From 8eba31cbf877eb8930d94e12867d2382a73cc3c5 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 30 Oct 2024 14:45:11 +0100 Subject: [PATCH 1/2] feat: inhouse freqs useable in seqvars query (#232) --- .gitattributes | 2 + src/seqvars/aggregate/mod.rs | 5 + src/seqvars/query/interpreter/frequency.rs | 37 +++ src/seqvars/query/mod.rs | 273 +++++++++++++++--- ...e_test@Case_1.ingested.vcf-no_inhouse.snap | 56 ++++ ...st@Case_1.ingested.vcf-with_inhouse-2.snap | 56 ++++ ...test@Case_1.ingested.vcf-with_inhouse.snap | 56 ++++ ...test@dragen.ingested.vcf-no_inhouse-2.snap | 6 + ...e_test@dragen.ingested.vcf-no_inhouse.snap | 6 + tests/seqvars/query/Case_1.query.json | 211 +++++++------- .../grch37/2024-10-30_13-33-30/paths.txt | 3 + .../2024-10-30_13-33-30/rocksdb/000017.sst | 3 + .../2024-10-30_13-33-30/rocksdb/000018.sst | 3 + .../2024-10-30_13-33-30/rocksdb/000019.sst | 3 + .../2024-10-30_13-33-30/rocksdb/CURRENT | 3 + .../2024-10-30_13-33-30/rocksdb/IDENTITY | 3 + .../grch37/2024-10-30_13-33-30/rocksdb/LOCK | 0 .../grch37/2024-10-30_13-33-30/rocksdb/LOG | 3 + .../rocksdb/LOG.old.1730295216382820 | 3 + .../rocksdb/MANIFEST-000014 | 3 + .../rocksdb/OPTIONS-000009 | 3 + .../rocksdb/OPTIONS-000016 | 3 + .../worker/seqvars/inhouse/grch37/active | 1 + tests/seqvars/query/dragen.query.json | 167 +++++------ 24 files changed, 667 insertions(+), 242 deletions(-) create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf-no_inhouse.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf-with_inhouse-2.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf-with_inhouse.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf-no_inhouse-2.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf-no_inhouse.snap create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/paths.txt create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/000017.sst create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/000018.sst create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/000019.sst create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/CURRENT create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/IDENTITY create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/LOCK create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/LOG create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/LOG.old.1730295216382820 create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/MANIFEST-000014 create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/OPTIONS-000009 create mode 100644 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/2024-10-30_13-33-30/rocksdb/OPTIONS-000016 create mode 120000 tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/active diff --git a/.gitattributes b/.gitattributes index 57191e29..3b322966 100644 --- a/.gitattributes +++ b/.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 diff --git a/src/seqvars/aggregate/mod.rs b/src/seqvars/aggregate/mod.rs index 7f055912..ec84fcc2 100644 --- a/src/seqvars/aggregate/mod.rs +++ b/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"); diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs index 8dbe3890..88aac4d8 100644 --- a/src/seqvars/query/interpreter/frequency.rs +++ b/src/seqvars/query/interpreter/frequency.rs @@ -45,6 +45,23 @@ pub fn passes(query: &CaseQuery, s: &VariantRecord) -> Result 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 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) diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs index af0045d4..f778c02a 100644 --- a/src/seqvars/query/mod.rs +++ b/src/seqvars/query/mod.rs @@ -49,6 +49,9 @@ pub struct Args { /// Path to worker database to use for querying. #[arg(long)] pub path_db: String, + /// Path to inhouse rocksdb folder. + #[arg(long)] + pub path_inhouse_db: Option, /// Path to query JSON file. #[arg(long)] pub path_query_json: String, @@ -260,6 +263,7 @@ async fn run_query( pb_query: &pbs_query::CaseQuery, args: &Args, annotator: &annonars::Annotator, + inhouse: &Option, rng: &mut rand::rngs::StdRng, ) -> Result { let start_time = common::now_as_pbjson_timestamp(); @@ -299,6 +303,14 @@ async fn run_query( .map_err(|e| anyhow::anyhow!("could not parse VCF record: {}", e))?; tracing::trace!("processing record {:?}", record_seqvar); + let record_seqvar = if let Some(inhouse) = inhouse.as_ref() { + inhouse.annotate_seqvar(record_seqvar).map_err(|e| { + anyhow::anyhow!("could not annotate record with inhouse data: {}", e) + })? + } else { + record_seqvar + }; + if interpreter.passes(&record_seqvar, annotator)?.pass_all { stats.count_passed += 1; if let Some(ann) = record_seqvar.ann_fields.first() { @@ -1140,7 +1152,7 @@ mod variant_related_annotation { het: seqvar.population_frequencies.inhouse.het, homalt: seqvar.population_frequencies.inhouse.hom, hemialt: seqvar.population_frequencies.inhouse.hemi, - af: seqvar.population_frequencies.inhouse.af(), + af: 0f32, }), }) } @@ -1593,6 +1605,173 @@ async fn create_and_write_record( .map_err(|e| anyhow::anyhow!