diff --git a/Cargo.lock b/Cargo.lock index 77ac5b31..6ba1b379 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -277,6 +277,9 @@ dependencies = [ "noodles-gff", "noodles-tabix", "noodles-vcf", + "pbjson", + "pbjson-build", + "pbjson-types", "pretty_assertions", "prost", "prost-build", @@ -1901,6 +1904,43 @@ version = "1.0.14" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "de3145af08024dea9fa9914f381a17b8fc6034dfb00f3a84013f7ff43f29ed4c" +[[package]] +name = "pbjson" +version = "0.6.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1030c719b0ec2a2d25a5df729d6cff1acf3cc230bf766f4f97833591f7577b90" +dependencies = [ + "base64", + "serde", +] + +[[package]] +name = "pbjson-build" +version = "0.6.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2580e33f2292d34be285c5bc3dba5259542b083cfad6037b6d70345f24dcb735" +dependencies = [ + "heck", + "itertools", + "prost", + "prost-types", +] + +[[package]] +name = "pbjson-types" +version = "0.6.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "18f596653ba4ac51bdecbb4ef6773bc7f56042dc13927910de1684ad3d32aa12" +dependencies = [ + "bytes", + "chrono", + "pbjson", + "pbjson-build", + "prost", + "prost-build", + "serde", +] + [[package]] name = "peeking_take_while" version = "0.1.2" diff --git a/Cargo.toml b/Cargo.toml index 238cdf96..6f6466a1 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -41,6 +41,8 @@ noodles-core = "0.12" noodles-csi = "0.28" noodles-tabix = "0.34" noodles-vcf = "0.47" +pbjson = "0.6" +pbjson-types = "0.6" prost = "0.12" rayon = "1.8" rocksdb-utils-lookup = "0.3" @@ -57,6 +59,8 @@ noodles-gff = "0.25.0" [build-dependencies] prost-build = "0.12" +pbjson-build = "0.6" +anyhow = "1.0" [dev-dependencies] insta = { version = "1.33", features = ["yaml"] } diff --git a/build.rs b/build.rs index 8bf78021..93fda381 100644 --- a/build.rs +++ b/build.rs @@ -1,67 +1,54 @@ -// The custom build script, needed as we use flatbuffers. +// The custo build script, used to (1) generate the Rust classes for the +// protobuf implementation and (2) use pbjson for proto3 JSON serialization. + +use std::{env, path::PathBuf}; + +fn main() -> Result<(), anyhow::Error> { + let root = PathBuf::from(env!("CARGO_MANIFEST_DIR")).join("protos"); + let proto_files = vec![ + "annonars/clinvar/minimal.proto", + "annonars/clinvar/per_gene.proto", + "annonars/clinvar/sv.proto", + "annonars/cons/base.proto", + "annonars/dbsnp/base.proto", + "annonars/functional/refseq.proto", + "annonars/genes/base.proto", + "annonars/gnomad/exac_cnv.proto", + "annonars/gnomad/gnomad2.proto", + "annonars/gnomad/gnomad3.proto", + "annonars/gnomad/gnomad_cnv4.proto", + "annonars/gnomad/gnomad_sv2.proto", + "annonars/gnomad/gnomad_sv4.proto", + "annonars/gnomad/mtdna.proto", + "annonars/gnomad/vep_common.proto", + "annonars/gnomad/vep_gnomad2.proto", + "annonars/gnomad/vep_gnomad3.proto", + "annonars/helixmtdb/base.proto", + ] + .iter() + .map(|f| root.join(f)) + .collect::>(); + + // Tell cargo to recompile if any of these proto files are changed + for proto_file in &proto_files { + println!("cargo:rerun-if-changed={}", proto_file.display()); + } + + let descriptor_path = PathBuf::from(env::var("OUT_DIR").unwrap()).join("proto_descriptor.bin"); -fn main() { - println!("cargo:rerun-if-changed=src/proto/annonars/clinvar/v1/minimal.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/clinvar/v1/per_gene.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/clinvar/v1/sv.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/cons/v1/base.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/dbsnp/v1/base.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/functional/v1/refseq.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gene/v1/base.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gnomad/v1/exac_cnv.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gnomad/v1/gnomad2.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gnomad/v1/gnomad3.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gnomad/v1/gnomad_cnv4.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gnomad/v1/gnomad_sv2.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gnomad/v1/gnomad_sv4.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gnomad/v1/mtdna.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gnomad/v1/vep_common.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gnomad/v1/vep_gnomad2.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/gnomad/v1/vep_gnomad3.proto"); - println!("cargo:rerun-if-changed=src/proto/annonars/helixmtdb/v1/base.proto"); prost_build::Config::new() - .protoc_arg("-Isrc/proto") - // Add serde serialization and deserialization to the generated code. - .type_attribute(".", "#[derive(serde::Serialize, serde::Deserialize)]") - // Skip serializing `None` values. - .type_attribute(".", "#[serde_with::skip_serializing_none]") - // Rename the field attributes such that we can properly decode - // ucsc-annotation TSV file with serde. - .field_attribute( - "annonars.cons.v1.base.Record.chrom", - "#[serde(rename = \"chromosome\")]", - ) - .field_attribute( - "annonars.cons.v1.base.Record.begin", - "#[serde(rename = \"start\")]", - ) - .field_attribute( - "annonars.cons.v1.base..Record.end", - "#[serde(rename = \"stop\")]", - ) + // Save descriptors to file + .file_descriptor_set_path(&descriptor_path) + // Override prost-types with pbjson-types + .compile_well_known_types() + .extern_path(".google.protobuf", "::pbjson_types") // Define the protobuf files to compile. - .compile_protos( - &[ - "annonars/clinvar/v1/minimal.proto", - "annonars/clinvar/v1/per_gene.proto", - "annonars/clinvar/v1/sv.proto", - "annonars/cons/v1/base.proto", - "annonars/dbsnp/v1/base.proto", - "annonars/gene/v1/base.proto", - "annonars/gnomad/v1/exac_cnv.proto", - "annonars/functional/v1/refseq.proto", - "annonars/gnomad/v1/gnomad2.proto", - "annonars/gnomad/v1/gnomad3.proto", - "annonars/gnomad/v1/gnomad_cnv4.proto", - "annonars/gnomad/v1/gnomad_sv2.proto", - "annonars/gnomad/v1/gnomad_sv4.proto", - "annonars/gnomad/v1/mtdna.proto", - "annonars/gnomad/v1/vep_common.proto", - "annonars/gnomad/v1/vep_gnomad2.proto", - "annonars/gnomad/v1/vep_gnomad3.proto", - "annonars/helixmtdb/v1/base.proto", - ], - &["src/"], - ) - .unwrap(); + .compile_protos(&proto_files, &[root])?; + + let descriptor_set = std::fs::read(descriptor_path).unwrap(); + pbjson_build::Builder::new() + .register_descriptors(&descriptor_set)? + .build(&[".annonars"])?; + + Ok(()) } diff --git a/src/proto/annonars/clinvar/v1/minimal.proto b/protos/annonars/clinvar/minimal.proto similarity index 98% rename from src/proto/annonars/clinvar/v1/minimal.proto rename to protos/annonars/clinvar/minimal.proto index ab5037bf..0344cddf 100644 --- a/src/proto/annonars/clinvar/v1/minimal.proto +++ b/protos/annonars/clinvar/minimal.proto @@ -2,7 +2,7 @@ syntax = "proto3"; -package annonars.clinvar.v1.minimal; +package annonars.clinvar.minimal; // Enumeration for variant type. enum VariantType { diff --git a/src/proto/annonars/clinvar/v1/per_gene.proto b/protos/annonars/clinvar/per_gene.proto similarity index 93% rename from src/proto/annonars/clinvar/v1/per_gene.proto rename to protos/annonars/clinvar/per_gene.proto index e96acb53..5e5d18bd 100644 --- a/src/proto/annonars/clinvar/v1/per_gene.proto +++ b/protos/annonars/clinvar/per_gene.proto @@ -2,9 +2,9 @@ syntax = "proto3"; -package annonars.clinvar.v1.per_gene; +package annonars.clinvar.per_gene; -import "annonars/clinvar/v1/minimal.proto"; +import "annonars/clinvar/minimal.proto"; // Impact on gene in ClinVar. enum Impact { @@ -73,7 +73,7 @@ message GeneVariantsForRelease { // Genome release / assembly string genome_release = 1; // Variants - repeated annonars.clinvar.v1.minimal.Record variants = 2; + repeated annonars.clinvar.minimal.Record variants = 2; } // ClinVar detailed information per gene. diff --git a/src/proto/annonars/clinvar/v1/sv.proto b/protos/annonars/clinvar/sv.proto similarity index 81% rename from src/proto/annonars/clinvar/v1/sv.proto rename to protos/annonars/clinvar/sv.proto index 36d715fe..1e840302 100644 --- a/src/proto/annonars/clinvar/v1/sv.proto +++ b/protos/annonars/clinvar/sv.proto @@ -2,9 +2,9 @@ syntax = "proto3"; -package annonars.clinvar.v1.sv; +package annonars.clinvar.sv; -import "annonars/clinvar/v1/minimal.proto"; +import "annonars/clinvar/minimal.proto"; // Record for storing minimal information on ClinVar for Mehari. message Record { @@ -32,10 +32,10 @@ message Record { optional uint32 outer_stop = 10; // The variant type. - annonars.clinvar.v1.minimal.VariantType variant_type = 11; + annonars.clinvar.minimal.VariantType variant_type = 11; // VCV accession identifier. string vcv = 12; // The reference assertions, sorted by (ClinicalSignificance, ReviewStatus). - repeated annonars.clinvar.v1.minimal.ReferenceAssertion reference_assertions = 13; + repeated annonars.clinvar.minimal.ReferenceAssertion reference_assertions = 13; } diff --git a/src/proto/annonars/cons/v1/base.proto b/protos/annonars/cons/base.proto similarity index 95% rename from src/proto/annonars/cons/v1/base.proto rename to protos/annonars/cons/base.proto index 83b1d765..1ed6a959 100644 --- a/src/proto/annonars/cons/v1/base.proto +++ b/protos/annonars/cons/base.proto @@ -1,6 +1,6 @@ syntax = "proto3"; -package annonars.cons.v1.base; +package annonars.cons.base; // List of `Record`s. message RecordList { diff --git a/src/proto/annonars/dbsnp/v1/base.proto b/protos/annonars/dbsnp/base.proto similarity index 91% rename from src/proto/annonars/dbsnp/v1/base.proto rename to protos/annonars/dbsnp/base.proto index ffa6d6d7..7df58e79 100644 --- a/src/proto/annonars/dbsnp/v1/base.proto +++ b/protos/annonars/dbsnp/base.proto @@ -1,6 +1,6 @@ syntax = "proto3"; -package annonars.dbsnp.v1.base; +package annonars.dbsnp.base; // Protocol buffer for the dbSNP VCF record. message Record { diff --git a/src/proto/annonars/functional/v1/refseq.proto b/protos/annonars/functional/refseq.proto similarity index 98% rename from src/proto/annonars/functional/v1/refseq.proto rename to protos/annonars/functional/refseq.proto index 4f21f3af..5f781f20 100644 --- a/src/proto/annonars/functional/v1/refseq.proto +++ b/protos/annonars/functional/refseq.proto @@ -2,7 +2,7 @@ syntax = "proto3"; -package annonars.functional.v1.refseq; +package annonars.functional.refseq; // Enumeration for `gbkey` field. enum Category { diff --git a/src/proto/annonars/gene/v1/base.proto b/protos/annonars/genes/base.proto similarity index 99% rename from src/proto/annonars/gene/v1/base.proto rename to protos/annonars/genes/base.proto index e19a7335..d731812b 100644 --- a/src/proto/annonars/gene/v1/base.proto +++ b/protos/annonars/genes/base.proto @@ -1,6 +1,6 @@ syntax = "proto3"; -package annonars.gene.v1.base; +package annonars.genes.base; // Information from ACMG secondary findings list. message AcmgSecondaryFindingRecord { diff --git a/src/proto/annonars/gnomad/v1/exac_cnv.proto b/protos/annonars/gnomad/exac_cnv.proto similarity index 96% rename from src/proto/annonars/gnomad/v1/exac_cnv.proto rename to protos/annonars/gnomad/exac_cnv.proto index 6da261d5..d2736b91 100644 --- a/src/proto/annonars/gnomad/v1/exac_cnv.proto +++ b/protos/annonars/gnomad/exac_cnv.proto @@ -2,7 +2,7 @@ syntax = "proto3"; -package annonars.gnomad.v1.exac_cnv; +package annonars.gnomad.exac_cnv; // Enumeration for the CNV type. enum CnvType { diff --git a/src/proto/annonars/gnomad/v1/gnomad2.proto b/protos/annonars/gnomad/gnomad2.proto similarity index 98% rename from src/proto/annonars/gnomad/v1/gnomad2.proto rename to protos/annonars/gnomad/gnomad2.proto index 48f574f1..d7d65dba 100644 --- a/src/proto/annonars/gnomad/v1/gnomad2.proto +++ b/protos/annonars/gnomad/gnomad2.proto @@ -1,8 +1,8 @@ syntax = "proto3"; -package annonars.gnomad.v1.gnomad2; +package annonars.gnomad.gnomad2; -import "annonars/gnomad/v1/vep_gnomad2.proto"; +import "annonars/gnomad/vep_gnomad2.proto"; // Protocol buffer enum for site-level filters. enum Filter { @@ -226,7 +226,7 @@ message Record { // Site-level filters. repeated Filter filters = 5; // VEP annotation records. - repeated annonars.gnomad.v1.vep_gnomad2.Vep vep = 6; + repeated annonars.gnomad.vep_gnomad2.Vep vep = 6; // Variant allele counts in the different cohorts and population. // diff --git a/src/proto/annonars/gnomad/v1/gnomad3.proto b/protos/annonars/gnomad/gnomad3.proto similarity index 98% rename from src/proto/annonars/gnomad/v1/gnomad3.proto rename to protos/annonars/gnomad/gnomad3.proto index a0cdb4e5..ae6f51cc 100644 --- a/src/proto/annonars/gnomad/v1/gnomad3.proto +++ b/protos/annonars/gnomad/gnomad3.proto @@ -1,8 +1,8 @@ syntax = "proto3"; -package annonars.gnomad.v1.gnomad3; +package annonars.gnomad.gnomad3; -import "annonars/gnomad/v1/vep_gnomad3.proto"; +import "annonars/gnomad/vep_gnomad3.proto"; // Protocol buffer enum for site-level filters. enum Filter { @@ -219,7 +219,7 @@ message Record { // Site-level filters. repeated Filter filters = 5; // VEP annotation records. - repeated annonars.gnomad.v1.vep_gnomad3.Vep vep = 6; + repeated annonars.gnomad.vep_gnomad3.Vep vep = 6; // Variant allele counts in the different cohorts and population. // diff --git a/src/proto/annonars/gnomad/v1/gnomad_cnv4.proto b/protos/annonars/gnomad/gnomad_cnv4.proto similarity index 94% rename from src/proto/annonars/gnomad/v1/gnomad_cnv4.proto rename to protos/annonars/gnomad/gnomad_cnv4.proto index caf549e4..fda8ea29 100644 --- a/src/proto/annonars/gnomad/v1/gnomad_cnv4.proto +++ b/protos/annonars/gnomad/gnomad_cnv4.proto @@ -2,9 +2,9 @@ syntax = "proto3"; -package annonars.gnomad.v1.gnomad_cnv4; +package annonars.gnomad.gnomad_cnv4; -import "annonars/gnomad/v1/exac_cnv.proto"; +import "annonars/gnomad/exac_cnv.proto"; // Carrier counts @@ -80,7 +80,7 @@ message Record { // Length of the SV. int32 sv_len = 9; // The type of the variant. - annonars.gnomad.v1.exac_cnv.CnvType sv_type = 10; + annonars.gnomad.exac_cnv.CnvType sv_type = 10; // Median number of callable exons spanned by variant passing QS // threshold. diff --git a/src/proto/annonars/gnomad/v1/gnomad_sv2.proto b/protos/annonars/gnomad/gnomad_sv2.proto similarity index 99% rename from src/proto/annonars/gnomad/v1/gnomad_sv2.proto rename to protos/annonars/gnomad/gnomad_sv2.proto index b06c25ad..44504722 100644 --- a/src/proto/annonars/gnomad/v1/gnomad_sv2.proto +++ b/protos/annonars/gnomad/gnomad_sv2.proto @@ -5,7 +5,7 @@ syntax = "proto3"; -package annonars.gnomad.v1.gnomad_sv2; +package annonars.gnomad.gnomad_sv2; // Protocol buffer enum for site-level filters. enum Filter { diff --git a/src/proto/annonars/gnomad/v1/gnomad_sv4.proto b/protos/annonars/gnomad/gnomad_sv4.proto similarity index 97% rename from src/proto/annonars/gnomad/v1/gnomad_sv4.proto rename to protos/annonars/gnomad/gnomad_sv4.proto index 783638ef..bdd80fce 100644 --- a/src/proto/annonars/gnomad/v1/gnomad_sv4.proto +++ b/protos/annonars/gnomad/gnomad_sv4.proto @@ -2,9 +2,9 @@ syntax = "proto3"; -package annonars.gnomad.v1.gnomad_sv4; +package annonars.gnomad.gnomad_sv4; -import "annonars/gnomad/v1/gnomad_sv2.proto"; +import "annonars/gnomad/gnomad_sv2.proto"; // Enumeration for filters. enum Filter { @@ -174,7 +174,7 @@ message Record { // SV Type. SvType sv_type = 8; // Refined complex type. - optional annonars.gnomad.v1.gnomad_sv2.CpxType cpx_type = 9; + optional annonars.gnomad.gnomad_sv2.CpxType cpx_type = 9; // Variant allele counts in the different cohorts and population. repeated CohortAlleleCounts allele_counts = 10; diff --git a/src/proto/annonars/gnomad/v1/mtdna.proto b/protos/annonars/gnomad/mtdna.proto similarity index 98% rename from src/proto/annonars/gnomad/v1/mtdna.proto rename to protos/annonars/gnomad/mtdna.proto index 45f6f2fd..1c491d2c 100644 --- a/src/proto/annonars/gnomad/v1/mtdna.proto +++ b/protos/annonars/gnomad/mtdna.proto @@ -1,8 +1,8 @@ syntax = "proto3"; -package annonars.gnomad.v1.mtdna; +package annonars.gnomad.mtdna; -import "annonars/gnomad/v1/vep_gnomad3.proto"; +import "annonars/gnomad/vep_gnomad3.proto"; // Protocol buffer enum for site-level filters. enum Filter { @@ -218,7 +218,7 @@ message Record { optional string pon_ml_probability_of_pathogenicity = 17; // VEP v3 annotation records. - repeated annonars.gnomad.v1.vep_gnomad3.Vep vep = 13; + repeated annonars.gnomad.vep_gnomad3.Vep vep = 13; // Summary information for variant quality interpretation. optional QualityInfo quality_info = 18; // Information related to heteroplasmy levels. diff --git a/src/proto/annonars/gnomad/v1/vep_common.proto b/protos/annonars/gnomad/vep_common.proto similarity index 90% rename from src/proto/annonars/gnomad/v1/vep_common.proto rename to protos/annonars/gnomad/vep_common.proto index 16e0ef72..a629ea39 100644 --- a/src/proto/annonars/gnomad/v1/vep_common.proto +++ b/protos/annonars/gnomad/vep_common.proto @@ -2,7 +2,7 @@ syntax = "proto3"; -package annonars.gnomad.v1.vep_common; +package annonars.gnomad.vep_common; // Protocol buffer for `Vep.domains` message Domain { diff --git a/src/proto/annonars/gnomad/v1/vep_gnomad2.proto b/protos/annonars/gnomad/vep_gnomad2.proto similarity index 94% rename from src/proto/annonars/gnomad/v1/vep_gnomad2.proto rename to protos/annonars/gnomad/vep_gnomad2.proto index 2595b42d..966ac830 100644 --- a/src/proto/annonars/gnomad/v1/vep_gnomad2.proto +++ b/protos/annonars/gnomad/vep_gnomad2.proto @@ -2,9 +2,9 @@ syntax = "proto3"; -package annonars.gnomad.v1.vep_gnomad2; +package annonars.gnomad.vep_gnomad2; -import "annonars/gnomad/v1/vep_common.proto"; +import "annonars/gnomad/vep_common.proto"; // Protocol buffer for the gnomAD-mtDNA VEP predictions. message Vep { @@ -79,11 +79,11 @@ message Vep { // Gene phenotype from VEP. optional string gene_pheno = 35; // SIFT prediction, e.g., `"tolerated(0.06)"`. - optional annonars.gnomad.v1.vep_common.Prediction sift = 36; + optional annonars.gnomad.vep_common.Prediction sift = 36; // PolyPhen prediction, e.g., `"benign(0.001)"`. - optional annonars.gnomad.v1.vep_common.Prediction polyphen = 37; + optional annonars.gnomad.vep_common.Prediction polyphen = 37; // Protein domains, e.g., `[["2p4e", "ENSP_mappings"], ["2qtw", "ENSP_mappings"]]`. - repeated annonars.gnomad.v1.vep_common.Domain domains = 38; + repeated annonars.gnomad.vep_common.Domain domains = 38; // HGVS offset. optional string hgvs_offset = 39; diff --git a/src/proto/annonars/gnomad/v1/vep_gnomad3.proto b/protos/annonars/gnomad/vep_gnomad3.proto similarity index 92% rename from src/proto/annonars/gnomad/v1/vep_gnomad3.proto rename to protos/annonars/gnomad/vep_gnomad3.proto index a9decb3f..7a2d2501 100644 --- a/src/proto/annonars/gnomad/v1/vep_gnomad3.proto +++ b/protos/annonars/gnomad/vep_gnomad3.proto @@ -2,9 +2,9 @@ syntax = "proto3"; -package annonars.gnomad.v1.vep_gnomad3; +package annonars.gnomad.vep_gnomad3; -import "annonars/gnomad/v1/vep_common.proto"; +import "annonars/gnomad/vep_common.proto"; // Protocol buffer for the gnomAD-mtDNA VEP predictions. message Vep { @@ -75,11 +75,11 @@ message Vep { // Gene phenotype from VEP. optional string gene_pheno = 33; // SIFT prediction, e.g., `"tolerated(0.06)"`. - optional annonars.gnomad.v1.vep_common.Prediction sift = 34; + optional annonars.gnomad.vep_common.Prediction sift = 34; // PolyPhen prediction, e.g., `"benign(0.001)"`. - optional annonars.gnomad.v1.vep_common.Prediction polyphen = 35; + optional annonars.gnomad.vep_common.Prediction polyphen = 35; // Protein domains, e.g., `[["2p4e", "ENSP_mappings"], ["2qtw", "ENSP_mappings"]]`. - repeated annonars.gnomad.v1.vep_common.Domain domains = 36; + repeated annonars.gnomad.vep_common.Domain domains = 36; // HGVS offset. optional string hgvs_offset = 37; // Motif name. diff --git a/src/proto/annonars/helixmtdb/v1/base.proto b/protos/annonars/helixmtdb/base.proto similarity index 94% rename from src/proto/annonars/helixmtdb/v1/base.proto rename to protos/annonars/helixmtdb/base.proto index e990615d..8c6a84fe 100644 --- a/src/proto/annonars/helixmtdb/v1/base.proto +++ b/protos/annonars/helixmtdb/base.proto @@ -1,6 +1,6 @@ syntax = "proto3"; -package annonars.helixmtdb.v1.base; +package annonars.helixmtdb.base; // Protocol buffer for the HelixMtDb VCF record. message Record { diff --git a/src/clinvar_genes/cli/import.rs b/src/clinvar_genes/cli/import.rs index 1fe71d23..7f88b886 100644 --- a/src/clinvar_genes/cli/import.rs +++ b/src/clinvar_genes/cli/import.rs @@ -5,10 +5,10 @@ use std::{collections::HashSet, io::BufRead, sync::Arc}; use clap::Parser; use prost::Message; -use crate::pbs::annonars::clinvar::v1::minimal::{ +use crate::pbs::clinvar::minimal::{ ClinicalSignificance, Record, ReferenceAssertion, ReviewStatus, }; -use crate::pbs::annonars::clinvar::v1::per_gene::{ +use crate::pbs::clinvar::per_gene::{ ClinvarPerGeneRecord, CoarseClinicalSignificance, GeneFreqRecordCounts, GeneImpactRecordCounts, GeneVariantsForRelease, Impact, }; diff --git a/src/clinvar_genes/cli/query.rs b/src/clinvar_genes/cli/query.rs index ac54673d..8ad86326 100644 --- a/src/clinvar_genes/cli/query.rs +++ b/src/clinvar_genes/cli/query.rs @@ -4,7 +4,7 @@ use std::sync::Arc; use prost::Message; -use crate::{common, pbs::annonars::clinvar::v1::per_gene::ClinvarPerGeneRecord}; +use crate::{common, pbs::clinvar::per_gene::ClinvarPerGeneRecord}; /// Command line arguments for `clinvar-gene query` sub command. #[derive(clap::Parser, Debug, Clone)] diff --git