diff --git a/src/gnomad_sv/cli/import/gnomad_cnv4.rs b/src/gnomad_sv/cli/import/gnomad_cnv4.rs index 21c77965..a83a59ac 100644 --- a/src/gnomad_sv/cli/import/gnomad_cnv4.rs +++ b/src/gnomad_sv/cli/import/gnomad_cnv4.rs @@ -79,6 +79,12 @@ impl Record { let outer_start = get_i32(record, "POSMIN").expect("no POSMIN?"); let inner_stop = get_i32(record, "ENDMIN").expect("no ENDMIN?"); let outer_stop = get_i32(record, "ENDMAX").expect("no ENDMAX?"); + let id = record + .ids() + .iter() + .next() + .map(|s| s.to_string()) + .ok_or_else(|| anyhow::anyhow!("no ID found in VCF record"))?; let sv_len = get_i32(record, "SVLEN").expect("no SVLEN?"); let sv_type = get_string(record, "SVTYPE")? .parse::() @@ -114,6 +120,7 @@ impl Record { inner_stop, outer_start, outer_stop, + id, sv_len, sv_type, n_exn_var, diff --git a/src/gnomad_sv/cli/query.rs b/src/gnomad_sv/cli/query.rs index f06c5cb9..2d6623ad 100644 --- a/src/gnomad_sv/cli/query.rs +++ b/src/gnomad_sv/cli/query.rs @@ -14,6 +14,9 @@ pub struct ArgsQuery { /// Query for all variants. #[arg(long, group = "query")] pub all: bool, + /// Query for variant with a specicic accession. + #[arg(long, group = "query")] + pub accession: Option, /// Specify range to query for. #[arg(long, group = "query")] pub range: Option, @@ -108,6 +111,7 @@ pub fn open_rocksdb_from_args( } /// Enumeration for the different record types that we have. +#[derive(Debug)] pub enum Record { /// ExAC SV record. ExacCnv(crate::gnomad_pbs::exac_cnv::Record), @@ -119,6 +123,50 @@ pub enum Record { GnomadSv4(crate::gnomad_pbs::gnomad_sv4::Record), } +/// The necessary data for the tree construction. +#[derive(Debug)] +pub struct TreeData { + /// The chromosome. + pub chromosome: String, + /// The start position. + pub start: u32, + /// The stop position. + pub stop: u32, +} + +impl Record { + fn tree_data(&self) -> TreeData { + match self { + Record::ExacCnv(record) => TreeData { + chromosome: record.chrom.clone(), + start: record.start as u32, + stop: record.stop as u32, + }, + Record::GnomadSv2(record) => TreeData { + chromosome: record.chrom.clone(), + start: record.pos as u32, + stop: record + .end + .map(|end| end as u32) + .unwrap_or(record.pos as u32 + 1), + }, + Record::GnomadCnv4(record) => TreeData { + chromosome: record.chrom.clone(), + start: record.start as u32, + stop: record.stop as u32, + }, + Record::GnomadSv4(record) => TreeData { + chromosome: record.chrom.clone(), + start: record.pos as u32, + stop: record + .end + .map(|end| end as u32) + .unwrap_or(record.pos as u32 + 1), + }, + } + } +} + /// Write a single record to `out_writer`. fn print_record( out_writer: &mut Box, @@ -203,7 +251,7 @@ fn print_all( /// Helper data structure that provides per-chromosome interval trees for querying. pub struct IntervalTrees { /// Per-chromosome interval trees. - trees: rustc_hash::FxHashMap>, + trees: rustc_hash::FxHashMap>>, /// Backing RocksDB. db: Arc>, /// Name of column family with data. @@ -239,7 +287,7 @@ impl IntervalTrees { anyhow::anyhow!("no column family with name {:?} found", cf_data_name) })?; Ok(Self { - trees: Self::build_trees(db.clone(), cf_data.clone())?, + trees: Self::build_trees(db.clone(), cf_data.clone(), &meta)?, db: db.clone(), cf_data_name: cf_data_name.to_string(), meta, @@ -250,9 +298,10 @@ impl IntervalTrees { fn build_trees( db: Arc>, cf_data: Arc, - ) -> Result>, anyhow::Error> + meta: &Meta, + ) -> Result>>, anyhow::Error> { - let mut result: rustc_hash::FxHashMap> = + let mut result: rustc_hash::FxHashMap>> = rustc_hash::FxHashMap::default(); // Obtain iterator and seek to start. @@ -260,27 +309,25 @@ impl IntervalTrees { iter.seek(b""); while iter.valid() { if let Some(raw_value) = iter.value() { - let record = crate::pbs::annonars::clinvar::v1::sv::Record::decode( - &mut std::io::Cursor::new(&raw_value), - ) - .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; - tracing::trace!("iterator at {:?} => {:?}", &iter.key(), &record); + let record = decode_record(&raw_value, &meta) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; + let key = iter.key().unwrap().to_vec(); + tracing::trace!("iterator at {:?} => {:?}", &key, &record); - let crate::pbs::annonars::clinvar::v1::sv::Record { + let TreeData { chromosome, start, stop, - vcv, - .. - } = record; + } = record.tree_data(); let interval = (start as u64 - 1)..(stop as u64); - tracing::trace!("contig = {} / {:?} / {}", &chromosome, &interval, &vcv); + let chrom = chromosome.strip_prefix("chr").unwrap_or(&chromosome); + tracing::trace!