("could not write record to output file: {}", e)) } +/// Code for accessing the in-house frequencies. +pub(crate) mod inhouse { + use std::{path::Path, sync::Arc}; + + use crate::seqvars::aggregate::ds::Counts; + + use super::schema::data::{InHouseFrequencies, PopulationFrequencies, VariantRecord}; + + /// Meta information of the database. + pub struct Meta { + /// Genome release. + pub genome_release: String, + } + + /// Container for the database structures. + pub struct Dbs { + /// Inhouse frequency RocksDB handle. + pub inhouse_db: Arc>, + /// Meta information. + #[allow(dead_code)] + pub inhouse_meta: Meta, + } + + /// Open RocksDb given path and column family name for data and metadata. + pub fn open_rocksdb>( + path_rocksdb: P, + cf_data: &str, + cf_meta: &str, + ) -> Result<(Arc>, Meta), anyhow::Error> { + tracing::info!("Opening RocksDB database ..."); + let before_open = std::time::Instant::now(); + let cf_names = &[cf_meta, cf_data]; + let resolved_path_rocksdb = annonars::common::readlink_f(&path_rocksdb)?; + let db = Arc::new(rocksdb::DB::open_cf_for_read_only( + &rocksdb::Options::default(), + resolved_path_rocksdb, + cf_names, + true, + )?); + tracing::info!(" reading meta information"); + let meta = { + let cf_meta = db.cf_handle(cf_meta).unwrap(); + let meta_genome_release = String::from_utf8( + db.get_cf(&cf_meta, "genome-release")? + .ok_or_else(|| anyhow::anyhow!("missing value meta:genome-release"))?, + )?; + Meta { + genome_release: meta_genome_release, + } + }; + + tracing::info!(" meta:genome-release = {}", &meta.genome_release); + tracing::info!( + "... opening RocksDB database took {:?}", + before_open.elapsed() + ); + + Ok((db, meta)) + } + + impl Dbs { + /// Initialize from path that contains the annonars databases. + pub fn with_path>( + path: P, + genome_release: &str, + ) -> Result { + let (inhouse_db, inhouse_meta) = + open_rocksdb(&path, "counts", "meta").map_err(|e| { + anyhow::anyhow!( + "problem opening {} metadata at {}: {}", + "counts", + path.as_ref().as_os_str().to_string_lossy(), + e + ) + })?; + + if inhouse_meta.genome_release != genome_release { + anyhow::bail!( + "genome release mismatch: expected {} but got {}", + genome_release, + inhouse_meta.genome_release + ); + } + + Ok(Self { + inhouse_db, + inhouse_meta, + }) + } + + /// Query for in-house data frequencies. + fn query( + &self, + key: &annonars::common::keys::Var, + ) -> Result, anyhow::Error> { + let cf_counts = self + .inhouse_db + .cf_handle("counts") + .expect("cannot find column family 'counts'"); + let key: Vec = key.clone().into(); + let res = self + .inhouse_db + .get_cf(&cf_counts, key) + .map_err(|e| anyhow::anyhow!("querying in-house RocksDB failed: {}", e))?; + Ok(res.as_ref().map(|res| Counts::from_vec(res))) + } + + /// Annotate the given seqvars record. + pub fn annotate_seqvar( + &self, + record: VariantRecord, + ) -> Result { + let VariantRecord { + vcf_variant, + call_infos, + ann_fields, + population_frequencies, + } = record; + let PopulationFrequencies { + gnomad_exomes, + gnomad_genomes, + gnomad_mtdna, + helixmtdb, + inhouse, + } = population_frequencies; + + let inhouse = if let Some(inhouse_counts) = + self.query(&annonars::common::keys::Var::from( + &vcf_variant.chrom, + vcf_variant.pos, + &vcf_variant.ref_allele, + &vcf_variant.alt_allele, + ))? { + let Counts { + count_homref, + count_hemiref, + count_het, + count_homalt, + count_hemialt, + } = inhouse_counts; + InHouseFrequencies { + an: (count_homref + count_hemiref + count_het + count_homalt + count_hemialt) + as i32, + hom: count_homalt as i32, + het: count_het as i32, + hemi: count_hemialt as i32, + } + } else { + inhouse + }; + + Ok(VariantRecord { + vcf_variant, + call_infos, + ann_fields, + population_frequencies: PopulationFrequencies { + gnomad_exomes, + gnomad_genomes, + gnomad_mtdna, + helixmtdb, + inhouse, + }, + }) + } + } +} + /// Main entry point for `seqvars query` sub command. pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow::Error> { let before_anything = Instant::now(); @@ -1633,6 +1812,11 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a ) })?; let annotator = annonars::Annotator::with_path(&args.path_db, args.genome_release)?; + let inhouse_db = args + .path_inhouse_db + .as_ref() + .map(|path| inhouse::Dbs::with_path(path, &format!("{}", args.genome_release))) + .transpose()?; tracing::info!( "...done loading databases in {:?}", before_loading.elapsed() @@ -1651,6 +1835,7 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a &pb_query.clone(), args, &annotator, + &inhouse_db, &mut rng, ) .await?; @@ -1768,37 +1953,57 @@ mod test { Ok(()) } - // TODO: re-enable smoke test - // #[tracing_test::traced_test] - // #[rstest::rstest] - // #[case::case_1_ingested_vcf("tests/seqvars/query/Case_1.ingested.vcf")] - // #[case::dragen_ingested_vcf("tests/seqvars/query/dragen.ingested.vcf")] - // #[tokio::test] - // async fn smoke_test(#[case] path_input: &str) -> Result<(), anyhow::Error> { - // mehari::common::set_snapshot_suffix!("{}", path_input.split('/').last().unwrap()); - - // let tmpdir = temp_testdir::TempDir::default(); - // let path_output = format!("{}/out.tsv", tmpdir.to_string_lossy()); - // let path_input: String = path_input.into(); - // let path_query_json = path_input.replace(".ingested.vcf", ".query.json"); - - // let args_common = Default::default(); - // let args = super::Args { - // genome_release: crate::common::GenomeRelease::Grch37, - // path_db: "tests/seqvars/query/db".into(), - // path_query_json, - // path_input, - // path_output, - // max_results: None, - // rng_seed: Some(42), - // max_tad_distance: 10_000, - // result_set_id: None, - // case_uuid_id: None, - // }; - // super::run(&args_common, &args).await?; - - // insta::assert_snapshot!