a/src/clinvar_genes/cli/reading.rs b/src/clinvar_genes/cli/reading.rs index 8f0c591a..31b3ed53 100644 --- a/src/clinvar_genes/cli/reading.rs +++ b/src/clinvar_genes/cli/reading.rs @@ -55,52 +55,44 @@ pub mod gene_impact { UpstreamGeneVariant, } - impl From for crate::pbs::annonars::clinvar::v1::per_gene::Impact { + impl From for crate::pbs::clinvar::per_gene::Impact { fn from(val: Impact) -> Self { match val { Impact::ThreePrimeUtrVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::ThreePrimeUtrVariant + crate::pbs::clinvar::per_gene::Impact::ThreePrimeUtrVariant } Impact::FivePrimeUtrVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::FivePrimeUtrVariant + crate::pbs::clinvar::per_gene::Impact::FivePrimeUtrVariant } Impact::DownstreamGeneVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::DownstreamTranscriptVariant + crate::pbs::clinvar::per_gene::Impact::DownstreamTranscriptVariant } Impact::FrameshiftVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::FrameshiftVariant - } - Impact::InframeIndel => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::InframeIndel - } - Impact::StartLost => crate::pbs::annonars::clinvar::v1::per_gene::Impact::StartLost, - Impact::IntronVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::IntronVariant - } - Impact::MissenseVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::MissenseVariant + crate::pbs::clinvar::per_gene::Impact::FrameshiftVariant } + Impact::InframeIndel => crate::pbs::clinvar::per_gene::Impact::InframeIndel, + Impact::StartLost => crate::pbs::clinvar::per_gene::Impact::StartLost, + Impact::IntronVariant => crate::pbs::clinvar::per_gene::Impact::IntronVariant, + Impact::MissenseVariant => crate::pbs::clinvar::per_gene::Impact::MissenseVariant, Impact::NonCodingTranscriptVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::NonCodingTranscriptVariant - } - Impact::StopGained => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::StopGained + crate::pbs::clinvar::per_gene::Impact::NonCodingTranscriptVariant } + Impact::StopGained => crate::pbs::clinvar::per_gene::Impact::StopGained, Impact::NoSequenceAlteration => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::NoSequenceAlteration + crate::pbs::clinvar::per_gene::Impact::NoSequenceAlteration } Impact::SpliceAcceptorVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::SpliceAcceptorVariant + crate::pbs::clinvar::per_gene::Impact::SpliceAcceptorVariant } Impact::SpliceDonorVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::SpliceDonorVariant + crate::pbs::clinvar::per_gene::Impact::SpliceDonorVariant } - Impact::StopLost => crate::pbs::annonars::clinvar::v1::per_gene::Impact::StopLost, + Impact::StopLost => crate::pbs::clinvar::per_gene::Impact::StopLost, Impact::SyonymousVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::SynonymousVariant + crate::pbs::clinvar::per_gene::Impact::SynonymousVariant } Impact::UpstreamGeneVariant => { - crate::pbs::annonars::clinvar::v1::per_gene::Impact::UpstreamTranscriptVariant + crate::pbs::clinvar::per_gene::Impact::UpstreamTranscriptVariant } } } @@ -153,18 +145,18 @@ pub mod counts_by_freq { } impl From - for crate::pbs::annonars::clinvar::v1::per_gene::CoarseClinicalSignificance + for crate::pbs::clinvar::per_gene::CoarseClinicalSignificance { fn from(val: CoarseClinicalSignificance) -> Self { match val { CoarseClinicalSignificance::Benign => { - crate::pbs::annonars::clinvar::v1::per_gene::CoarseClinicalSignificance::CoarseBenign + crate::pbs::clinvar::per_gene::CoarseClinicalSignificance::CoarseBenign } CoarseClinicalSignificance::Uncertain => { - crate::pbs::annonars::clinvar::v1::per_gene::CoarseClinicalSignificance::CoarseUncertain + crate::pbs::clinvar::per_gene::CoarseClinicalSignificance::CoarseUncertain } CoarseClinicalSignificance::Pathogenic => { - crate::pbs::annonars::clinvar::v1::per_gene::CoarseClinicalSignificance::CoarsePathogenic + crate::pbs::clinvar::per_gene::CoarseClinicalSignificance::CoarsePathogenic } } } diff --git a/src/clinvar_minimal/cli/import.rs b/src/clinvar_minimal/cli/import.rs index 0913bcda..8e98099b 100644 --- a/src/clinvar_minimal/cli/import.rs +++ b/src/clinvar_minimal/cli/import.rs @@ -8,7 +8,7 @@ use prost::Message; use crate::{ clinvar_minimal, common::{self, keys}, - pbs::annonars::clinvar::v1::minimal::ReferenceAssertion, + pbs::clinvar::minimal::ReferenceAssertion, }; /// Command line arguments for `clinvar-minimal import` sub command. @@ -74,10 +74,9 @@ fn jsonl_import( sequence_location, .. } = record; - let clinical_significance: crate::pbs::annonars::clinvar::v1::minimal::ClinicalSignificance = + let clinical_significance: crate::pbs::clinvar::minimal::ClinicalSignificance = clinical_significance.into(); - let review_status: crate::pbs::annonars::clinvar::v1::minimal::ReviewStatus = - review_status.into(); + let review_status: crate::pbs::clinvar::minimal::ReviewStatus = review_status.into(); let clinvar_minimal::cli::reading::SequenceLocation { assembly, chr, @@ -111,10 +110,9 @@ fn jsonl_import( db.put_cf(&cf_by_accession, vcv.as_bytes(), &key)?; let record = if let Some(data) = data { - let mut record = - crate::pbs::annonars::clinvar::v1::minimal::Record::decode(&data[..])?; + let mut record = crate::pbs::clinvar::minimal::Record::decode(&data[..])?; record.reference_assertions.push( - crate::pbs::annonars::clinvar::v1::minimal::ReferenceAssertion { + crate::pbs::clinvar::minimal::ReferenceAssertion { rcv, title, clinical_significance: clinical_significance.into(), @@ -126,7 +124,7 @@ fn jsonl_import( .sort_by_key(|a| (a.clinical_significance, a.review_status)); record } else { - crate::pbs::annonars::clinvar::v1::minimal::Record { + crate::pbs::clinvar::minimal::Record { release: assembly, chromosome: chr, start, diff --git a/src/clinvar_minimal/cli/query.rs b/src/clinvar_minimal/cli/query.rs index 5af61fe7..4039f8ac 100644 --- a/src/clinvar_minimal/cli/query.rs +++ b/src/clinvar_minimal/cli/query.rs @@ -93,7 +93,7 @@ pub fn open_rocksdb_from_args( fn print_record( out_writer: &mut Box, output_format: common::cli::OutputFormat, - value: &crate::pbs::annonars::clinvar::v1::minimal::Record, + value: &crate::pbs::clinvar::minimal::Record, ) -> Result<(), anyhow::Error> { match output_format { common::cli::OutputFormat::Jsonl => { @@ -110,7 +110,7 @@ pub fn query_for_variant( meta: &Meta, db: &rocksdb::DBWithThreadMode, cf_data: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { // Split off the genome release (checked) and convert to key as used in database. let query = spdi::Var { sequence: extract_chrom::from_var(variant, Some(&meta.genome_release))?, @@ -126,10 +126,8 @@ pub fn query_for_variant( raw_value .map(|raw_value| { // Decode via prost. - crate::pbs::annonars::clinvar::v1::minimal::Record::decode(&mut std::io::Cursor::new( - &raw_value, - )) - .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) + crate::pbs::clinvar::minimal::Record::decode(&mut std::io::Cursor::new(&raw_value)) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) }) .transpose() } @@ -140,7 +138,7 @@ pub fn query_for_accession( db: &rocksdb::DBWithThreadMode, cf_data: &Arc, cf_data_by_rsid: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { let accession = accession.to_uppercase(); // VCV*, RCV* // First, lookup accession. @@ -156,10 +154,8 @@ pub fn query_for_accession( raw_value .map(|raw_value| { // Decode via prost. - crate::pbs::annonars::clinvar::v1::minimal::Record::decode(&mut std::io::Cursor::new( - &raw_value, - )) - .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) + crate::pbs::clinvar::minimal::Record::decode(&mut std::io::Cursor::new(&raw_value)) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) }) .transpose() } @@ -250,7 +246,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> } } - let record = crate::pbs::annonars::clinvar::v1::minimal::Record::decode( + let record = crate::pbs::clinvar::minimal::Record::decode( &mut std::io::Cursor::new(&raw_value), ) .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; diff --git a/src/clinvar_minimal/cli/reading.rs b/src/clinvar_minimal/cli/reading.rs index e119130a..88fcf443 100644 --- a/src/clinvar_minimal/cli/reading.rs +++ b/src/clinvar_minimal/cli/reading.rs @@ -71,23 +71,15 @@ impl<'de> Deserialize<'de> for VariantType { } } -impl From for crate::pbs::annonars::clinvar::v1::minimal::VariantType { +impl From for crate::pbs::clinvar::minimal::VariantType { fn from(value: VariantType) -> Self { match value { - VariantType::Deletion => { - crate::pbs::annonars::clinvar::v1::minimal::VariantType::Deletion - } - VariantType::Duplication => { - crate::pbs::annonars::clinvar::v1::minimal::VariantType::Duplication - } - VariantType::Indel => crate::pbs::annonars::clinvar::v1::minimal::VariantType::Indel, - VariantType::Insertion => { - crate::pbs::annonars::clinvar::v1::minimal::VariantType::Insertion - } - VariantType::Inversion => { - crate::pbs::annonars::clinvar::v1::minimal::VariantType::Inversion - } - VariantType::Snv => crate::pbs::annonars::clinvar::v1::minimal::VariantType::Snv, + VariantType::Deletion => crate::pbs::clinvar::minimal::VariantType::Deletion, + VariantType::Duplication => crate::pbs::clinvar::minimal::VariantType::Duplication, + VariantType::Indel => crate::pbs::clinvar::minimal::VariantType::Indel, + VariantType::Insertion => crate::pbs::clinvar::minimal::VariantType::Insertion, + VariantType::Inversion => crate::pbs::clinvar::minimal::VariantType::Inversion, + VariantType::Snv => crate::pbs::clinvar::minimal::VariantType::Snv, } } } @@ -167,25 +159,23 @@ impl<'de> Deserialize<'de> for ClinicalSignificance { } } -impl From - for crate::pbs::annonars::clinvar::v1::minimal::ClinicalSignificance -{ +impl From for crate::pbs::clinvar::minimal::ClinicalSignificance { fn from(value: ClinicalSignificance) -> Self { match value { ClinicalSignificance::Pathogenic => { - crate::pbs::annonars::clinvar::v1::minimal::ClinicalSignificance::Pathogenic + crate::pbs::clinvar::minimal::ClinicalSignificance::Pathogenic } ClinicalSignificance::LikelyPathogenic => { - crate::pbs::annonars::clinvar::v1::minimal::ClinicalSignificance::LikelyPathogenic + crate::pbs::clinvar::minimal::ClinicalSignificance::LikelyPathogenic } ClinicalSignificance::UncertainSignificance => { - crate::pbs::annonars::clinvar::v1::minimal::ClinicalSignificance::UncertainSignificance + crate::pbs::clinvar::minimal::ClinicalSignificance::UncertainSignificance } ClinicalSignificance::LikelyBenign => { - crate::pbs::annonars::clinvar::v1::minimal::ClinicalSignificance::LikelyBenign + crate::pbs::clinvar::minimal::ClinicalSignificance::LikelyBenign } ClinicalSignificance::Benign => { - crate::pbs::annonars::clinvar::v1::minimal::ClinicalSignificance::Benign + crate::pbs::clinvar::minimal::ClinicalSignificance::Benign } } } @@ -287,24 +277,24 @@ impl<'de> Deserialize<'de> for ReviewStatus { } } -impl From for crate::pbs::annonars::clinvar::v1::minimal::ReviewStatus { +impl From for crate::pbs::clinvar::minimal::ReviewStatus { fn from(value: ReviewStatus) -> Self { match value { - ReviewStatus::NoAssertionProvided => crate::pbs::annonars::clinvar::v1::minimal::ReviewStatus::NoAssertionProvided, + ReviewStatus::NoAssertionProvided => crate::pbs::clinvar::minimal::ReviewStatus::NoAssertionProvided, ReviewStatus::NoAssertionCriteriaProvided => { - crate::pbs::annonars::clinvar::v1::minimal::ReviewStatus::NoAssertionCriteriaProvided + crate::pbs::clinvar::minimal::ReviewStatus::NoAssertionCriteriaProvided } ReviewStatus::CriteriaProvidedConflictingInterpretations => { - crate::pbs::annonars::clinvar::v1::minimal::ReviewStatus::CriteriaProvidedConflictingInterpretations + crate::pbs::clinvar::minimal::ReviewStatus::CriteriaProvidedConflictingInterpretations } ReviewStatus::CriteriaProvidedSingleSubmitter => { - crate::pbs::annonars::clinvar::v1::minimal::ReviewStatus::CriteriaProvidedSingleSubmitter + crate::pbs::clinvar::minimal::ReviewStatus::CriteriaProvidedSingleSubmitter } ReviewStatus::CriteriaProvidedMultipleSubmittersNoConflicts => { - crate::pbs::annonars::clinvar::v1::minimal::ReviewStatus::CriteriaProvidedMultipleSubmittersNoConflicts + crate::pbs::clinvar::minimal::ReviewStatus::CriteriaProvidedMultipleSubmittersNoConflicts } - ReviewStatus::ReviewedByExpertPanel => crate::pbs::annonars::clinvar::v1::minimal::ReviewStatus::ReviewedByExpertPanel, - ReviewStatus::PracticeGuideline => crate::pbs::annonars::clinvar::v1::minimal::ReviewStatus::PracticeGuideline, + ReviewStatus::ReviewedByExpertPanel => crate::pbs::clinvar::minimal::ReviewStatus::ReviewedByExpertPanel, + ReviewStatus::PracticeGuideline => crate::pbs::clinvar::minimal::ReviewStatus::PracticeGuideline, } } } diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_all.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_all.snap index 7cec8d3c..3523b9f0 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_all.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_all.snap @@ -2,73 +2,73 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95227055,"stop":95227055,"reference":"A","alternative":"G","vcv":"VCV001309690","reference_assertions":[{"rcv":"RCV001756758","title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95227093,"stop":95227093,"reference":"T","alternative":"C","vcv":"VCV000792370","reference_assertions":[{"rcv":"RCV000975465","title":"NM_014305.4(TGDS):c.996A>G (p.Arg332=) AND not provided","clinical_significance":3,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95227114,"stop":95227114,"reference":"G","alternative":"A","vcv":"VCV000720702","reference_assertions":[{"rcv":"RCV000894054","title":"NM_014305.4(TGDS):c.983-8C>T AND not provided","clinical_significance":3,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95227128,"stop":95227129,"reference":"C","alternative":"CA","vcv":"VCV001261515","reference_assertions":[{"rcv":"RCV001674093","title":"NM_014305.4(TGDS):c.983-34dup AND not provided","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95227129,"stop":95227129,"reference":"CA","alternative":"C","vcv":"VCV001244089","reference_assertions":[{"rcv":"RCV001648355","title":"NM_014305.4(TGDS):c.983-23del AND not provided","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95227139,"stop":95227141,"reference":"AAAG","alternative":"A","vcv":"VCV001282312","reference_assertions":[{"rcv":"RCV001695704","title":"NM_014305.4(TGDS):c.983-35_983-33del AND not provided","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95227140,"stop":95227141,"reference":"AAG","alternative":"A","vcv":"VCV001228958","reference_assertions":[{"rcv":"RCV001616589","title":"NM_014305.4(TGDS):c.983-35_983-34del AND not provided","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95227340,"stop":95227340,"reference":"C","alternative":"T","vcv":"VCV001288190","reference_assertions":[{"rcv":"RCV001707165","title":"NM_014305.4(TGDS):c.983-234G>A AND not provided","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95228593,"stop":95228593,"reference":"A","alternative":"G","vcv":"VCV001575281","reference_assertions":[{"rcv":"RCV002083442","title":"NM_014305.4(TGDS):c.957T>C (p.Pro319=) AND not provided","clinical_significance":3,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95228658,"stop":95228658,"reference":"T","alternative":"C","vcv":"VCV000162460","reference_assertions":[{"rcv":"RCV000149822","title":"NM_014305.4(TGDS):c.892A>G (p.Asn298Asp) AND Catel-Manzke syndrome","clinical_significance":0,"review_status":5}]} -{"release":"GRCh37","chromosome":"13","start":95228667,"stop":95228667,"reference":"T","alternative":"G","vcv":"VCV002437068","reference_assertions":[{"rcv":"RCV003140988","title":"NM_014305.4(TGDS):c.885-2A>C AND Catel-Manzke syndrome","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95229675,"stop":95229675,"reference":"C","alternative":"G","vcv":"VCV002278206","reference_assertions":[{"rcv":"RCV002822699","title":"NM_014305.4(TGDS):c.834G>C (p.Glu278Asp) AND Inborn genetic diseases","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95229697,"stop":95229697,"reference":"A","alternative":"G","vcv":"VCV001617317","reference_assertions":[{"rcv":"RCV002076513","title":"NM_014305.4(TGDS):c.826-14T>C AND not provided","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95229735,"stop":95229735,"reference":"A","alternative":"G","vcv":"VCV001260430","reference_assertions":[{"rcv":"RCV001669248","title":"NM_014305.4(TGDS):c.826-52T>C AND not provided","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95230107,"stop":95230111,"reference":"CTTAAT","alternative":"C","vcv":"VCV001266539","reference_assertions":[{"rcv":"RCV001676362","title":"NM_014305.4(TGDS):c.825+148_825+152del AND not provided","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95230255,"stop":95230255,"reference":"A","alternative":"T","vcv":"VCV001523917","reference_assertions":[{"rcv":"RCV002031328","title":"NM_014305.4(TGDS):c.825+4T>A AND not provided","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95230291,"stop":95230291,"reference":"C","alternative":"T","vcv":"VCV002246034","reference_assertions":[{"rcv":"RCV002738091","title":"NM_014305.4(TGDS):c.793G>A (p.Val265Ile) AND Inborn genetic diseases","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95230343,"stop":95230343,"reference":"T","alternative":"C","vcv":"VCV001932516","reference_assertions":[{"rcv":"RCV002605801","title":"NM_014305.4(TGDS):c.741A>G (p.Lys247=) AND not provided","clinical_significance":3,"review_status":3}]} 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-{"release":"GRCh37","chromosome":"13","start":95230624,"stop":95230625,"reference":"A","alternative":"AAGTGGCAAACATATT","vcv":"VCV001241711","reference_assertions":[{"rcv":"RCV001645456","title":"NM_014305.4(TGDS):c.660-201_660-200insCACTAATATGTTTGC AND not provided","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95230877,"stop":95230877,"reference":"G","alternative":"A","vcv":"VCV001244948","reference_assertions":[{"rcv":"RCV001649156","title":"NM_014305.4(TGDS):c.659+107C>T AND not provided","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95230976,"stop":95230976,"reference":"T","alternative":"C","vcv":"VCV000738027","reference_assertions":[{"rcv":"RCV000913870","title":"NM_014305.4(TGDS):c.659+8A>G AND not provided","clinical_significance":3,"review_status":3}]} 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genetic diseases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95233400,"stop":95233400,"reference":"G","alternative":"T","vcv":"VCV001480501","referenceAssertions":[{"rcv":"RCV001993954","title":"NM_014305.4(TGDS):c.500C>A (p.Ala167Glu) AND not provided","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95233409,"stop":95233409,"reference":"T","alternative":"G","vcv":"VCV002437069","referenceAssertions":[{"rcv":"RCV003140989","title":"NM_014305.4(TGDS):c.491A>C (p.Asn164Thr) AND Catel-Manzke syndrome","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} 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+{"release":"GRCh37","chromosome":"13","start":95243126,"stop":95243126,"reference":"A","alternative":"C","vcv":"VCV000162458","referenceAssertions":[{"rcv":"RCV000149820","title":"NM_014305.4(TGDS):c.294T>G (p.Phe98Leu) AND Catel-Manzke syndrome","reviewStatus":"NO_ASSERTION_CRITERIA_PROVIDED"}]} +{"release":"GRCh37","chromosome":"13","start":95243134,"stop":95243134,"reference":"G","alternative":"T","vcv":"VCV000521407","referenceAssertions":[{"rcv":"RCV000622534","title":"NM_014305.4(TGDS):c.286C>A (p.Leu96Ile) AND Inborn genetic diseases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95243135,"stop":95243135,"reference":"T","alternative":"C","vcv":"VCV002160065","referenceAssertions":[{"rcv":"RCV003075760","title":"NM_014305.4(TGDS):c.285A>G (p.Val95=) AND not provided","clinicalSignificance":"LIKELY_BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95243151,"stop":95243151,"reference":"T","alternative":"C","vcv":"VCV000162457","referenceAssertions":[{"rcv":"RCV000149819","title":"NM_014305.4(TGDS):c.269A>G (p.Glu90Gly) AND Catel-Manzke syndrome","reviewStatus":"NO_ASSERTION_CRITERIA_PROVIDED"}]} +{"release":"GRCh37","chromosome":"13","start":95243156,"stop":95243156,"reference":"T","alternative":"C","vcv":"VCV000753804","referenceAssertions":[{"rcv":"RCV000931075","title":"NM_014305.4(TGDS):c.264A>G (p.Glu88=) AND not provided","clinicalSignificance":"LIKELY_BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95243270,"stop":95243270,"reference":"G","alternative":"A","vcv":"VCV001289640","referenceAssertions":[{"rcv":"RCV001714148","title":"NM_014305.4(TGDS):c.223-73C>T AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95244490,"stop":95244490,"reference":"C","alternative":"T","vcv":"VCV002066159","referenceAssertions":[{"rcv":"RCV002966071","title":"NM_014305.4(TGDS):c.222+5G>A AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95244537,"stop":95244537,"reference":"A","alternative":"T","vcv":"VCV000521406","referenceAssertions":[{"rcv":"RCV000624236","title":"NM_014305.4(TGDS):c.180T>A (p.Asn60Lys) AND Inborn genetic diseases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95244548,"stop":95244548,"reference":"T","alternative":"A","vcv":"VCV001475013","referenceAssertions":[{"rcv":"RCV001973800","title":"NM_014305.4(TGDS):c.169A>T (p.Ser57Cys) AND not