fix: changing protobuf and others as needed (#455)

protos/varfish/v1/seqvars/output.proto

@@ -159,7 +159,7 @@ message GeneIdentity {
 /// Gene-related consequences of a variant.
 message GeneRelatedConsequences {
   // HGVS. {c,n} code of variant.
-  string hgvs_t = 1;
+  optional string hgvs_t = 1;
   // HGVS.p code of variant.
   optional string hgvs_p = 2;
   // Predicted variant consequences.

protos/varfish/v1/seqvars/query.proto

@@ -190,61 +190,81 @@ enum Consequence {
   CONSEQUENCE_START_LOST = 8;
   // Transcript amplification
   CONSEQUENCE_TRANSCRIPT_AMPLIFICATION = 9;
+  // Feature elongation.
+  CONSEQUENCE_FEATURE_ELONGATION = 10;
+  // Feature truncation.
+  CONSEQUENCE_FEATURE_TRUNCATION = 11;
   /*
    * moderate impact
    */
   // Disruptive inframe insertion
-  CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION = 10;
+  CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION = 12;
   // Disruptive inframe deletion
-  CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION = 11;
+  CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION = 13;
   // Conservative inframe insertion
-  CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION = 12;
+  CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION = 14;
   // Conservative inframe deletion
-  CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION = 13;
+  CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION = 15;
   // Missense variant
-  CONSEQUENCE_MISSENSE_VARIANT = 14;
+  CONSEQUENCE_MISSENSE_VARIANT = 16;
   /*
    * low impact
    */
   // Splice donor 5th base variant.
-  CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT = 15;
+  CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT = 17;
   // Splice region variant.
-  CONSEQUENCE_SPLICE_REGION_VARIANT = 16;
+  CONSEQUENCE_SPLICE_REGION_VARIANT = 18;
   // Splice donor region variant.
-  CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT = 17;
+  CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT = 19;
   // Splice polypyrimidine tract variant.
-  CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT = 18;
+  CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT = 20;
   // Start retained variant.
-  CONSEQUENCE_START_RETAINED_VARIANT = 19;
+  CONSEQUENCE_START_RETAINED_VARIANT = 21;
   // Stop retained variant.
-  CONSEQUENCE_STOP_RETAINED_VARIANT = 20;
+  CONSEQUENCE_STOP_RETAINED_VARIANT = 22;
   // Synonymous variant.
-  CONSEQUENCE_SYNONYMOUS_VARIANT = 21;
+  CONSEQUENCE_SYNONYMOUS_VARIANT = 23;
   /*
    * modifier
    */
   // Coding sequence variant.
-  CONSEQUENCE_CODING_SEQUENCE_VARIANT = 22;
+  CONSEQUENCE_CODING_SEQUENCE_VARIANT = 24;
+  // Mature miRNA variant.
+  CONSEQUENCE_MATURE_MIRNA_VARIANT = 25;
   // 5' UTR exon variant.
-  CONSEQUENCE_FIVE_PRIME_UTR_EXON_VARIANT = 23;
+  CONSEQUENCE_FIVE_PRIME_UTR_EXON_VARIANT = 26;
   // 5' UTR intron variant.
-  CONSEQUENCE_FIVE_PRIME_UTR_INTRON_VARIANT = 24;
+  CONSEQUENCE_FIVE_PRIME_UTR_INTRON_VARIANT = 27;
   // 3' UTR exon variant.
-  CONSEQUENCE_THREE_PRIME_UTR_EXON_VARIANT = 25;
+  CONSEQUENCE_THREE_PRIME_UTR_EXON_VARIANT = 28;
   // 3' UTR intron variant.
-  CONSEQUENCE_THREE_PRIME_UTR_INTRON_VARIANT = 26;
+  CONSEQUENCE_THREE_PRIME_UTR_INTRON_VARIANT = 29;
   // Non-coding transcript exon variant.
-  CONSEQUENCE_NON_CODING_TRANSCRIPT_EXON_VARIANT = 27;
+  CONSEQUENCE_NON_CODING_TRANSCRIPT_EXON_VARIANT = 30;
   // Non-coding transcript intron variant.
-  CONSEQUENCE_NON_CODING_TRANSCRIPT_INTRON_VARIANT = 28;
+  CONSEQUENCE_NON_CODING_TRANSCRIPT_INTRON_VARIANT = 31;
   // Upstream gene variant.
-  CONSEQUENCE_UPSTREAM_GENE_VARIANT = 29;
+  CONSEQUENCE_UPSTREAM_GENE_VARIANT = 32;
   // Downstream gene variant.
-  CONSEQUENCE_DOWNSTREAM_GENE_VARIANT = 30;
+  CONSEQUENCE_DOWNSTREAM_GENE_VARIANT = 33;
+  // TFBS ablation.
+  CONSEQUENCE_TFBS_ABLATION = 34;
+  // TFBS amplification.
+  CONSEQUENCE_TFBS_AMPLIFICATION = 35;
+  // TFBS binding site variant.
+  CONSEQUENCE_TF_BINDING_SITE_VARIANT = 36;
+  // Regulatory region ablation.
+  CONSEQUENCE_REGULATORY_REGION_ABLATION = 37;
+  // Regulatory region amplification.
+  CONSEQUENCE_REGULATORY_REGION_AMPLIFICATION = 38;
+  // Regulatory region variant.
+  CONSEQUENCE_REGULATORY_REGION_VARIANT = 39;
   // Intergenic variant.
-  CONSEQUENCE_INTERGENIC_VARIANT = 31;
+  CONSEQUENCE_INTERGENIC_VARIANT = 40;
   // Intron variant.
-  CONSEQUENCE_INTRON_VARIANT = 32;
+  CONSEQUENCE_INTRON_VARIANT = 41;
+  // Gene variant.
+  CONSEQUENCE_GENE_VARIANT = 42;
 }
 