(std::fs::read_to_string(args.path_output.as_str())?); - - // Ok(()) - // } + #[tracing_test::traced_test] + #[rstest::rstest] + #[case::case_1_ingested_vcf_with_inhouse("tests/seqvars/query/Case_1.ingested.vcf", true)] + #[case::dragen_ingested_vcf_no_inhouse("tests/seqvars/query/dragen.ingested.vcf", false)] + #[case::case_1_ingested_vcf_with_inhouse("tests/seqvars/query/Case_1.ingested.vcf", true)] + #[case::dragen_ingested_vcf_no_inhouse("tests/seqvars/query/dragen.ingested.vcf", false)] + #[tokio::test] + async fn smoke_test( + #[case] path_input: &str, + #[case] with_inhouse: bool, + ) -> Result<(), anyhow::Error> { + mehari::common::set_snapshot_suffix!( + "{}-{}", + path_input.split('/').last().unwrap(), + if with_inhouse { + "with_inhouse" + } else { + "no_inhouse" + } + ); + + let tmpdir = temp_testdir::TempDir::default(); + let path_output = format!("{}/out.tsv", tmpdir.to_string_lossy()); + let path_input: String = path_input.into(); + let path_query_json = path_input.replace(".ingested.vcf", ".query.json"); + + let args_common = Default::default(); + let args = super::Args { + genome_release: crate::common::GenomeRelease::Grch37, + path_db: "tests/seqvars/query/db".into(), + path_inhouse_db: if with_inhouse { + Some( + "tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/active/rocksdb" + .into(), + ) + } else { + None + }, + path_query_json, + path_input, + path_output, + max_results: None, + rng_seed: Some(42), + max_tad_distance: 10_000, + result_set_id: None, + case_uuid: None, + }; + super::run(&args_common, &args).await?; + + insta::assert_snapshot!(std::fs::read_to_string(args.path_output.as_str())?); + + Ok(()) + } } diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf-no_inhouse.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf-no_inhouse.snap new file mode 100644 index 00000000..5ba7fff8 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf-no_inhouse.snap @@ -0,0 +1,56 @@ +--- +source: src/seqvars/query/mod.rs +expression: "std::fs::read_to_string(args.path_output.as_str())?" +--- +{"genomeRelease":"GENOME_RELEASE_GRCH37","versions":[{"name":"varfish-worker","version":"x.y.z"}],"query":{"genotype":{"recessiveMode":"RECESSIVE_MODE_DISABLED","sampleGenotypes":[{"sample":"Case_1_index-N1-DNA1-WGS1","genotype":"GENOTYPE_CHOICE_ANY","enabled":true},{"sample":"Case_1_father-N1-DNA1-WGS1","genotype":"GENOTYPE_CHOICE_ANY","enabled":true},{"sample":"Case_1_mother-N1-DNA1-WGS1","genotype":"GENOTYPE_CHOICE_ANY","enabled":true}]},"quality":{"sampleQualities":[{"sample":"Case_1_index-N1-DNA1-WGS1","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3},{"sample":"Case_1_father-N1-DNA1-WGS1","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3},{"sample":"Case_1_mother-N1-DNA1-WGS1","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3}]},"frequency":{"gnomadExomes":{"enabled":true,"maxHet":1,"maxHom":0,"maxAf":0.002},"gnomadGenomes":{"enabled":true,"maxHet":1,"maxHom":0,"maxAf":0.002},"gnomadMtdna":{},"helixmtdb":{},"inhouse":{"enabled":true,"maxCarriers":20}},"consequence":{"variantTypes":["VARIANT_TYPE_SNV","VARIANT_TYPE_INDEL","VARIANT_TYPE_MNV","VARIANT_TYPE_COMPLEX_SUBSTITUTION"],"transcriptTypes":["TRANSCRIPT_TYPE_CODING"],"consequences":["CONSEQUENCE_TRANSCRIPT_ABLATION","CONSEQUENCE_EXON_LOSS_VARIANT","CONSEQUENCE_SPLICE_ACCEPTOR_VARIANT","CONSEQUENCE_SPLICE_DONOR_VARIANT","CONSEQUENCE_STOP_GAINED","CONSEQUENCE_FRAMESHIFT_VARIANT","CONSEQUENCE_STOP_LOST","CONSEQUENCE_START_LOST","CONSEQUENCE_TRANSCRIPT_AMPLIFICATION","CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION","CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION","CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION","CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION","CONSEQUENCE_MISSENSE_VARIANT","CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT","CONSEQUENCE_SPLICE_REGION_VARIANT","CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT","CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT"]},"locus":{},"clinvar":{}},"caseUuid":"00000000-0000-0000-0000-000000000000","resources":{"startTime":"2024-10-30T11:05:52.075513534+00:00","endTime":"2024-10-30T11:05:52.131177831+00:00","memoryUsed":"1092222976"},"statistics":{"countTotal":"63","countPassed":"51"},"variantScoreColumns":[{"name":"cadd_phred","label":"CADD","description":"PHRED-scaled CADD score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"mmsplice","label":"MMSplice","description":"MMSplice score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"mmsplice_argmax","label":"MMSplice (which)","description":"Which MMSplice score is maximal","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"polyphen","label":"PolyPhen","description":"PolyPhen score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"sift","label":"SIFT","description":"SIFT score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"spliceai","label":"SpliceAI","description":"SpliceAI score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"spliceai_argmax","label":"SpliceAI (which)","description":"Which SpliceAI score is maximal","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"alphamissense","label":"AlphaMissense","description":"AlphaMissense score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"bayesdel_addaf","label":"BayesDel","description":"BayesDel AddAF