provided","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95244583,"stop":95244583,"reference":"G","alternative":"C","vcv":"VCV001897819","referenceAssertions":[{"rcv":"RCV002569866","title":"NM_014305.4(TGDS):c.154-20C>G AND not provided","clinicalSignificance":"LIKELY_BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95246122,"stop":95246122,"reference":"T","alternative":"C","vcv":"VCV001583659","referenceAssertions":[{"rcv":"RCV002093757","title":"NM_014305.4(TGDS):c.126A>G (p.Pro42=) AND not provided","clinicalSignificance":"LIKELY_BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95246151,"stop":95246151,"reference":"T","alternative":"C","vcv":"VCV000747821","referenceAssertions":[{"rcv":"RCV000924565","title":"NM_014305.4(TGDS):c.97A>G (p.Met33Val) AND not provided","clinicalSignificance":"LIKELY_BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95246440,"stop":95246440,"reference":"C","alternative":"T","vcv":"VCV001244800","referenceAssertions":[{"rcv":"RCV001649008","title":"NM_014305.4(TGDS):c.87-279G>A AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248289,"stop":95248289,"reference":"C","alternative":"T","vcv":"VCV001601222","referenceAssertions":[{"rcv":"RCV002136792","title":"NM_014305.4(TGDS):c.86+16G>A AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248302,"stop":95248302,"reference":"T","alternative":"G","vcv":"VCV001900006","referenceAssertions":[{"rcv":"RCV002576293","title":"NM_014305.4(TGDS):c.86+3A>C AND not provided","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248348,"stop":95248348,"reference":"C","alternative":"T","vcv":"VCV000777433","referenceAssertions":[{"rcv":"RCV000957904","title":"NM_014305.4(TGDS):c.43G>A (p.Gly15Ser) AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248354,"stop":95248354,"reference":"G","alternative":"A","vcv":"VCV002476739","referenceAssertions":[{"rcv":"RCV003198638","title":"NM_014305.4(TGDS):c.37C>T (p.Pro13Ser) AND Inborn genetic diseases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248366,"stop":95248366,"reference":"G","alternative":"A","vcv":"VCV002564467","referenceAssertions":[{"rcv":"RCV003310965","title":"NM_014305.4(TGDS):c.25C>T (p.Pro9Ser) AND Inborn genetic diseases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248379,"stop":95248379,"reference":"C","alternative":"T","vcv":"VCV000778479","referenceAssertions":[{"rcv":"RCV000959128","title":"NM_014305.4(TGDS):c.12G>A (p.Ala4=) AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248566,"stop":95248566,"reference":"C","alternative":"T","vcv":"VCV001255243","referenceAssertions":[{"rcv":"RCV001653352","title":"NC_000013.11:g.94596312C>T AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248751,"stop":95248751,"reference":"C","alternative":"T","vcv":"VCV001269376","referenceAssertions":[{"rcv":"RCV001681009","title":"NC_000013.11:g.94596497C>T AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@RCV001679107.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@RCV001679107.snap index 1812f548..56c849b8 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@RCV001679107.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@RCV001679107.snap @@ -2,5 +2,5 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95235557,"stop":95235557,"reference":"A","alternative":"G","vcv":"VCV001273284","reference_assertions":[{"rcv":"RCV001679107","title":"NM_014305.4(TGDS):c.314-67T>C AND not provided","clinical_significance":4,"review_status":3}]} +{"release":"GRCh37","chromosome":"13","start":95235557,"stop":95235557,"reference":"A","alternative":"G","vcv":"VCV001273284","referenceAssertions":[{"rcv":"RCV001679107","title":"NM_014305.4(TGDS):c.314-67T>C AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@VCV001307216.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@VCV001307216.snap index 97dba2bf..98cdeac3 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@VCV001307216.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@VCV001307216.snap @@ -2,5 +2,5 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95232181,"stop":95232181,"reference":"A","alternative":"C","vcv":"VCV001307216","reference_assertions":[{"rcv":"RCV001760634","title":"NM_014305.4(TGDS):c.582T>G (p.Ser194Arg) AND not provided","clinical_significance":2,"review_status":3}]} +{"release":"GRCh37","chromosome":"13","start":95232181,"stop":95232181,"reference":"A","alternative":"C","vcv":"VCV001307216","referenceAssertions":[{"rcv":"RCV001760634","title":"NM_014305.4(TGDS):c.582T>G (p.Ser194Arg) AND not provided","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_all.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_all.snap index 7cec8d3c..3523b9f0 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_all.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_all.snap @@ -2,73 +2,73 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95227055,"stop":95227055,"reference":"A","alternative":"G","vcv":"VCV001309690","reference_assertions":[{"rcv":"RCV001756758","title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"13","start":95227093,"stop":95227093,"reference":"T","alternative":"C","vcv":"VCV000792370","reference_assertions":[{"rcv":"RCV000975465","title":"NM_014305.4(TGDS):c.996A>G (p.Arg332=) AND not provided","clinical_significance":3,"review_status":3}]} 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provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248354,"stop":95248354,"reference":"G","alternative":"A","vcv":"VCV002476739","referenceAssertions":[{"rcv":"RCV003198638","title":"NM_014305.4(TGDS):c.37C>T (p.Pro13Ser) AND Inborn genetic diseases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248366,"stop":95248366,"reference":"G","alternative":"A","vcv":"VCV002564467","referenceAssertions":[{"rcv":"RCV003310965","title":"NM_014305.4(TGDS):c.25C>T (p.Pro9Ser) AND Inborn genetic diseases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248379,"stop":95248379,"reference":"C","alternative":"T","vcv":"VCV000778479","referenceAssertions":[{"rcv":"RCV000959128","title":"NM_014305.4(TGDS):c.12G>A (p.Ala4=) AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248566,"stop":95248566,"reference":"C","alternative":"T","vcv":"VCV001255243","referenceAssertions":[{"rcv":"RCV001653352","title":"NC_000013.11:g.94596312C>T AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"13","start":95248751,"stop":95248751,"reference":"C","alternative":"T","vcv":"VCV001269376","referenceAssertions":[{"rcv":"RCV001681009","title":"NC_000013.11:g.94596497C>T AND not provided","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_first.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_first.snap index 3755625d..ffd6dd4c 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_first.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_first.snap @@ -2,5 +2,5 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95227055,"stop":95227055,"reference":"A","alternative":"G","vcv":"VCV001309690","reference_assertions":[{"rcv":"RCV001756758","title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided","clinical_significance":2,"review_status":3}]} +{"release":"GRCh37","chromosome":"13","start":95227055,"stop":95227055,"reference":"A","alternative":"G","vcv":"VCV001309690","referenceAssertions":[{"rcv":"RCV001756758","title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_second.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_second.snap index e9836973..3aa9ff21 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_second.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_second.snap @@ -2,5 +2,5 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95227093,"stop":95227093,"reference":"T","alternative":"C","vcv":"VCV000792370","reference_assertions":[{"rcv":"RCV000975465","title":"NM_014305.4(TGDS):c.996A>G (p.Arg332=) AND not provided","clinical_significance":3,"review_status":3}]} +{"release":"GRCh37","chromosome":"13","start":95227093,"stop":95227093,"reference":"T","alternative":"C","vcv":"VCV000792370","referenceAssertions":[{"rcv":"RCV000975465","title":"NM_014305.4(TGDS):c.996A>G (p.Arg332=) AND not provided","clinicalSignificance":"LIKELY_BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_var_single.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_var_single.snap index 3755625d..ffd6dd4c 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_var_single.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_var_single.snap @@ -2,5 +2,5 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95227055,"stop":95227055,"reference":"A","alternative":"G","vcv":"VCV001309690","reference_assertions":[{"rcv":"RCV001756758","title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided","clinical_significance":2,"review_status":3}]} +{"release":"GRCh37","chromosome":"13","start":95227055,"stop":95227055,"reference":"A","alternative":"G","vcv":"VCV001309690","referenceAssertions":[{"rcv":"RCV001756758","title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_sv/cli/import.rs b/src/clinvar_sv/cli/import.rs index 63d988db..e01b68a2 100644 --- a/src/clinvar_sv/cli/import.rs +++ b/src/clinvar_sv/cli/import.rs @@ -75,10 +75,9 @@ fn jsonl_import( variant_type, .. } = record; - let clinical_significance: crate::pbs::annonars::clinvar::v1::minimal::ClinicalSignificance = + let clinical_significance: crate::pbs::clinvar::minimal::ClinicalSignificance = clinical_significance.into(); - let review_status: crate::pbs::annonars::clinvar::v1::minimal::ReviewStatus = - review_status.into(); + let review_status: crate::pbs::clinvar::minimal::ReviewStatus = review_status.into(); let clinvar_minimal::cli::reading::SequenceLocation { assembly, chr, @@ -154,10 +153,9 @@ fn jsonl_import( } Ok(data) => { let record = if let Some(data) = data { - let mut record = - crate::pbs::annonars::clinvar::v1::sv::Record::decode(&data[..])?; + let mut record = crate::pbs::clinvar::sv::Record::decode(&data[..])