("contig = {} / {:?} / {:?}", &chrom, &interval, &key); result - .entry(chromosome.clone()) + .entry(chrom.to_string()) .or_default() - .insert(interval, vcv); - assert!(result.contains_key(&chromosome)); + .insert(interval, key); + assert!(result.contains_key(chrom)); iter.next(); } else { @@ -295,6 +342,7 @@ impl IntervalTrees { /// Query for a range. pub fn query(&self, range: &spdi::Range) -> Result, anyhow::Error> { + tracing::trace!("query for {:?}", &range); let contig = extract_chrom::from_range(range, Some(&self.meta.genome_release))?; let cf_data = self.db.cf_handle(&self.cf_data_name).ok_or_else(|| { anyhow::anyhow!("no column family with name {:?} found", &self.cf_data_name) @@ -303,7 +351,8 @@ impl IntervalTrees { let mut result = Vec::new(); if let Some(tree) = self.trees.get(&contig) { for entry in tree.find(&interval) { - if let Some(raw_value) = self.db.get_cf(&cf_data, entry.data().as_bytes())? { + tracing::info!("found entry: {:?}", &entry); + if let Some(raw_value) = self.db.get_cf(&cf_data, entry.data())? { result.push(decode_record(&raw_value, &self.meta)?); } } @@ -349,6 +398,18 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> print_record(&mut out_writer, args.out_format, record)?; } tracing::info!("... done running query"); + } else if let Some(accession) = args.query.accession.as_ref() { + tracing::info!("for accession {}", accession); + let buf = db + .get_cf(&cf_data, accession.as_bytes()) + .map_err(|e| anyhow::anyhow!("failed to query RocksDB: {}", e))?; + if let Some(buf) = buf { + let record = decode_record(&buf, &meta)?; + print_record(&mut out_writer, args.out_format, &record)?; + } else { + tracing::warn!("no record found for accession {}", accession); + } + tracing::info!("... done running query"); } else if args.query.all { tracing::info!("for all"); print_all(&mut out_writer, args.out_format, &db, &cf_data, &meta)?; @@ -363,6 +424,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> #[cfg(test)] mod test { + use std::str::FromStr as _; use temp_testdir::TempDir; use crate::common; @@ -383,6 +445,7 @@ mod test { (common, args, temp) } + #[tracing_test::traced_test] #[rstest::rstest] #[case("tests/gnomad-sv/exac-cnv/rocksdb", "exac-cnv")] #[case("tests/gnomad-sv/gnomad-sv2/rocksdb", "gnomad-sv2")] @@ -410,4 +473,111 @@ mod test { Ok(()) } + + #[tracing_test::traced_test] + #[rstest::rstest] + #[case( + "tests/gnomad-sv/gnomad-sv2/rocksdb", + "gnomAD-SV_v2.1_BND_1_1", + "gnomad-sv2" + )] + #[case( + "tests/gnomad-sv/gnomad-cnv4/rocksdb", + "variant_is_80_2__DEL", + "gnomad-cnv4" + )] + #[case( + "tests/gnomad-sv/gnomad-sv4/rocksdb", + "gnomAD-SV_v3_DUP_chr1_01c2781c", + "gnomad-sv4" + )] + fn smoke_query_var_accession( + #[case] path_rocksdb: &str, + #[case] accession: &str, + #[case] label: &str, + args_args_temp: (common::cli::Args, super::Args, TempDir), + ) -> Result<(), anyhow::Error> { + crate::common::set_snapshot_suffix!("{}", &label); + + let (common, args, _temp) = args_args_temp; + let args = super::Args { + path_rocksdb: path_rocksdb.to_string(), + query: super::ArgsQuery { + accession: Some(accession.to_string()), + ..Default::default() + }, + ..args + }; + super::run(&common, &args)?; + let out_data = std::fs::read_to_string(&args.out_file)?; + insta::assert_snapshot!(&out_data); + + Ok(()) + } + + #[tracing_test::traced_test] + #[rstest::rstest] + #[case( + "tests/gnomad-sv/exac-cnv/rocksdb", + "10:51620321:51748701", + "exac-cnv-some" + )] + #[case( + "tests/gnomad-sv/exac-cnv/rocksdb", + "1:51620321:51748701", + "exac-cnv-none" + )] + #[case( + "tests/gnomad-sv/gnomad-sv2/rocksdb", + "1:94000:94010", + "gnomad-sv2-some" + )] + #[case( + "tests/gnomad-sv/gnomad-sv2/rocksdb", + "10:94000:94010", + "gnomad-sv2-none" + )] + #[case( + "tests/gnomad-sv/gnomad-cnv4/rocksdb", + "chr1:925634:925635", + "gnomad-cnv4-some" + )] + #[case( + "tests/gnomad-sv/gnomad-cnv4/rocksdb", + "chr10:925634:925635", + "gnomad-cnv4-none" + )] + #[case( + "tests/gnomad-sv/gnomad-sv4/rocksdb", + "chr1:120937:120938", + "gnomad-sv4-some" + )] + #[case( + "tests/gnomad-sv/gnomad-sv4/rocksdb", + "chr10:120937:120938", + "gnomad-sv4-none" + )] + fn smoke_query_range( + #[case] path_rocksdb: &str, + #[case] range: &str, + #[case] label: &str, + args_args_temp: (common::cli::Args, super::Args, TempDir), + ) -> Result<(), anyhow::Error> { + crate::common::set_snapshot_suffix!