score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"fathmm","label":"FATHMM","description":"FATHMM score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"fitcons_integrated","label":"fitCons","description":"The integrated fitCons score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"lrt","label":"LRT","description":"LRT score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"metasvm","label":"MetaSVM","description":"MetaSVM score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"polyphen2_hdiv","label":"Polyphen2 HDIV","description":"Polyphen2 HDIV score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"polyphen2_hvar","label":"Polyphen2 HVAR","description":"Polyphen2 HVAR score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"primateai","label":"PrimateAI","description":"PrimateAI score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"provean","label":"PROVEAN","description":"PROVEAN score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"revel","label":"REVEL","description":"REVEL score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"}]} 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+{"genomeRelease":"GENOME_RELEASE_GRCH37","versions":[{"name":"varfish-worker","version":"x.y.z"}],"query":{"genotype":{"recessiveMode":"RECESSIVE_MODE_DISABLED","sampleGenotypes":[{"sample":"CASE","genotype":"GENOTYPE_CHOICE_ANY","enabled":true}]},"quality":{"sampleQualities":[{"sample":"CASE","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3}]},"frequency":{"gnomadExomes":{"enabled":true,"maxHet":1,"maxHom":0,"maxAf":0.002},"gnomadGenomes":{"enabled":true,"maxHet":1,"maxHom":0,"maxAf":0.002},"gnomadMtdna":{},"helixmtdb":{},"inhouse":{"enabled":true,"maxCarriers":20}},"consequence":{"variantTypes":["VARIANT_TYPE_SNV","VARIANT_TYPE_INDEL","VARIANT_TYPE_MNV","VARIANT_TYPE_COMPLEX_SUBSTITUTION"],"transcriptTypes":["TRANSCRIPT_TYPE_CODING"],"consequences":["CONSEQUENCE_TRANSCRIPT_ABLATION","CONSEQUENCE_EXON_LOSS_VARIANT","CONSEQUENCE_SPLICE_ACCEPTOR_VARIANT","CONSEQUENCE_SPLICE_DONOR_VARIANT","CONSEQUENCE_STOP_GAINED","CONSEQUENCE_FRAMESHIFT_VARIANT","CONSEQUENCE_STOP_LOST","CONSEQUENCE_START_LOST","CONSEQUENCE_TRANSCRIPT_AMPLIFICATION","CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION","CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION","CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION","CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION","CONSEQUENCE_MISSENSE_VARIANT","CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT","CONSEQUENCE_SPLICE_REGION_VARIANT","CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT","CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT"]},"locus":{},"clinvar":{}},"caseUuid":"00000000-0000-0000-0000-000000000000","resources":{"startTime":"2024-10-30T13:41:06.488235079+00:00","endTime":"2024-10-30T13:41:06.493710229+00:00","memoryUsed":"2081452032"},"statistics":{"countTotal":"2","countPassed":"1"},"variantScoreColumns":[{"name":"cadd_phred","label":"CADD","description":"PHRED-scaled 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score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"fathmm","label":"FATHMM","description":"FATHMM score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"fitcons_integrated","label":"fitCons","description":"The integrated fitCons score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"lrt","label":"LRT","description":"LRT score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"metasvm","label":"MetaSVM","description":"MetaSVM score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"polyphen2_hdiv","label":"Polyphen2 HDIV","description":"Polyphen2 HDIV score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"polyphen2_hvar","label":"Polyphen2 HVAR","description":"Polyphen2 HVAR score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"primateai","label":"PrimateAI","description":"PrimateAI score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"provean","label":"PROVEAN","description":"PROVEAN score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"revel","label":"REVEL","description":"REVEL score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"}]} +{"uuid":"a2242722-6377-cc86-7d51-ad3f130af08a","caseUuid":"00000000-0000-0000-0000-000000000000","vcfVariant":{"genomeRelease":"GENOME_RELEASE_GRCH37","chrom":"MT","chromNo":25,"pos":750,"refAllele":"A","altAllele":"G"},"variantAnnotation":{"gene":{},"variant":{"frequency":{"gnomadExomes":{},"gnomadGenomes":{},"gnomadMtdna":{},"helixmtdb":{},"inhouse":{}},"clinvar":{"vcvAccession":"VCV000441148.2","germlineSignificanceDescription":"association not found","germlineReviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED","effectiveGermlineSignificanceDescription":"association not found"},"scores":{}},"call":{"callInfos":[{"sample":"CASE","genotype":"/1/1","dp":5608,"ad":5607,"gq":98.0}]}}} diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf-no_inhouse.