refactor: consolidating protobuf definitions (#508)

protos/varfish/v1/seqvars/output.proto

@@ -335,9 +335,9 @@ message FrequencyAnnotation {
   // gnomAD-genomes filter
   optional NuclearFrequency gnomad_genomes = 2;
   // gnomAD-MT filter
-  optional GnomadMitochondrialFrequency gnomad_mtdna = 3;
+  optional MitochondrialFrequency gnomad_mtdna = 3;
   // HelixMtDb filter
-  optional HelixMtDbFrequency helixmtdb = 4;
+  optional MitochondrialFrequency helixmtdb = 4;
   // In-house filter
   optional NuclearFrequency inhouse = 5;
 }
@@ -356,8 +356,8 @@ message NuclearFrequency {
   float af = 5;
 }
 
-// gnomAD mitochondrial frequency information.
-message GnomadMitochondrialFrequency {
+// Mitochondrial frequency information.
+message MitochondrialFrequency {
   // Number of covered alleles.
   int32 an = 1;
   // Number of heteroplasmic carriers.
@@ -368,18 +368,6 @@ message GnomadMitochondrialFrequency {
   float af = 4;
 }
 
-// HelixMtDb frequency information.
-message HelixMtDbFrequency {
-  // Number of covered alleles.
-  int32 an = 1;
-  // Number of heterozygous carriers in HelixMtDb
-  int32 het = 2;
-  // Number of homozygous carriers in HelixMtDb
-  int32 homalt = 3;
-  // Frequency in HelixMtDb
-  float af = 4;
-}
-
 // Database identifiers.
 message DbIds {
   // dbSNP ID.

protos/varfish/v1/seqvars/query.proto

@@ -102,8 +102,8 @@ message NuclearFrequencySettings {
   optional float frequency = 5;
 }
 
-// gnomAD mitochondrial filter options.
-message GnomadMitochondrialFrequencySettings {
+// Mitochondrial filter options.
+message MitochondrialFrequencySettings {
   // Whether to enable filtration by 1000 Genomes.
   bool enabled = 1;
   // Maximal number of heteroplasmic carriers.
@@ -114,29 +114,16 @@ message GnomadMitochondrialFrequencySettings {
   optional float frequency = 4;
 }
 
-// HelixMtDb filter options.
-message HelixMtDbFrequencySettings {
-  // Whether to enable filtration by mtDB
-  bool enabled = 1;
-  // Maximal number of heterozygous carriers in HelixMtDb
-  optional int32 heteroplasmic = 2;
-  // Maximal number of homozygous carriers in HelixMtDb
-  optional int32 homoplasmic = 3;
-  // Maximal frequency in HelixMtDb
-  optional float frequency = 4;
-}
-
-
 // Population frequency filter options.
 message QuerySettingsFrequency {
   // gnomAD-exomes filter
   NuclearFrequencySettings gnomad_exomes = 1;
   // gnomAD-genomes filter
   NuclearFrequencySettings gnomad_genomes = 2;
   // gnomAD-MT filter
-  GnomadMitochondrialFrequencySettings gnomad_mtdna = 3;
+  MitochondrialFrequencySettings gnomad_mtdna = 3;
   // HelixMtDb filter
-  HelixMtDbFrequencySettings helixmtdb = 4;
+  MitochondrialFrequencySettings helixmtdb = 4;
   // In-house filter
   NuclearFrequencySettings inhouse = 5;
 }
@@ -284,7 +271,7 @@ message Range {
   // 1-based start position.
   int32 start = 1;
   // 1-based end position.
-  int32 end = 2;
+  int32 stop = 2;
 }
 
 // Genomic region.

src/seqvars/query/interpreter/frequency.rs

@@ -108,8 +108,8 @@ mod test {
             VcfVariant,
         },
         query::{
-            CaseQuery, GnomadMitochondrialFrequencySettings, HelixMtDbFrequencySettings,
-            NuclearFrequencySettings, QuerySettingsFrequency,
+            CaseQuery, MitochondrialFrequencySettings, NuclearFrequencySettings,
+            QuerySettingsFrequency,
         },
     };
 