("{}", &label); + + let (common, args, _temp) = args_args_temp; + let args = super::Args { + path_rocksdb: path_rocksdb.to_string(), + query: super::ArgsQuery { + range: Some(crate::common::spdi::Range::from_str(range)?), + ..Default::default() + }, + ..args + }; + super::run(&common, &args)?; + let out_data = std::fs::read_to_string(&args.out_file)?; + insta::assert_snapshot!(&out_data); + + Ok(()) + } } diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@exac-cnv-none.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@exac-cnv-none.snap new file mode 100644 index 00000000..35939be0 --- /dev/null +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@exac-cnv-none.snap @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:004cb911026d67a969cb2e871fb38f265a795d61e2a71496adcf3a2bbd7f4d2b +size 68 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@exac-cnv-some.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@exac-cnv-some.snap new file mode 100644 index 00000000..11eb32ac --- /dev/null +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@exac-cnv-some.snap @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid 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b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-cnv4-some.snap @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6c288dcf2e0d26732160a8ea1d50c101d38ff9f3d554187bb9572635ea6005da +size 10975 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv2-none.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv2-none.snap new file mode 100644 index 00000000..35939be0 --- /dev/null +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv2-none.snap @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:004cb911026d67a969cb2e871fb38f265a795d61e2a71496adcf3a2bbd7f4d2b +size 68 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv2-some.snap 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b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_accession@gnomad-sv4.snap @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:159b060e61613440d04ee6564df0bdd27bbece00503329176d1912a435cb8796 +size 21282 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-cnv4.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-cnv4.snap index d9efa9ed..fa006f78 100644 --- a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-cnv4.snap +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-cnv4.snap @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:c6d27e476f3d3e0d7231430133318b2ab9e225c582a640b8430ef9534eddb7b8 -size 104550 +oid sha256:6fcea22ca14cc0e97baf57c598fbaebd6b6a40ac92cd7b17f000e1b907c8ec57 +size 106643 diff --git a/src/proto/annonars/gnomad/v1/gnomad_cnv4.proto b/src/proto/annonars/gnomad/v1/gnomad_cnv4.proto index e83f7b58..caf549e4 100644 --- a/src/proto/annonars/gnomad/v1/gnomad_cnv4.proto +++ b/src/proto/annonars/gnomad/v1/gnomad_cnv4.proto @@ -74,22 +74,25 @@ message Record { // 1-based inner stop position. int32 outer_stop = 7; + // Unique identifier for the variant. + string id = 8; + // Length of the SV. - int32 sv_len = 8; + int32 sv_len = 9; // The type of the variant. - annonars.gnomad.v1.exac_cnv.CnvType sv_type = 9; + annonars.gnomad.v1.exac_cnv.CnvType sv_type = 10; // Median number of callable exons spanned by variant passing QS // threshold. - int32 n_exn_var = 10; + int32 n_exn_var = 11; // Median number of callable intervals spanned by variant passing // QS threshold. - int32 n_int_var = 11; + int32 n_int_var = 12; // Symbols of genes predicted to be impacted by variant - repeated string genes = 12; + repeated string genes = 13; // Global carrier counts. - CarrierCountsBySex counts = 13; + CarrierCountsBySex counts = 14; // Carrier counts in the different population. - repeated PopulationAlleleCounts by_population = 14; + repeated PopulationAlleleCounts by_population = 15; } diff --git a/tests/gnomad-sv/gnomad-cnv4/rocksdb/000014.sst b/tests/gnomad-sv/gnomad-cnv4/rocksdb/000014.sst index 649ec422..3c422113 100644 --- a/tests/gnomad-sv/gnomad-cnv4/rocksdb/000014.sst +++ b/tests/gnomad-sv/gnomad-cnv4/rocksdb/000014.sst @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:0bf43f23ae027b1ea188c750f267c5fc2cec5492b0b64ae8a0ec5f751fbe9420 +oid sha256:19a1e93080d47585699ad3ce06382ca2c9c2901182a24800daffc899077fab1c size 1339 diff --git a/tests/gnomad-sv/gnomad-cnv4/rocksdb/000016.sst b/tests/gnomad-sv/gnomad-cnv4/rocksdb/000016.sst index c8b3b60c..c658ce71 100644 --- a/tests/gnomad-sv/gnomad-cnv4/rocksdb/000016.sst +++ b/tests/gnomad-sv/gnomad-cnv4/rocksdb/000016.sst @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid 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