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf-no_inhouse.snap new file mode 100644 index 00000000..7231d551 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf-no_inhouse.snap @@ -0,0 +1,6 @@ +--- +source: src/seqvars/query/mod.rs +expression: "std::fs::read_to_string(args.path_output.as_str())?" +--- +{"genomeRelease":"GENOME_RELEASE_GRCH37","versions":[{"name":"varfish-worker","version":"x.y.z"}],"query":{"genotype":{"recessiveMode":"RECESSIVE_MODE_DISABLED","sampleGenotypes":[{"sample":"CASE","genotype":"GENOTYPE_CHOICE_ANY","enabled":true}]},"quality":{"sampleQualities":[{"sample":"CASE","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3}]},"frequency":{"gnomadExomes":{"enabled":true,"maxHet":1,"maxHom":0,"maxAf":0.002},"gnomadGenomes":{"enabled":true,"maxHet":1,"maxHom":0,"maxAf":0.002},"gnomadMtdna":{},"helixmtdb":{},"inhouse":{"enabled":true,"maxCarriers":20}},"consequence":{"variantTypes":["VARIANT_TYPE_SNV","VARIANT_TYPE_INDEL","VARIANT_TYPE_MNV","VARIANT_TYPE_COMPLEX_SUBSTITUTION"],"transcriptTypes":["TRANSCRIPT_TYPE_CODING"],"consequences":["CONSEQUENCE_TRANSCRIPT_ABLATION","CONSEQUENCE_EXON_LOSS_VARIANT","CONSEQUENCE_SPLICE_ACCEPTOR_VARIANT","CONSEQUENCE_SPLICE_DONOR_VARIANT","CONSEQUENCE_STOP_GAINED","CONSEQUENCE_FRAMESHIFT_VARIANT","CONSEQUENCE_STOP_LOST","CONSEQUENCE_START_LOST","CONSEQUENCE_TRANSCRIPT_AMPLIFICATION","CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION","CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION","CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION","CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION","CONSEQUENCE_MISSENSE_VARIANT","CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT","CONSEQUENCE_SPLICE_REGION_VARIANT","CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT","CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT"]},"locus":{},"clinvar":{}},"caseUuid":"00000000-0000-0000-0000-000000000000","resources":{"startTime":"2024-10-30T13:41:00.506568048+00:00","endTime":"2024-10-30T13:41:00.531182639+00:00","memoryUsed":"1855889408"},"statistics":{"countTotal":"2","countPassed":"1"},"variantScoreColumns":[{"name":"cadd_phred","label":"CADD","description":"PHRED-scaled 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score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"revel","label":"REVEL","description":"REVEL score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"}]} +{"uuid":"a2242722-6377-cc86-7d51-ad3f130af08a","caseUuid":"00000000-0000-0000-0000-000000000000","vcfVariant":{"genomeRelease":"GENOME_RELEASE_GRCH37","chrom":"MT","chromNo":25,"pos":750,"refAllele":"A","altAllele":"G"},"variantAnnotation":{"gene":{},"variant":{"frequency":{"gnomadExomes":{},"gnomadGenomes":{},"gnomadMtdna":{},"helixmtdb":{},"inhouse":{}},"clinvar":{"vcvAccession":"VCV000441148.2","germlineSignificanceDescription":"association not found","germlineReviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED","effectiveGermlineSignificanceDescription":"association not found"},"scores":{}},"call":{"callInfos":[{"sample":"CASE","genotype":"/1/1","dp":5608,"ad":5607,"gq":98.0}]}}} diff --git a/tests/seqvars/query/Case_1.query.json b/tests/seqvars/query/Case_1.query.json index e841f1ca..a2879881 100644 --- a/tests/seqvars/query/Case_1.query.json +++ b/tests/seqvars/query/Case_1.query.json @@ -1,121 +1,106 @@ { - "consequences": [ - "chromosome_number_variation", - "exon_loss_variant", - "frameshift_variant", - "rare_amino_acid_variant", - "splice_acceptor_variant", - "splice_donor_variant", - "start_lost", - "stop_gained", - "stop_lost", - "transcript_ablation", - "3_prime_UTR_truncation", - "5_prime_UTR_truncation", - "conservative_inframe_deletion", - "conservative_inframe_insertion", - "disruptive_inframe_deletion", - "disruptive_inframe_insertion", - "missense_variant", - "regulatory_region_ablation", - "splice_region_variant", - "TFBS_ablation", - "5_prime_UTR_premature_start_codon_gain_variant", - "initiator_codon_variant", - "start_retained", - "stop_retained_variant", - "synonymous_variant", - "3_prime_UTR_variant", - "5_prime_UTR_variant", - "coding_sequence_variant", - "conserved_intergenic_variant", - "conserved_intron_variant", - "downstream_gene_variant", - "exon_variant", - "feature_elongation", - "feature_truncation", - "gene_variant", - "intergenic_variant", - "intron_variant", - "mature_miRNA_variant", - "miRNA", - "NMD_transcript_variant", - "non_coding_transcript_exon_variant", - "non_coding_transcript_intron_variant", - "regulatory_region_amplification", - "regulatory_region_variant", - "TF_binding_site_variant", - "TFBS_amplification", - "transcript_amplification", - "transcript_variant", - "upstream_gene_variant" - ], - "gnomad_exomes_enabled": false, - "gnomad_genomes_enabled": false, - "inhouse_enabled": false, - "helixmtdb_enabled": false, + "genotype": { + "recessiveMode": "RECESSIVE_MODE_DISABLED", + "sampleGenotypes": [ + { + "sample": "Case_1_index-N1-DNA1-WGS1", + "genotype": "GENOTYPE_CHOICE_ANY", + "enabled": true + }, + { + "sample": "Case_1_father-N1-DNA1-WGS1", + "genotype": "GENOTYPE_CHOICE_ANY", + "enabled": true + }, + { + "sample": "Case_1_mother-N1-DNA1-WGS1", + "genotype": "GENOTYPE_CHOICE_ANY", + "enabled": true + } + ] + }, "quality": { - "Case_1_index-N1-DNA1-WGS1": { - "dp_het": 10, - "dp_hom": 5, - "gq": 10, - "ab": 0.2, - "ad": 3, - "ad_max": null, - "filter_active": "drop-variant" + "sampleQualities": [ + { + "sample": "Case_1_index-N1-DNA1-WGS1", + "filterActive": true, + "minDpHet": 10, + "minDpHom": 5, + "minGq": 10, + "minAb": 0.2, + "minAd": 3 + }, + { + "sample": "Case_1_father-N1-DNA1-WGS1", + "filterActive": true, + "minDpHet": 10, + "minDpHom": 5, + "minGq": 10, + "minAb": 0.2, + "minAd": 3 + }, + { + "sample": "Case_1_mother-N1-DNA1-WGS1", + "filterActive": true, + "minDpHet": 