?; record.reference_assertions.push( - crate::pbs::annonars::clinvar::v1::minimal::ReferenceAssertion { + crate::pbs::clinvar::minimal::ReferenceAssertion { rcv: rcv.clone(), title, clinical_significance: clinical_significance.into(), @@ -169,7 +167,7 @@ fn jsonl_import( .sort_by_key(|a| (a.clinical_significance, a.review_status)); record } else { - crate::pbs::annonars::clinvar::v1::sv::Record { + crate::pbs::clinvar::sv::Record { release: assembly, chromosome: chr, start, @@ -178,7 +176,7 @@ fn jsonl_import( alternative: alternate_allele_vcf, vcv: vcv.clone(), reference_assertions: vec![ - crate::pbs::annonars::clinvar::v1::minimal::ReferenceAssertion { + crate::pbs::clinvar::minimal::ReferenceAssertion { rcv: rcv.clone(), title, clinical_significance: clinical_significance.into(), @@ -189,9 +187,8 @@ fn jsonl_import( inner_stop, outer_start, outer_stop, - variant_type: crate::pbs::annonars::clinvar::v1::minimal::VariantType::from( - variant_type, - ) as i32, + variant_type: crate::pbs::clinvar::minimal::VariantType::from(variant_type) + as i32, } }; let buf = record.encode_to_vec(); diff --git a/src/clinvar_sv/cli/query.rs b/src/clinvar_sv/cli/query.rs index 9fc9ce23..8b817589 100644 --- a/src/clinvar_sv/cli/query.rs +++ b/src/clinvar_sv/cli/query.rs @@ -109,7 +109,7 @@ pub fn open_rocksdb_from_args( fn print_record( out_writer: &mut Box, output_format: common::cli::OutputFormat, - value: &crate::pbs::annonars::clinvar::v1::sv::Record, + value: &crate::pbs::clinvar::sv::Record, ) -> Result<(), anyhow::Error> { match output_format { common::cli::OutputFormat::Jsonl => { @@ -126,7 +126,7 @@ pub fn query_for_accession( db: &rocksdb::DBWithThreadMode, cf_data: &Arc, cf_by_rcv: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { // Execute query. tracing::debug!("accession = {:?}", &accession); let vcv = if accession.starts_with("VCV") { @@ -145,10 +145,8 @@ pub fn query_for_accession( raw_value .map(|raw_value| { // Decode via prost. - 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)) + crate::pbs::clinvar::sv::Record::decode(&mut std::io::Cursor::new(&raw_value)) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) }) .transpose() } @@ -166,10 +164,9 @@ fn print_all( 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))?; + let record = + crate::pbs::clinvar::sv::Record::decode(&mut std::io::Cursor::new(&raw_value)) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; print_record(out_writer, out_format, &record)?; iter.next(); } else { @@ -241,13 +238,12 @@ 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))?; + let record = + crate::pbs::clinvar::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 crate::pbs::annonars::clinvar::v1::sv::Record { + let crate::pbs::clinvar::sv::Record { chromosome, start, stop, @@ -278,7 +274,7 @@ impl IntervalTrees { pub fn query( &self, range: &spdi::Range, - ) -> Result, anyhow::Error> { + ) -> Result, anyhow::Error> { 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) @@ -288,7 +284,7 @@ impl IntervalTrees { 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())? { - let record = crate::pbs::annonars::clinvar::v1::sv::Record::decode( + let record = crate::pbs::clinvar::sv::Record::decode( &mut std::io::Cursor::new(&raw_value), ) .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_all.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_all.snap index 8ad20402..5609f83c 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_all.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_all.snap @@ -2,24 +2,24 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"X","start":155210040,"stop":155242832,"reference":null,"alternative":null,"inner_start":155210040,"inner_stop":null,"outer_start":155242832,"outer_stop":null,"variant_type":0,"vcv":"VCV000057500","reference_assertions":[{"rcv":"RCV000051210","title":"GRCh38/hg38 Xq28(chrX:155980375-156013167)x0 AND See cases","clinical_significance":4,"review_status":3}]} -{"release":"GRCh37","chromosome":"7","start":64691936,"stop":64866073,"reference":null,"alternative":null,"inner_start":64691936,"inner_stop":null,"outer_start":64866073,"outer_stop":null,"variant_type":0,"vcv":"VCV000057566","reference_assertions":[{"rcv":"RCV000051294","title":"GRCh38/hg38 7q11.21(chr7:65231558-65401160)x1 AND See cases","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"reference":null,"alternative":null,"inner_start":34150132,"inner_stop":null,"outer_start":34182300,"outer_stop":null,"variant_type":0,"vcv":"VCV000057627","reference_assertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","clinical_significance":0,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":73055208,"stop":73059460,"reference":null,"alternative":null,"inner_start":73055208,"inner_stop":null,"outer_start":73059460,"outer_stop":null,"variant_type":0,"vcv":"VCV000057653","reference_assertions":[{"rcv":"RCV000051388","title":"GRCh38/hg38 Xq13.2(chrX:73835373-73839625)x1 AND See cases","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":78605903,"stop":79090819,"reference":null,"alternative":null,"inner_start":78605903,"inner_stop":null,"outer_start":79090819,"outer_stop":null,"variant_type":0,"vcv":"VCV000057654","reference_assertions":[{"rcv":"RCV000051389","title":"GRCh38/hg38 Xq21.1(chrX:79350406-79835322)x0 AND See cases","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":89330088,"stop":89853974,"reference":null,"alternative":null,"inner_start":89330088,"inner_stop":null,"outer_start":89853974,"outer_stop":null,"variant_type":0,"vcv":"VCV000057686","reference_assertions":[{"rcv":"RCV000051424","title":"GRCh38/hg38 Xq21.31(chrX:90075089-90598975)x1 AND See cases","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":102885179,"stop":102967225,"reference":null,"alternative":null,"inner_start":102885179,"inner_stop":null,"outer_start":102967225,"outer_stop":null,"variant_type":0,"vcv":"VCV000057688","reference_assertions":[{"rcv":"RCV000051426","title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"1","start":196757278,"stop":196796716,"reference":null,"alternative":null,"inner_start":196757278,"inner_stop":null,"outer_start":196796716,"outer_stop":null,"variant_type":0,"vcv":"VCV000058538","reference_assertions":[{"rcv":"RCV000052307","title":"GRCh38/hg38 1q31.3(chr1:196788148-196827586)x1 AND See cases","clinical_significance":0,"review_status":3}]} -{"release":"GRCh37","chromosome":"7","start":27194426,"stop":27461954,"reference":null,"alternative":null,"inner_start":27194426,"inner_stop":null,"outer_start":27461954,"outer_stop":null,"variant_type":0,"vcv":"VCV000058544","reference_assertions":[{"rcv":"RCV000052313","title":"GRCh38/hg38 7p15.2(chr7:27154807-27422335)x1 AND See cases","clinical_significance":0,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":8595045,"stop":8704378,"reference":null,"alternative":null,"inner_start":8595045,"inner_stop":null,"outer_start":8704378,"outer_stop":null,"variant_type":1,"vcv":"VCV000058565","reference_assertions":[{"rcv":"RCV000052334","title":"GRCh38/hg38 Xp22.31(chrX:8627004-8736337)x2 AND See cases","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":8596894,"stop":8705494,"reference":null,"alternative":null,"inner_start":8596894,"inner_stop":null,"outer_start":8705494,"outer_stop":null,"variant_type":1,"vcv":"VCV000058566","reference_assertions":[{"rcv":"RCV000052337","title":"GRCh38/hg38 Xp22.31(chrX:8628853-8737453)x2 AND See cases","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":8597747,"stop":8674356,"reference":null,"alternative":null,"inner_start":8597747,"inner_stop":null,"outer_start":8674356,"outer_stop":null,"variant_type":1,"vcv":"VCV000058567","reference_assertions":[{"rcv":"RCV000052338","title":"GRCh38/hg38 Xp22.31(chrX:8629706-8706315)x3 AND See cases","clinical_significance":2,"review_status":5}]} -{"release":"GRCh37","chromosome":"X","start":28777940,"stop":29112528,"reference":null,"alternative":null,"inner_start":28777940,"inner_stop":null,"outer_start":29112528,"outer_stop":null,"variant_type":1,"vcv":"VCV000058611","reference_assertions":[{"rcv":"RCV000052386","title":"GRCh38/hg38 Xp21.3(chrX:28759823-29094411)x2 AND See cases","clinical_significance":0,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":29731388,"stop":29759068,"reference":null,"alternative":null,"inner_start":29731388,"inner_stop":null,"outer_start":29759068,"outer_stop":null,"variant_type":1,"vcv":"VCV000058612","reference_assertions":[{"rcv":"RCV000052387","title":"GRCh38/hg38 Xp21.2(chrX:29713271-29740951)x3 AND See cases","clinical_significance":0,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":32680483,"stop":32777081,"reference":null,"alternative":null,"inner_start":32680483,"inner_stop":null,"outer_start":32777081,"outer_stop":null,"variant_type":1,"vcv":"VCV000058614","reference_assertions":[{"rcv":"RCV000052389","title":"GRCh38/hg38 Xp21.1(chrX:32662366-32758964)x2 AND See cases","clinical_significance":0,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":105135228,"stop":105669012,"reference":null,"alternative":null,"inner_start":105135228,"inner_stop":null,"outer_start":105669012,"outer_stop":null,"variant_type":1,"vcv":"VCV000058665","reference_assertions":[{"rcv":"RCV000052442","title":"GRCh38/hg38 Xq22.3(chrX:105891235-106425782)x2 AND See cases","clinical_significance":0,"review_status":3}]} -{"release":"GRCh37","chromosome":"Y","start":2651665,"stop":4972987,"reference":null,"alternative":null,"inner_start":2651665,"inner_stop":null,"outer_start":4972987,"outer_stop":null,"variant_type":1,"vcv":"VCV000058795","reference_assertions":[{"rcv":"RCV000052584","title":"GRCh38/hg38 Yp11.2(chrY:2783624-5104946)x2 AND See cases","clinical_significance":0,"review_status":3}]} -{"release":"GRCh37","chromosome":"Y","start":2654967,"stop":2862993,"reference":null,"alternative":null,"inner_start":2654967,"inner_stop":null,"outer_start":2862993,"outer_stop":null,"variant_type":1,"vcv":"VCV000058800","reference_assertions":[{"rcv":"RCV000052589","title":"GRCh38/hg38 Yp11.2(chrY:2786926-2994952)x2 AND See cases","clinical_significance":0,"review_status":3}]} -{"release":"GRCh37","chromosome":"19","start":54104552,"stop":54276282,"reference":null,"alternative":null,"inner_start":54104552,"inner_stop":null,"outer_start":54276282,"outer_stop":null,"variant_type":1,"vcv":"VCV000058805","reference_assertions":[{"rcv":"RCV000052594","title":"GRCh38/hg38 19q13.42(chr19:53601298-53773028)x3 AND See cases","clinical_significance":2,"review_status":3}]} -{"release":"GRCh37","chromosome":"X","start":8595045,"stop":8704378,"reference":null,"alternative":null,"inner_start":8595045,"inner_stop":null,"outer_start":8704378,"outer_stop":null,"variant_type":1,"vcv":"VCV000144128","reference_assertions":[{"rcv":"RCV000052335","title":"GRCh38/hg38 Xp22.31(chrX:8627004-8736337)x3 AND See cases","clinical_significance":2,"review_status":3}]} +{"release":"GRCh37","chromosome":"X","start":155210040,"stop":155242832,"innerStart":155210040,"outerStart":155242832,"vcv":"VCV000057500","referenceAssertions":[{"rcv":"RCV000051210","title":"GRCh38/hg38 Xq28(chrX:155980375-156013167)x0 AND See cases","clinicalSignificance":"BENIGN","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"7","start":64691936,"stop":64866073,"innerStart":64691936,"outerStart":64866073,"vcv":"VCV000057566","referenceAssertions":[{"rcv":"RCV000051294","title":"GRCh38/hg38 7q11.21(chr7:65231558-65401160)x1 