 // Consequence-related filter settings.

src/seqvars/aggregate/mod.rs

@@ -459,102 +459,76 @@ mod test {
 
     #[test]
     fn test_is_par() {
-        assert_eq!(
-            super::is_par(super::Chrom::X, 60000, crate::common::GenomeRelease::Grch37),
-            false
-        );
-        assert_eq!(
-            super::is_par(super::Chrom::X, 60001, crate::common::GenomeRelease::Grch37),
-            true
-        );
-        assert_eq!(
-            super::is_par(
-                super::Chrom::X,
-                2699520,
-                crate::common::GenomeRelease::Grch37
-            ),
-            true
-        );
-        assert_eq!(
-            super::is_par(
-                super::Chrom::X,
-                2699521,
-                crate::common::GenomeRelease::Grch37
-            ),
-            false
-        );
-        assert_eq!(
-            super::is_par(
-                super::Chrom::X,
-                154931043,
-                crate::common::GenomeRelease::Grch37
-            ),
-            false
-        );
-        assert_eq!(
-            super::is_par(
-                super::Chrom::X,
-                154931044,
-                crate::common::GenomeRelease::Grch37
-            ),
-            true
-        );
-        assert_eq!(
-            super::is_par(
-                super::Chrom::X,
-                155260560,
-                crate::common::GenomeRelease::Grch37
-            ),
-            true
-        );
-        assert_eq!(
-            super::is_par(
-                super::Chrom::X,
-                155260561,
-                crate::common::GenomeRelease::Grch37
-            ),
-            false
-        );
-        assert_eq!(
-            super::is_par(
-                super::Chrom::X,
-                155260561,
-                crate::common::GenomeRelease::Grch38
-            ),
-            false
-        );
-        assert_eq!(
-            super::is_par(
-                super::Chrom::X,
-                155701383,
-                crate::common::GenomeRelease::Grch38
-            ),
-            true
-        );
-        assert_eq!(
-            super::is_par(
-                super::Chrom::X,
-                156030895,
-                crate::common::GenomeRelease::Grch38
-            ),
-            true
-        );
-        assert_eq!(
-            super::is_par(
-                super::Chrom::X,
-                156030896,
-                crate::common::GenomeRelease::Grch38
-            ),
-            false
-        );
-        assert_eq!(
-            super::is_par(super::Chrom::Y, 10000, crate::common::GenomeRelease::Grch37),
-            false
-        );
-        assert_eq!(
-            super::is_par(super::Chrom::Y, 10001, crate::common::GenomeRelease::Grch37),
-            true
-        );
+        assert!(!super::is_par(
+            super::Chrom::X,
+            60000,
+            crate::common::GenomeRelease::Grch37
+        ));
+        assert!(super::is_par(
+            super::Chrom::X,
+            60001,
+            crate::common::GenomeRelease::Grch37
+        ));
+        assert!(super::is_par(
+            super::Chrom::X,
+            2699520,
+            crate::common::GenomeRelease::Grch37
+        ));
+        assert!(!super::is_par(
+            super::Chrom::X,
+            2699521,
+            crate::common::GenomeRelease::Grch37
+        ));
+        assert!(!super::is_par(
+            super::Chrom::X,
+            154931043,
+            crate::common::GenomeRelease::Grch37
+        ));
+        assert!(super::is_par(
+            super::Chrom::X,
+            154931044,
+            crate::common::GenomeRelease::Grch37
+        ));
+        assert!(super::is_par(
+            super::Chrom::X,
+            155260560,
+            crate::common::GenomeRelease::Grch37
+        ));
+        assert!(!super::is_par(
+            super::Chrom::X,
+            155260561,
+            crate::common::GenomeRelease::Grch37
+        ));
+        assert!(!super::is_par(
+            super::Chrom::X,
+            155260561,
+            crate::common::GenomeRelease::Grch38
+        ));
+        assert!(super::is_par(
+            super::Chrom::X,
+            155701383,
+            crate::common::GenomeRelease::Grch38
+        ));
+        assert!(super::is_par(
+            super::Chrom::X,
+            156030895,
+            crate::common::GenomeRelease::Grch38
+        ));
+        assert!(!super::is_par(
+            super::Chrom::X,
+            156030896,
+            crate::common::GenomeRelease::Grch38
+        ));
+        assert!(!super::is_par(
+            super::Chrom::Y,
+            10000,
+            crate::common::GenomeRelease::Grch37
+        ));
+        assert!(super::is_par(
+            super::Chrom::Y,
+            10001,
+            crate::common::GenomeRelease::Grch37
+        ));
     }
 