10, + "minDpHom": 5, + "minGq": 10, + "minAb": 0.2, + "minAd": 3 + } + ] + }, + "frequency": { + "gnomadExomes": { + "enabled": true, + "maxHet": 1, + "maxHom": 0, + "maxAf": 0.002 }, - "Case_1_father-N1-DNA1-WGS1": { - "dp_het": 10, - "dp_hom": 5, - "gq": 10, - "ab": 0.2, - "ad": 3, - "ad_max": null, - "filter_active": "drop-variant" + "gnomadGenomes": { + "enabled": true, + "maxHet": 1, + "maxHom": 0, + "maxAf": 0.002 }, - "Case_1_mother-N1-DNA1-WGS1": { - "dp_het": 10, - "dp_hom": 5, - "gq": 10, - "ab": 0.2, - "ad": 3, - "ad_max": null, - "filter_active": "drop-variant" + "gnomadMtdna": {}, + "helixmtdb": {}, + "inhouse": { + "enabled": true, + "maxCarriers": 20 } }, - "genotype": { - "Case_1_index-N1-DNA1-WGS1": "any", - "Case_1_father-N1-DNA1-WGS1": "any", - "Case_1_mother-N1-DNA1-WGS1": "any" + "consequence": { + "variantTypes": [ + "VARIANT_TYPE_SNV", + "VARIANT_TYPE_INDEL", + "VARIANT_TYPE_MNV", + "VARIANT_TYPE_COMPLEX_SUBSTITUTION" + ], + "transcriptTypes": [ + "TRANSCRIPT_TYPE_CODING" + ], + "consequences": [ + "CONSEQUENCE_TRANSCRIPT_ABLATION", + "CONSEQUENCE_EXON_LOSS_VARIANT", + "CONSEQUENCE_SPLICE_ACCEPTOR_VARIANT", + "CONSEQUENCE_SPLICE_DONOR_VARIANT", + "CONSEQUENCE_STOP_GAINED", + "CONSEQUENCE_FRAMESHIFT_VARIANT", + "CONSEQUENCE_STOP_LOST", + "CONSEQUENCE_START_LOST", + "CONSEQUENCE_TRANSCRIPT_AMPLIFICATION", + "CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION", + "CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION", + "CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION", + "CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION", + "CONSEQUENCE_MISSENSE_VARIANT", + "CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT", + "CONSEQUENCE_SPLICE_REGION_VARIANT", + "CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT", + "CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT" + ] }, - "selected_variants": null, - "transcripts_coding": true, - "transcripts_noncoding": true, - "var_type_snv": true, - "var_type_indel": true, - "var_type_mnv": true, - "max_exon_dist": 100, - "gene_allowlist": [], - "genomic_regions": null, - "require_in_clinvar": false, - "clinvar_include_benign": false, - "clinvar_include_pathogenic": true, - "clinvar_include_likely_benign": false, - "clinvar_include_likely_pathogenic": true, - "clinvar_include_uncertain_significance": false, - "gnomad_exomes_frequency": 0.002, - "gnomad_exomes_heterozygous": 20, - "gnomad_exomes_homozygous": 0, - "gnomad_exomes_hemizygous": null, - 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/dev/null +++ b/tests/seqvars/query/db-dynamic/worker/seqvars/inhouse/grch37/active @@ -0,0 +1 @@ +2024-10-30_13-33-30 \ No newline at end of file diff --git a/tests/seqvars/query/dragen.query.json b/tests/seqvars/query/dragen.query.json index 1e6b33f4..a7d0f2fd 100644 --- a/tests/seqvars/query/dragen.query.json +++ b/tests/seqvars/query/dragen.query.json @@ -1,101 +1,78 @@ { - "consequences": [ - "chromosome_number_variation", - "exon_loss_variant", - "frameshift_variant", - "rare_amino_acid_variant", - "splice_acceptor_variant", - "splice_donor_variant", - "start_lost", - "stop_gained", - "stop_lost", - "transcript_ablation", - "3_prime_UTR_truncation", - "5_prime_UTR_truncation", - "conservative_inframe_deletion", - "conservative_inframe_insertion", - "disruptive_inframe_deletion", - "disruptive_inframe_insertion", - "missense_variant", - "regulatory_region_ablation", - "splice_region_variant", - "TFBS_ablation", - "5_prime_UTR_premature_start_codon_gain_variant", - "initiator_codon_variant", - "start_retained", - "stop_retained_variant", - "synonymous_variant", - "3_prime_UTR_variant", - "5_prime_UTR_variant", - "coding_sequence_variant", - "conserved_intergenic_variant", - "conserved_intron_variant", - "downstream_gene_variant", - "exon_variant", - "feature_elongation", - "feature_truncation", - "gene_variant", - "intergenic_variant", - "intron_variant", - "mature_miRNA_variant", - "miRNA", - "NMD_transcript_variant", - "non_coding_transcript_exon_variant", - "non_coding_transcript_intron_variant", - "regulatory_region_amplification", - "regulatory_region_variant", - "TF_binding_site_variant", - "TFBS_amplification", - "transcript_amplification", - "transcript_variant", - "upstream_gene_variant" - ], - "gnomad_exomes_enabled": false, - "gnomad_genomes_enabled": false, - "inhouse_enabled": false, - "helixmtdb_enabled": false, + "genotype": { + "recessiveMode": "RECESSIVE_MODE_DISABLED", + "sampleGenotypes": [ + { + "sample": "CASE", + "genotype": "GENOTYPE_CHOICE_ANY", + "enabled": true + } + ] + }, "quality": { - "CASE": { - "dp_het": 10, - "dp_hom": 5, - "gq": 10, - "ab": 0.2, - "ad": 3, - "ad_max": null, - "filter_active": "drop-variant" + "sampleQualities": [ + { + "sample": "CASE", + "filterActive": true, + "minDpHet": 10, + "minDpHom": 5, + "minGq": 10, + "minAb": 0.2, + "minAd": 3 + } + ] + }, + "frequency": { + "gnomadExomes": { + "enabled": true, + "maxHet": 1, + "maxHom": 0, + "maxAf": 0.002 + }, + "gnomadGenomes": { + "enabled": true, + "maxHet": 1, + "maxHom": 0, + "maxAf": 0.002 + }, + "gnomadMtdna": {}, + "helixmtdb": {}, + "inhouse": { + "enabled": true, + "maxCarriers": 20 } }, - "genotype": { - "CASE": "variant" + "consequence": { + "variantTypes": [ + "VARIANT_TYPE_SNV", + "VARIANT_TYPE_INDEL", + "VARIANT_TYPE_MNV", + "VARIANT_TYPE_COMPLEX_SUBSTITUTION" + ], + "transcriptTypes": [ + "TRANSCRIPT_TYPE_CODING" + ], + "consequences": [ + "CONSEQUENCE_TRANSCRIPT_ABLATION", + "CONSEQUENCE_EXON_LOSS_VARIANT", + "CONSEQUENCE_SPLICE_ACCEPTOR_VARIANT", + "CONSEQUENCE_SPLICE_DONOR_VARIANT", + "CONSEQUENCE_STOP_GAINED", + "CONSEQUENCE_FRAMESHIFT_VARIANT", + "CONSEQUENCE_STOP_LOST", + "CONSEQUENCE_START_LOST", + "CONSEQUENCE_TRANSCRIPT_AMPLIFICATION", + "CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION", + "CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION", + "CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION", + "CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION", + "CONSEQUENCE_MISSENSE_VARIANT", + "CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT", + "CONSEQUENCE_SPLICE_REGION_VARIANT", + "CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT", + "CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT" + ] }, - "selected_variants": null, - "transcripts_coding": true, - "transcripts_noncoding": true, - "var_type_snv": true, - "var_type_indel": true, - "var_type_mnv": true, - "max_exon_dist": 100, - "gene_allowlist": [], - "genomic_regions": null, - "require_in_clinvar": false, - "clinvar_include_benign": false, - "clinvar_include_pathogenic": true, - "clinvar_include_likely_benign": false, - "clinvar_include_likely_pathogenic": true, - "clinvar_include_uncertain_significance": false, - "gnomad_exomes_frequency": 0.002, - "gnomad_exomes_heterozygous": 20, - "gnomad_exomes_homozygous": 0, - "gnomad_exomes_hemizygous": null, - "gnomad_genomes_frequency": 0.002, - "gnomad_genomes_heterozygous": 4, - "gnomad_genomes_homozygous": 0, - "gnomad_genomes_hemizygous": null, - "inhouse_carriers": 20, - "inhouse_heterozygous": null, - "inhouse_homozygous": null, - "inhouse_hemizygous": null, - "helixmtdb_frequency": 0.01, - "helixmtdb_heterozygous": null, - "helixmtdb_homozygous": null + "locus": {}, + "clinvar": {} } From 1b1a37f219666987c8c945198c563629929fc12e Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 30 Oct 2024 14:57:52 +0100 Subject: [PATCH 2/2] invariant output time/memory --- src/seqvars/query/mod.rs | 18 +++++++++++++----- ...est@Case_1.ingested.vcf-with_inhouse-2.snap | 2 +- ..._test@Case_1.ingested.vcf-with_inhouse.snap | 2 +- ..._test@dragen.ingested.vcf-no_inhouse-2.snap | 2 +- ...ke_test@dragen.ingested.vcf-no_inhouse.snap | 2 +- 5 files changed, 17 insertions(+), 9 deletions(-) diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs index f778c02a..2d8d0791 100644 --- a/src/seqvars/query/mod.rs +++ b/src/seqvars/query/mod.rs @@ -557,11 +557,19 @@ fn write_header( }) .collect::>(), }), - resources: Some(pbs_output::ResourcesUsed { - start_time: Some(start_time), - end_time: Some(common::now_as_pbjson_timestamp()), - memory_used: common::rss_size()?, - }), + resources: if cfg!(test) { + Some(pbs_output::ResourcesUsed { + start_time: None, + end_time: None, + memory_used: 0, + }) + } else { + Some(pbs_output::ResourcesUsed { + start_time: Some(start_time), + end_time: Some(common::now_as_pbjson_timestamp()), + memory_used: common::rss_size()?, + }) + }, variant_score_columns: variant_related_annotation::score_columns(), }; writeln!( diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf-with_inhouse-2.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf-with_inhouse-2.snap index c45c4d5e..97dd4512 100644 --- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf-with_inhouse-2.snap +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf-with_inhouse-2.snap @@ -2,7 +2,7 @@ source: src/seqvars/query/mod.rs expression: "std::fs::read_to_string(args.path_output.as_str())?" --- -{"genomeRelease":"GENOME_RELEASE_GRCH37","versions":[{"name":"varfish-worker","version":"x.y.z"}],"query":{"genotype":{"recessiveMode":"RECESSIVE_MODE_DISABLED","sampleGenotypes":[{"sample":"Case_1_index-N1-DNA1-WGS1","genotype":"GENOTYPE_CHOICE_ANY","enabled":true},{"sample":"Case_1_father-N1-DNA1-WGS1","genotype":"GENOTYPE_CHOICE_ANY","enabled":true},{"sample":"Case_1_mother-N1-DNA1-WGS1","genotype":"GENOTYPE_CHOICE_ANY","enabled":true}]},"quality":{"sampleQualities":[{"sample":"Case_1_index-N1-DNA1-WGS1","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3},{"sample":"Case_1_father-N1-DNA1-WGS1","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3},{"sample":"Case_1_mother-N1-DNA1-WGS1","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3}]},"frequency":{"gnomadExomes":{"enabled":true,"maxHet":1,"maxHom":0,"maxAf":0.002},"gnomadGenomes":{"enabled":true,"maxHet":1,"maxHom":0,"maxAf":0.002},"gnomadMtdna":{},"helixmtdb":{},"inhouse":{"enabled":true,"maxCarriers":20}},"consequence":{"variantTypes":["VARIANT_TYPE_SNV","VARIANT_TYPE_INDEL","VARIANT_TYPE_MNV","VARIANT_TYPE_COMPLEX_SUBSTITUTION"],"transcriptTypes":["TRANSCRIPT_TYPE_CODING"],"consequences":["CONSEQUENCE_TRANSCRIPT_ABLATION","CONSEQUENCE_EXON_LOSS_VARIANT","CONSEQUENCE_SPLICE_ACCEPTOR_VARIANT","CONSEQUENCE_SPLICE_DONOR_VARIANT","CONSEQUENCE_STOP_GAINED","CONSEQUENCE_FRAMESHIFT_VARIANT","CONSEQUENCE_STOP_LOST","CONSEQUENCE_START_LOST","CONSEQUENCE_TRANSCRIPT_AMPLIFICATION","CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION","CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION","CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION","CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION","CONSEQUENCE_MISSENSE_VARIANT","CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT","CONSEQUENCE_SPLICE_REGION_VARIANT","CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT","CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT"]},"locus":{},"clinvar":{}},"caseUuid":"00000000-0000-0000-0000-000000000000","resources":{"startTime":"2024-10-30T13:41:03.863109086+00:00","endTime":"2024-10-30T13:41:03.899274255+00:00","memoryUsed":"1999933440"},"statistics":{"countTotal":"63","countPassed":"51"},"variantScoreColumns":[{"name":"cadd_phred","label":"CADD","description":"PHRED-scaled