml_snapshot!(result);
+
+        Ok(())
+    }
+
     /// Test `is_protein_coding`.
     #[tracing_test::traced_test]
     #[rstest::rstest]

tests/data/strucvars/hi_ts/bootstrap.sh

@@ -77,6 +77,20 @@ annonars db-utils copy \
     --path-out tests/data/strucvars/hi_ts/clinvar-empty/rocksdb \
     --path-beds /dev/null
 
+# -- clinvar-sv --
+
+wget -O $TMPDIR/clinvar-data-extract-vars-20231112+0.12.0.tar.gz \
+    https://github.com/bihealth/clinvar-data-jsonl/releases/download/clinvar-weekly-20231112/clinvar-data-extract-vars-20231112+0.12.0.tar.gz
+tar -C $TMPDIR -xvf $TMPDIR/clinvar-data-extract-vars-20231112+0.12.0.tar.gz
+
+mkdir -p tests/data/strucvars/hi_ts/clinvar-sv
+rm -rf tests/data/strucvars/hi_ts/clinvar-sv/rocksdb
+
+annonars clinvar-sv import \
+    --genome-release grch37 \
+    --path-out-rocksdb tests/data/strucvars/hi_ts/clinvar-sv/rocksdb \
+    --path-in-jsonl $TMPDIR/clinvar-data-extract-vars-*/clinvar-variants-grch37-strucvars.jsonl.gz
+
 # -- functional elements --
 
 wget \