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"innerStart":34150132,"outerStart":34182300,"vcv":"VCV000057627","referenceAssertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":73055208,"stop":73059460,"innerStart":73055208,"outerStart":73059460,"vcv":"VCV000057653","referenceAssertions":[{"rcv":"RCV000051388","title":"GRCh38/hg38 Xq13.2(chrX:73835373-73839625)x1 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":78605903,"stop":79090819,"innerStart":78605903,"outerStart":79090819,"vcv":"VCV000057654","referenceAssertions":[{"rcv":"RCV000051389","title":"GRCh38/hg38 Xq21.1(chrX:79350406-79835322)x0 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":89330088,"stop":89853974,"innerStart":89330088,"outerStart":89853974,"vcv":"VCV000057686","referenceAssertions":[{"rcv":"RCV000051424","title":"GRCh38/hg38 Xq21.31(chrX:90075089-90598975)x1 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":102885179,"stop":102967225,"innerStart":102885179,"outerStart":102967225,"vcv":"VCV000057688","referenceAssertions":[{"rcv":"RCV000051426","title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"1","start":196757278,"stop":196796716,"innerStart":196757278,"outerStart":196796716,"vcv":"VCV000058538","referenceAssertions":[{"rcv":"RCV000052307","title":"GRCh38/hg38 1q31.3(chr1:196788148-196827586)x1 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"7","start":27194426,"stop":27461954,"innerStart":27194426,"outerStart":27461954,"vcv":"VCV000058544","referenceAssertions":[{"rcv":"RCV000052313","title":"GRCh38/hg38 7p15.2(chr7:27154807-27422335)x1 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":8595045,"stop":8704378,"innerStart":8595045,"outerStart":8704378,"variantType":"DUPLICATION","vcv":"VCV000058565","referenceAssertions":[{"rcv":"RCV000052334","title":"GRCh38/hg38 Xp22.31(chrX:8627004-8736337)x2 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":8596894,"stop":8705494,"innerStart":8596894,"outerStart":8705494,"variantType":"DUPLICATION","vcv":"VCV000058566","referenceAssertions":[{"rcv":"RCV000052337","title":"GRCh38/hg38 Xp22.31(chrX:8628853-8737453)x2 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":8597747,"stop":8674356,"innerStart":8597747,"outerStart":8674356,"variantType":"DUPLICATION","vcv":"VCV000058567","referenceAssertions":[{"rcv":"RCV000052338","title":"GRCh38/hg38 Xp22.31(chrX:8629706-8706315)x3 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"NO_ASSERTION_CRITERIA_PROVIDED"}]} +{"release":"GRCh37","chromosome":"X","start":28777940,"stop":29112528,"innerStart":28777940,"outerStart":29112528,"variantType":"DUPLICATION","vcv":"VCV000058611","referenceAssertions":[{"rcv":"RCV000052386","title":"GRCh38/hg38 Xp21.3(chrX:28759823-29094411)x2 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":29731388,"stop":29759068,"innerStart":29731388,"outerStart":29759068,"variantType":"DUPLICATION","vcv":"VCV000058612","referenceAssertions":[{"rcv":"RCV000052387","title":"GRCh38/hg38 Xp21.2(chrX:29713271-29740951)x3 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":32680483,"stop":32777081,"innerStart":32680483,"outerStart":32777081,"variantType":"DUPLICATION","vcv":"VCV000058614","referenceAssertions":[{"rcv":"RCV000052389","title":"GRCh38/hg38 Xp21.1(chrX:32662366-32758964)x2 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":105135228,"stop":105669012,"innerStart":105135228,"outerStart":105669012,"variantType":"DUPLICATION","vcv":"VCV000058665","referenceAssertions":[{"rcv":"RCV000052442","title":"GRCh38/hg38 Xq22.3(chrX:105891235-106425782)x2 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"Y","start":2651665,"stop":4972987,"innerStart":2651665,"outerStart":4972987,"variantType":"DUPLICATION","vcv":"VCV000058795","referenceAssertions":[{"rcv":"RCV000052584","title":"GRCh38/hg38 Yp11.2(chrY:2783624-5104946)x2 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"Y","start":2654967,"stop":2862993,"innerStart":2654967,"outerStart":2862993,"variantType":"DUPLICATION","vcv":"VCV000058800","referenceAssertions":[{"rcv":"RCV000052589","title":"GRCh38/hg38 Yp11.2(chrY:2786926-2994952)x2 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"19","start":54104552,"stop":54276282,"innerStart":54104552,"outerStart":54276282,"variantType":"DUPLICATION","vcv":"VCV000058805","referenceAssertions":[{"rcv":"RCV000052594","title":"GRCh38/hg38 19q13.42(chr19:53601298-53773028)x3 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} +{"release":"GRCh37","chromosome":"X","start":8595045,"stop":8704378,"innerStart":8595045,"outerStart":8704378,"variantType":"DUPLICATION","vcv":"VCV000144128","referenceAssertions":[{"rcv":"RCV000052335","title":"GRCh38/hg38 Xp22.31(chrX:8627004-8736337)x3 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_exact.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_exact.snap index 3df2ec6c..832aa213 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_exact.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_exact.snap @@ -2,5 +2,5 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"reference":null,"alternative":null,"inner_start":34150132,"inner_stop":null,"outer_start":34182300,"outer_stop":null,"variant_type":0,"vcv":"VCV000057627","reference_assertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","clinical_significance":0,"review_status":3}]} +{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"innerStart":34150132,"outerStart":34182300,"vcv":"VCV000057627","referenceAssertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_no_overlap.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_no_overlap.snap index 3df2ec6c..832aa213 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_no_overlap.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_no_overlap.snap @@ -2,5 +2,5 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"reference":null,"alternative":null,"inner_start":34150132,"inner_stop":null,"outer_start":34182300,"outer_stop":null,"variant_type":0,"vcv":"VCV000057627","reference_assertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","clinical_significance":0,"review_status":3}]} +{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"innerStart":34150132,"outerStart":34182300,"vcv":"VCV000057627","referenceAssertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_overlap.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_overlap.snap index 3df2ec6c..832aa213 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_overlap.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_overlap.snap @@ -2,5 +2,5 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"reference":null,"alternative":null,"inner_start":34150132,"inner_stop":null,"outer_start":34182300,"outer_stop":null,"variant_type":0,"vcv":"VCV000057627","reference_assertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","clinical_significance":0,"review_status":3}]} +{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"innerStart":34150132,"outerStart":34182300,"vcv":"VCV000057627","referenceAssertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_rcv.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_rcv.snap index ad5d73c1..7df6e1d6 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_rcv.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_rcv.snap @@ -2,5 +2,5 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"X","start":102885179,"stop":102967225,"reference":null,"alternative":null,"inner_start":102885179,"inner_stop":null,"outer_start":102967225,"outer_stop":null,"variant_type":0,"vcv":"VCV000057688","reference_assertions":[{"rcv":"RCV000051426","title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases","clinical_significance":2,"review_status":3}]} +{"release":"GRCh37","chromosome":"X","start":102885179,"stop":102967225,"innerStart":102885179,"outerStart":102967225,"vcv":"VCV000057688","referenceAssertions":[{"rcv":"RCV000051426","title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_vcv.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_vcv.snap index ad5d73c1..7df6e1d6 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_vcv.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_vcv.snap @@ -2,5 +2,5 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"X","start":102885179,"stop":102967225,"reference":null,"alternative":null,"inner_start":102885179,"inner_stop":null,"outer_start":102967225,"outer_stop":null,"variant_type":0,"vcv":"VCV000057688","reference_assertions":[{"rcv":"RCV000051426","title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases","clinical_significance":2,"review_status":3}]} +{"release":"GRCh37","chromosome":"X","start":102885179,"stop":102967225,"innerStart":102885179,"outerStart":102967225,"vcv":"VCV000057688","referenceAssertions":[{"rcv":"RCV000051426","title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases","clinicalSignificance":"UNCERTAIN_SIGNIFICANCE","reviewStatus":"CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} diff --git a/src/cons/cli/import.rs b/src/cons/cli/import.rs index 6f3667b7..36301a48 100644 --- a/src/cons/cli/import.rs +++ b/src/cons/cli/import.rs @@ -5,10 +5,47 @@ use std::sync::Arc; use clap::Parser; use prost::Message; -use crate::{ - common::{self, keys}, - cons, -}; +use crate::common::{self, keys}; + +/// Helper data structures for reading CSV files. +pub mod reading { + + /// Protocol buffer for the UCSC conservation record. + #[derive(Debug, Clone, PartialEq, serde::Deserialize, serde::Serialize)] + pub struct Record { + /// Chromosome name. + pub chromosome: String, + /// 1-based, inclusive start position. + pub start: i32, + /// 1-based, inclusive stop position. + pub stop: i32, + /// HGNC identifier. + pub hgnc_id: String, + /// ENST identifier. + pub enst_id: String, + /// Exon number (1-based). + pub exon_num: i32, + /// Exon count. + pub exon_count: i32, + /// Alignment. + pub alignment: String, + } + + impl Into for Record { + fn into(self) -> crate::pbs::cons::Record { + crate::pbs::cons::Record { + chrom: self.chromosome, + start: self.start, + stop: self.start, + hgnc_id: self.hgnc_id, + enst_id: self.enst_id, + exon_num: self.exon_num, + exon_count: self.exon_count, + alignment: self.alignment, + } + } + } +} /// Command line arguments for `tsv import` sub command. #[derive(Parser, Debug, Clone)] @@ -32,10 +69,10 @@ pub struct Args { pub path_wal_dir: Option, } -/// Utility to make a `Vec` unique. +/// Utility to make a `Vec` unique. /// /// Will sort the records first. -fn dedup_records(records: &mut Vec) { +fn dedup_records(records: &mut Vec) { records.sort_by(|a, b| { (a.chrom.as_str(), a.start, a.enst_id.as_str()).cmp(&( b.chrom.as_str(), @@ -76,10 +113,11 @@ fn tsv_import( // Read through all records. Collect all at the same position into a `RecordList` and // insert these into the database. - let mut record_list = cons::pbs::RecordList::default(); + let mut