     #[tracing_test::traced_test]

src/seqvars/query/interpreter/quality.rs

@@ -179,8 +179,8 @@ mod test {
         Ok(())
     }
 
-    #[rstest::rstest]
     #[allow(clippy::too_many_arguments)]
+    #[rstest::rstest]
     // het, pass dp
     #[case(
         Some(10), // q_min_dp_het
@@ -421,7 +421,6 @@ mod test {
         None, // c_ad
         true, // expected
     )]
-    #[allow(clippy::too_many_arguments)]
     fn passes_for_sample(
         #[case] q_min_dp_het: Option<i32>,
         #[case] q_min_dp_hom: Option<i32>,

src/seqvars/query/mod.rs

@@ -44,7 +44,7 @@ pub struct Args {
     pub result_set_id: Option<String>,
     /// The case UUID.
     #[arg(long)]
-    pub case_uuid_id: Option<uuid::Uuid>,
+    pub case_uuid: Option<uuid::Uuid>,
     /// Path to worker database to use for querying.
     #[arg(long)]
     pub path_db: String,
@@ -522,18 +522,27 @@ fn write_header(
             version: common::worker_version().to_string(),
         }],
         query: Some(pb_query.clone()),
-        case_uuid: args.case_uuid_id.unwrap_or_default().to_string(),
+        case_uuid: args.case_uuid.unwrap_or_default().to_string(),
         statistics: Some(pbs_output::OutputStatistics {
             count_total: stats.count_total as u64,
             count_passed: stats.count_passed as u64,
             passed_by_consequences: stats
                 .passed_by_consequences
                 .iter()
-                .map(|(k, v)| pbs_output::ConsequenceCount {
-                    consequence: *k as i32,
-                    count: *v as u32,
-                })
-                .collect(),
+                .map(
+                    |(csq, count)| -> Result<pbs_output::ConsequenceCount, anyhow::Error> {
+                        Ok(pbs_output::ConsequenceCount {
+                            consequence: TryInto::<pbs_query::Consequence>::try_into(*csq).map_err(
+                                |e| {
+                                    anyhow::anyhow!("could not convert consequence {}: {}", *csq, e)
+                                },
+                            )? as i32,
+                            count: *count as u32,
+                        })
+                    },
+                )
+                .collect::<Result<_, _>>()
+                .map_err(|e| anyhow::anyhow!("could not convert consequences: {}", e))?,
         }),
         resources: Some(pbs_output::ResourcesUsed {
             start_time: Some(start_time),
@@ -727,11 +736,9 @@ mod gene_related_annotation {
     pub(crate) fn consequences(
         ann: &mehari::annotate::seqvars::ann::AnnField,
     ) -> Result<Option<pbs_output::GeneRelatedConsequences>, anyhow::Error> {
+        eprintln!("{:?}", &ann);
         Ok(Some(pbs_output::GeneRelatedConsequences {
-            hgvs_t: ann
-                .hgvs_t
-                .clone()
-                .ok_or_else(|| anyhow::anyhow!("missing hgvs_t annotation"))?,
+            hgvs_t: ann.hgvs_t.clone(),
             hgvs_p: ann.hgvs_p.clone(),
             consequences: ann
                 .consequences
@@ -1309,7 +1316,7 @@ async fn create_and_write_record(
             *uuid_buf
         })
         .to_string(),
-        case_uuid: args.case_uuid_id.unwrap_or_default().to_string(),
+        case_uuid: args.case_uuid.unwrap_or_default().to_string(),
         vcf_variant: Some(pbs_output::VcfVariant {
             genome_release: Into::<pbs_output::GenomeRelease>::into(args.genome_release) as i32,
             chrom: seqvar.vcf_variant.chrom.clone(),
@@ -1350,12 +1357,12 @@ async fn create_and_write_record(
         &mut buf,
         "{}",
         serde_json::to_string(&record)
-            .map_err(|e| anyhow::anyhow!("could not convert header to JSON: {}", e))?
+            .map_err(|e| anyhow::anyhow!("could not convert record to JSON: {}", e))?
     )?;
     writer
         .write_all(&buf)
         .await
-        .map_err(|e| anyhow::anyhow!("could not write header to output file: {}", e))
+        .map_err(|e| anyhow::anyhow!("could not write record to output file: {}", e))
 }
 
 /// Main entry point for `seqvars query` sub command.