CADD score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"mmsplice","label":"MMSplice","description":"MMSplice score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"mmsplice_argmax","label":"MMSplice (which)","description":"Which MMSplice score is maximal","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"polyphen","label":"PolyPhen","description":"PolyPhen score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"sift","label":"SIFT","description":"SIFT score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"spliceai","label":"SpliceAI","description":"SpliceAI score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"spliceai_argmax","label":"SpliceAI (which)","description":"Which SpliceAI score is maximal","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"alphamissense","label":"AlphaMissense","description":"AlphaMissense score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"bayesdel_addaf","label":"BayesDel","description":"BayesDel AddAF score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"fathmm","label":"FATHMM","description":"FATHMM score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"fitcons_integrated","label":"fitCons","description":"The integrated fitCons score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"lrt","label":"LRT","description":"LRT score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"metasvm","label":"MetaSVM","description":"MetaSVM score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"polyphen2_hdiv","label":"Polyphen2 HDIV","description":"Polyphen2 HDIV score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"polyphen2_hvar","label":"Polyphen2 HVAR","description":"Polyphen2 HVAR score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"primateai","label":"PrimateAI","description":"PrimateAI score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"provean","label":"PROVEAN","description":"PROVEAN score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"},{"name":"revel","label":"REVEL","description":"REVEL score","type":"VARIANT_SCORE_COLUMN_TYPE_NUMBER"}]} +{"genomeRelease":"GENOME_RELEASE_GRCH37","versions":[{"name":"varfish-worker","version":"x.y.z"}],"query":{"genotype":{"recessiveMode":"RECESSIVE_MODE_DISABLED","sampleGenotypes":[{"sample":"Case_1_index-N1-DNA1-WGS1","genotype":"GENOTYPE_CHOICE_ANY","enabled":true},{"sample":"Case_1_father-N1-DNA1-WGS1","genotype":"GENOTYPE_CHOICE_ANY","enabled":true},{"sample":"Case_1_mother-N1-DNA1-WGS1","genotype":"GENOTYPE_CHOICE_ANY","enabled":true}]},"quality":{"sampleQualities":[{"sample":"Case_1_index-N1-DNA1-WGS1","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3},{"sample":"Case_1_father-N1-DNA1-WGS1","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3},{"sample":"Case_1_mother-N1-DNA1-WGS1","filterActive":true,"minDpHet":10,"minDpHom":5,"minGq":10,"minAb":0.2,"minAd":3}]},"frequency":{"gnomadExomes":{"enabled":true,"maxHet":1,"maxHom":0,"maxAf":0.002},"gnomadGenomes":{"enabled":true,"maxHet":1,"maxHom":0,"maxAf":0.002},"gnomadMtdna":{},"helixmtdb":{},"inhouse":{"enabled":true,"maxCarriers":20}},"consequence":{"variantTypes":["VARIANT_TYPE_SNV","VARIANT_TYPE_INDEL","VARIANT_TYPE_MNV","VARIANT_TYPE_COMPLEX_SUBSTITUTION"],"transcriptTypes":["TRANSCRIPT_TYPE_CODING"],"consequences":["CONSEQUENCE_TRANSCRIPT_ABLATION","CONSEQUENCE_EXON_LOSS_VARIANT","CONSEQUENCE_SPLICE_ACCEPTOR_VARIANT","CONSEQUENCE_SPLICE_DONOR_VARIANT","CONSEQUENCE_STOP_GAINED","CONSEQUENCE_FRAMESHIFT_VARIANT","CONSEQUENCE_STOP_LOST","CONSEQUENCE_START_LOST","CONSEQUENCE_TRANSCRIPT_AMPLIFICATION","CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION","CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION","CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION","CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION","CONSEQUENCE_MISSENSE_VARIANT","CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT","CONSEQUENCE_SPLICE_REGION_VARIANT","CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT","CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT"]},"locus":{},"clinvar":{}},"caseUuid":"00000000-0000-0000-0000-000000000000","resources":{},"statistics":{"countTotal":"63","countPassed":"51"},"variantScoreColumns":[{"name":"cadd_phred","label":"CADD","description":"PHRED-scaled 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a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf-no_inhouse.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf-no_inhouse.snap index 7231d551..f28f2aba 100644 --- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf-no_inhouse.snap +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf-no_inhouse.snap @@ -2,5 +2,5 @@ source: src/seqvars/query/mod.rs expression: "std::fs::read_to_string(args.path_output.as_str())?" --- 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