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refactor!: more protobuf cleaning #511

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Oct 28, 2024
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refactor!: more protobuf cleaning #511

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14 changes: 7 additions & 7 deletions protos/varfish/v1/seqvars/query.proto
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Original file line number Diff line number Diff line change
Expand Up @@ -93,25 +93,25 @@ message NuclearFrequencySettings {
// Whether to enable filtration by 1000 Genomes.
bool enabled = 1;
// Maximal number of in-house heterozygous carriers
optional int32 heterozygous = 2;
optional int32 max_het = 2;
// Maximal number of in-house homozygous carriers
optional int32 homozygous = 3;
optional int32 max_hom = 3;
// Maximal number of in-house hemizygous carriers
optional int32 hemizygous = 4;
optional int32 max_hemi = 4;
// Maximal allele frequency.
optional float frequency = 5;
optional float max_af = 5;
}

// Mitochondrial filter options.
message MitochondrialFrequencySettings {
// Whether to enable filtration by 1000 Genomes.
bool enabled = 1;
// Maximal number of heteroplasmic carriers.
optional int32 heteroplasmic = 2;
optional int32 max_het = 2;
// Maximal number of homoplasmic carriers.
optional int32 homoplasmic = 3;
optional int32 max_hom = 3;
// Maximal allele frequency.
optional float frequency = 4;
optional float max_af = 4;
}

// Population frequency filter options.
Expand Down
93 changes: 45 additions & 48 deletions src/seqvars/query/interpreter/frequency.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -10,15 +10,15 @@ pub fn passes(query: &CaseQuery, s: &VariantRecord) -> Result<bool, anyhow::Erro