@@ -423,7 +423,7 @@ mod test {
     ) -> Result<(), anyhow::Error> {
         let query = CaseQuery {
             frequency: QuerySettingsFrequency {
-                helixmtdb: HelixMtDbFrequencySettings {
+                helixmtdb: MitochondrialFrequencySettings {
                     enabled: query_helixmtdb_enabled,
                     frequency: query_helixmtdb_frequency,
                     heteroplasmic: query_helixmtdb_heteroplasmic,
@@ -534,7 +534,7 @@ mod test {
     ) -> Result<(), anyhow::Error> {
         let query = CaseQuery {
             frequency: QuerySettingsFrequency {
-                gnomad_mtdna: GnomadMitochondrialFrequencySettings {
+                gnomad_mtdna: MitochondrialFrequencySettings {
                     enabled: query_gnomad_mtdna_enabled,
                     frequency: query_gnomad_mtdna_frequency,
                     heteroplasmic: query_gnomad_mtdna_heteroplasmic,

src/seqvars/query/interpreter/regions_allowlist.rs

@@ -25,7 +25,7 @@ pub fn passes(query: &CaseQuery, seqvar: &VariantRecord) -> bool {
     }
 }
 
-fn overlaps(region: &GenomicRegion, seqvar_chrom: &str, seqvar_pos: i32, seqvar_end: i32) -> bool {
+fn overlaps(region: &GenomicRegion, seqvar_chrom: &str, seqvar_pos: i32, seqvar_stop: i32) -> bool {
     let GenomicRegion {
         chrom: region_chrom,
         range: region_range,
@@ -39,10 +39,10 @@ fn overlaps(region: &GenomicRegion, seqvar_chrom: &str, seqvar_pos: i32, seqvar_
 
     if let Some(Range {
         start: region_start,
-        end: region_end,
+        stop: region_stop,
     }) = region_range
     {
-        *region_start <= seqvar_end && *region_end >= seqvar_pos
+        *region_start <= seqvar_stop && *region_stop >= seqvar_pos
     } else {
         true
     }
@@ -64,18 +64,18 @@ mod test {
         #[case] region_range: Option<(i32, i32)>,
         #[case] seqvar_chrom: &str,
         #[case] seqvar_start: i32,
-        #[case] seqvar_end: i32,
+        #[case] seqvar_stop: i32,
         #[case] expected: bool,
     ) {
         let region = super::GenomicRegion {
             chrom: String::from(region_chrom),
-            range: region_range.map(|(region_start, region_end)| super::Range {
+            range: region_range.map(|(region_start, region_stop)| super::Range {
                 start: region_start,
-                end: region_end,
+                stop: region_stop,
             }),
         };
         assert_eq!(
-            super::overlaps(&region, seqvar_chrom, seqvar_start, seqvar_end),
+            super::overlaps(&region, seqvar_chrom, seqvar_start, seqvar_stop),
             expected
         );
     }

src/seqvars/query/mod.rs

@@ -1123,13 +1123,13 @@ mod variant_related_annotation {
                 hemialt: seqvar.population_frequencies.gnomad_genomes.hemi,
                 af: seqvar.population_frequencies.gnomad_genomes.af(),
             }),
-            gnomad_mtdna: Some(pbs_output::GnomadMitochondrialFrequency {
+            gnomad_mtdna: Some(pbs_output::MitochondrialFrequency {
                 an: seqvar.population_frequencies.gnomad_mtdna.an,
                 het: seqvar.population_frequencies.gnomad_mtdna.het,
                 homalt: seqvar.population_frequencies.gnomad_mtdna.hom,
                 af: seqvar.population_frequencies.gnomad_mtdna.af(),
             }),
-            helixmtdb: Some(pbs_output::HelixMtDbFrequency {
+            helixmtdb: Some(pbs_output::MitochondrialFrequency {
                 an: seqvar.population_frequencies.helixmtdb.an,
                 het: seqvar.population_frequencies.helixmtdb.het,
                 homalt: seqvar.population_frequencies.helixmtdb.hom,