if is_mtdna {
if frequency.helixmtdb.enabled
&& (frequency.helixmtdb.frequency.is_some()
&& (frequency.helixmtdb.max_af.is_some()
&& s.population_frequencies.helixmtdb.af()
> frequency.helixmtdb.frequency.expect("tested before")
|| frequency.helixmtdb.heteroplasmic.is_some()
> frequency.helixmtdb.max_af.expect("tested before")
|| frequency.helixmtdb.max_het.is_some()
&& s.population_frequencies.helixmtdb.het
> frequency.helixmtdb.heteroplasmic.expect("tested before")
|| frequency.helixmtdb.homoplasmic.is_some()
> frequency.helixmtdb.max_het.expect("tested before")
|| frequency.helixmtdb.max_hom.is_some()
&& s.population_frequencies.helixmtdb.hom
> frequency.helixmtdb.homoplasmic.expect("tested before"))
> frequency.helixmtdb.max_hom.expect("tested before"))
{
tracing::trace!(
"variant {:?} fails HelixMtDb frequency filter {:?}",
Expand All @@ -28,15 +28,15 @@ pub fn passes(query: &CaseQuery, s: &VariantRecord) -> Result<bool, anyhow::Erro
return Ok(false);
}
if frequency.gnomad_mtdna.enabled
&& (frequency.gnomad_mtdna.frequency.is_some()
&& (frequency.gnomad_mtdna.max_af.is_some()
&& s.population_frequencies.gnomad_mtdna.af()
> frequency.gnomad_mtdna.frequency.expect("tested before")
|| frequency.gnomad_mtdna.heteroplasmic.is_some()
> frequency.gnomad_mtdna.max_af.expect("tested before")
|| frequency.gnomad_mtdna.max_het.is_some()
&& s.population_frequencies.gnomad_mtdna.het
> frequency.gnomad_mtdna.heteroplasmic.expect("tested before")
|| frequency.gnomad_mtdna.homoplasmic.is_some()
> frequency.gnomad_mtdna.max_het.expect("tested before")
|| frequency.gnomad_mtdna.max_hom.is_some()
&& s.population_frequencies.gnomad_mtdna.hom
> frequency.gnomad_mtdna.homoplasmic.expect("tested before"))
> frequency.gnomad_mtdna.max_hom.expect("tested before"))
{
tracing::trace!(
"variant {:?} fails gnomAD-MT frequency filter {:?}",
Expand All @@ -47,18 +47,18 @@ pub fn passes(query: &CaseQuery, s: &VariantRecord) -> Result<bool, anyhow::Erro
}
} else {
if frequency.gnomad_exomes.enabled
&& (frequency.gnomad_exomes.frequency.is_some()
&& (frequency.gnomad_exomes.max_af.is_some()
&& s.population_frequencies.gnomad_exomes.af()
> frequency.gnomad_exomes.frequency.expect("tested before")
|| frequency.gnomad_exomes.heterozygous.is_some()
> frequency.gnomad_exomes.max_af.expect("tested before")
|| frequency.gnomad_exomes.max_het.is_some()
&& s.population_frequencies.gnomad_exomes.het
> frequency.gnomad_exomes.heterozygous.expect("tested before")
|| frequency.gnomad_exomes.homozygous.is_some()
> frequency.gnomad_exomes.max_het.expect("tested before")
|| frequency.gnomad_exomes.max_hom.is_some()
&& s.population_frequencies.gnomad_exomes.hom
> frequency.gnomad_exomes.homozygous.expect("tested before")
|| frequency.gnomad_exomes.hemizygous.is_some()
> frequency.gnomad_exomes.max_hom.expect("tested before")
|| frequency.gnomad_exomes.max_hemi.is_some()
&& s.population_frequencies.gnomad_exomes.hemi
> frequency.gnomad_exomes.hemizygous.expect("tested before"))
> frequency.gnomad_exomes.max_hemi.expect("tested before"))
{
tracing::trace!(
"variant {:?} fails gnomAD-exomes frequency filter {:?}",
Expand All @@ -68,21 +68,18 @@ pub fn passes(query: &CaseQuery, s: &VariantRecord) -> Result<bool, anyhow::Erro
return Ok(false);
}
if frequency.gnomad_genomes.enabled
&& (frequency.gnomad_genomes.frequency.is_some()
&& (frequency.gnomad_genomes.max_af.is_some()
&& s.population_frequencies.gnomad_genomes.af()
> frequency.gnomad_genomes.frequency.expect("tested before")
|| frequency.gnomad_genomes.heterozygous.is_some()
> frequency.gnomad_genomes.max_af.expect("tested before")
|| frequency.gnomad_genomes.max_het.is_some()
&& s.population_frequencies.gnomad_genomes.het
> frequency
.gnomad_genomes
.heterozygous
.expect("tested before")
|| frequency.gnomad_genomes.homozygous.is_some()
> frequency.gnomad_genomes.max_het.expect("tested before")
|| frequency.gnomad_genomes.max_hom.is_some()
&& s.population_frequencies.gnomad_genomes.hom
> frequency.gnomad_genomes.homozygous.expect("tested before")
|| frequency.gnomad_genomes.hemizygous.is_some()
> frequency.gnomad_genomes.max_hom.expect("tested before")
|| frequency.gnomad_genomes.max_hemi.is_some()
&& s.population_frequencies.gnomad_genomes.hemi
> frequency.gnomad_genomes.hemizygous.expect("tested before"))
> frequency.gnomad_genomes.max_hemi.expect("tested before"))
{
tracing::trace!(
"variant {:?} fails gnomAD-genomes frequency filter {:?}",
Expand Down Expand Up @@ -182,10 +179,10 @@ mod test {
frequency: QuerySettingsFrequency {
gnomad_exomes: NuclearFrequencySettings {
enabled: query_gnomad_exomes_enabled,
frequency: query_gnomad_exomes_frequency,
heterozygous: query_gnomad_exomes_heterozygous,
homozygous: query_gnomad_exomes_homozygous,
hemizygous: query_gnomad_exomes_hemizygous,
max_af: query_gnomad_exomes_frequency,
max_het: query_gnomad_exomes_heterozygous,
max_hom: query_gnomad_exomes_homozygous,
max_hemi: query_gnomad_exomes_hemizygous,
},
..Default::default()
},
Expand Down Expand Up @@ -313,10 +310,10 @@ mod test {
frequency: QuerySettingsFrequency {
gnomad_genomes: NuclearFrequencySettings {
enabled: query_gnomad_genomes_enabled,
frequency: query_gnomad_genomes_frequency,
heterozygous: query_gnomad_genomes_heterozygous,
homozygous: query_gnomad_genomes_homozygous,
hemizygous: query_gnomad_genomes_hemizygous,
max_af: query_gnomad_genomes_frequency,
max_het: query_gnomad_genomes_heterozygous,
max_hom: query_gnomad_genomes_homozygous,
max_hemi: query_gnomad_genomes_hemizygous,
},
..Default::default()
},
Expand Down Expand Up @@ -416,18 +413,18 @@ mod test {
#[case] seqvar_helix_het: i32,
#[case] seqvar_helix_hom: i32,
#[case] query_helixmtdb_enabled: bool,
#[case] query_helixmtdb_frequency: Option<f32>,
#[case] query_helixmtdb_heteroplasmic: Option<i32>,
#[case] query_helixmtdb_homoplasmic: Option<i32>,
#[case] query_helixmtdb_af: Option<f32>,
#[case] query_helixmtdb_het: Option<i32>,
#[case] query_helixmtdb_hom: Option<i32>,
#[case] expected_pass_all: bool,
) -> Result<(), anyhow::Error> {
let query = CaseQuery {
frequency: QuerySettingsFrequency {
helixmtdb: MitochondrialFrequencySettings {
enabled: query_helixmtdb_enabled,
frequency: query_helixmtdb_frequency,
heteroplasmic: query_helixmtdb_heteroplasmic,
homoplasmic: query_helixmtdb_homoplasmic,
max_af: query_helixmtdb_af,
max_het: query_helixmtdb_het,
max_hom: query_helixmtdb_hom,
},
..Default::default()
},
Expand Down Expand Up @@ -536,9 +533,9 @@ mod test {
frequency: QuerySettingsFrequency {
gnomad_mtdna: MitochondrialFrequencySettings {
enabled: query_gnomad_mtdna_enabled,
frequency: query_gnomad_mtdna_frequency,
heteroplasmic: query_gnomad_mtdna_heteroplasmic,
homoplasmic: query_gnomad_mtdna_homoplasmic,
max_af: query_gnomad_mtdna_frequency,
max_het: query_gnomad_mtdna_heteroplasmic,
max_hom: query_gnomad_mtdna_homoplasmic,
},
..Default::default()
},
Expand Down
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