record_list = crate::pbs::cons::RecordList::default(); let mut last_pos = keys::Pos::default(); for result in csv_reader.deserialize() { - let record: cons::pbs::Record = result?; + let record: reading::Record = result?; + let record: crate::pbs::cons::Record = record.into(); let pos = keys::Pos::from(&record.chrom, record.start); if pos != last_pos { @@ -92,7 +130,7 @@ fn tsv_import( db.put_cf(&cf_data, &key, &buf)?; } - record_list = cons::pbs::RecordList::default(); + record_list = crate::pbs::cons::RecordList::default(); last_pos = pos; } diff --git a/src/cons/cli/query.rs b/src/cons/cli/query.rs index a6a2aae0..8ca5d1fa 100644 --- a/src/cons/cli/query.rs +++ b/src/cons/cli/query.rs @@ -4,10 +4,7 @@ use std::sync::Arc; use prost::Message; -use crate::{ - common::{self, cli::extract_chrom, keys, spdi}, - cons, -}; +use crate::common::{self, cli::extract_chrom, keys, spdi}; /// Command line arguments for `cons query` sub command. #[derive(clap::Parser, Debug, Clone)] @@ -100,7 +97,7 @@ pub fn open_rocksdb_from_args( fn print_values( out_writer: &mut Box, output_format: common::cli::OutputFormat, - record: &cons::pbs::Record, + record: &crate::pbs::cons::Record, ) -> Result<(), anyhow::Error> { match output_format { common::cli::OutputFormat::Jsonl => { @@ -184,7 +181,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> } // Decode the record list and iterate it. - let record_list = cons::pbs::RecordList::decode(value)?; + let record_list = crate::pbs::cons::RecordList::decode(value)?; for record in &record_list.records { // Skip record if end of iterator is before start of range. This can happen as we // jump two base pairs before the start position as alignment columns span one codon. diff --git a/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_all_without_hgnc_id_result.snap b/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_all_without_hgnc_id_result.snap index 88c750fb..c60dd6e3 100644 --- a/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_all_without_hgnc_id_result.snap +++ b/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_all_without_hgnc_id_result.snap @@ -2,10 +2,10 @@ source: src/cons/cli/query.rs expression: "&out_data" --- -{"chromosome":"13","start":95248334,"stop":95248336,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"RRRRRRRRRRRRRRRR-RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR--RR-RRR---RRRR-R--RRR----------------"} -{"chromosome":"13","start":95248337,"stop":95248339,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"KKKKKKKKKKKKKKKK-KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK--KK-KKK---KKKK-K--KKK----------------"} -{"chromosome":"13","start":95248340,"stop":95248342,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"AAAAAAAAAAAAAAAA-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADAAAAAAAAA--EE-EEE---EEED-A--ASS----------------"} -{"chromosome":"13","start":95248343,"stop":95248345,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"FFFFFFFFFFFFFFFY-YFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF-FFF----LLF-F---FF----------------"} -{"chromosome":"13","start":95248346,"stop":95248348,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"GGGGSGGGGGDGGS-S-GSSSSSSSSSSSGGSSSSSSSSSSSSGGCSSGSRHNDNNNTGGGG--------------------GG----------------"} -{"chromosome":"13","start":95248349,"stop":95248351,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"GGGGGGGGGGGSSGGG-GGGGGGGCGNSSNNDDDDSRGSSSSSSSSSSRSSGGGSGSSSSSS--------------------R-----------------"} +{"chrom":"13","start":95248334,"stop":95248336,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"RRRRRRRRRRRRRRRR-RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR--RR-RRR---RRRR-R--RRR----------------"} +{"chrom":"13","start":95248337,"stop":95248339,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"KKKKKKKKKKKKKKKK-KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK--KK-KKK---KKKK-K--KKK----------------"} +{"chrom":"13","start":95248340,"stop":95248342,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"AAAAAAAAAAAAAAAA-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADAAAAAAAAA--EE-EEE---EEED-A--ASS----------------"} +{"chrom":"13","start":95248343,"stop":95248345,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"FFFFFFFFFFFFFFFY-YFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF-FFF----LLF-F---FF----------------"} +{"chrom":"13","start":95248346,"stop":95248348,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"GGGGSGGGGGDGGS-S-GSSSSSSSSSSSGGSSSSSSSSSSSSGGCSSGSRHNDNNNTGGGG--------------------GG----------------"} +{"chrom":"13","start":95248349,"stop":95248351,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"GGGGGGGGGGGSSGGG-GGGGGGGCGNSSNNDDDDSRGSSSSSSSSSSRSSGGGSGSSSSSS--------------------R-----------------"} diff --git a/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_range_with_hgnc_id_result.snap b/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_range_with_hgnc_id_result.snap index 88c750fb..c60dd6e3 100644 --- a/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_range_with_hgnc_id_result.snap +++ b/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_range_with_hgnc_id_result.snap @@ -2,10 +2,10 @@ source: src/cons/cli/query.rs expression: "&out_data" --- -{"chromosome":"13","start":95248334,"stop":95248336,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"RRRRRRRRRRRRRRRR-RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR--RR-RRR---RRRR-R--RRR----------------"} -{"chromosome":"13","start":95248337,"stop":95248339,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"KKKKKKKKKKKKKKKK-KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK--KK-KKK---KKKK-K--KKK----------------"} -{"chromosome":"13","start":95248340,"stop":95248342,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"AAAAAAAAAAAAAAAA-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADAAAAAAAAA--EE-EEE---EEED-A--ASS----------------"} -{"chromosome":"13","start":95248343,"stop":95248345,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"FFFFFFFFFFFFFFFY-YFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF-FFF----LLF-F---FF----------------"} -{"chromosome":"13","start":95248346,"stop":95248348,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"GGGGSGGGGGDGGS-S-GSSSSSSSSSSSGGSSSSSSSSSSSSGGCSSGSRHNDNNNTGGGG--------------------GG----------------"} -{"chromosome":"13","start":95248349,"stop":95248351,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"GGGGGGGGGGGSSGGG-GGGGGGGCGNSSNNDDDDSRGSSSSSSSSSSRSSGGGSGSSSSSS--------------------R-----------------"} +{"chrom":"13","start":95248334,"stop":95248336,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"RRRRRRRRRRRRRRRR-RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR--RR-RRR---RRRR-R--RRR----------------"} +{"chrom":"13","start":95248337,"stop":95248339,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"KKKKKKKKKKKKKKKK-KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK--KK-KKK---KKKK-K--KKK----------------"} +{"chrom":"13","start":95248340,"stop":95248342,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"AAAAAAAAAAAAAAAA-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADAAAAAAAAA--EE-EEE---EEED-A--ASS----------------"} +{"chrom":"13","start":95248343,"stop":95248345,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"FFFFFFFFFFFFFFFY-YFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF-FFF----LLF-F---FF----------------"} +{"chrom":"13","start":95248346,"stop":95248348,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"GGGGSGGGGGDGGS-S-GSSSSSSSSSSSGGSSSSSSSSSSSSGGCSSGSRHNDNNNTGGGG--------------------GG----------------"} +{"chrom":"13","start":95248349,"stop":95248351,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"GGGGGGGGGGGSSGGG-GGGGGGGCGNSSNNDDDDSRGSSSSSSSSSSRSSGGGSGSSSSSS--------------------R-----------------"} diff --git a/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_range_without_hgnc_id.snap b/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_range_without_hgnc_id.snap index 88c750fb..c60dd6e3 100644 --- a/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_range_without_hgnc_id.snap +++ b/src/cons/cli/snapshots/annonars__cons__cli__query__test__smoke_query_range_without_hgnc_id.snap @@ -2,10 +2,10 @@ source: src/cons/cli/query.rs expression: "&out_data" --- -{"chromosome":"13","start":95248334,"stop":95248336,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"RRRRRRRRRRRRRRRR-RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR--RR-RRR---RRRR-R--RRR----------------"} -{"chromosome":"13","start":95248337,"stop":95248339,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"KKKKKKKKKKKKKKKK-KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK--KK-KKK---KKKK-K--KKK----------------"} -{"chromosome":"13","start":95248340,"stop":95248342,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"AAAAAAAAAAAAAAAA-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADAAAAAAAAA--EE-EEE---EEED-A--ASS----------------"} -{"chromosome":"13","start":95248343,"stop":95248345,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"FFFFFFFFFFFFFFFY-YFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF-FFF----LLF-F---FF----------------"} -{"chromosome":"13","start":95248346,"stop":95248348,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"GGGGSGGGGGDGGS-S-GSSSSSSSSSSSGGSSSSSSSSSSSSGGCSSGSRHNDNNNTGGGG--------------------GG----------------"} -{"chromosome":"13","start":95248349,"stop":95248351,"hgnc_id":"HGNC:20324","enst_id":"ENST00000261296","exon_num":1,"exon_count":12,"alignment":"GGGGGGGGGGGSSGGG-GGGGGGGCGNSSNNDDDDSRGSSSSSSSSSSRSSGGGSGSSSSSS--------------------R-----------------"} +{"chrom":"13","start":95248334,"stop":95248336,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"RRRRRRRRRRRRRRRR-RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR--RR-RRR---RRRR-R--RRR----------------"} +{"chrom":"13","start":95248337,"stop":95248339,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"KKKKKKKKKKKKKKKK-KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK--KK-KKK---KKKK-K--KKK----------------"} +{"chrom":"13","start":95248340,"stop":95248342,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"AAAAAAAAAAAAAAAA-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADAAAAAAAAA--EE-EEE---EEED-A--ASS----------------"} +{"chrom":"13","start":95248343,"stop":95248345,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"FFFFFFFFFFFFFFFY-YFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF-FFF----LLF-F---FF----------------"} +{"chrom":"13","start":95248346,"stop":95248348,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"GGGGSGGGGGDGGS-S-GSSSSSSSSSSSGGSSSSSSSSSSSSGGCSSGSRHNDNNNTGGGG--------------------GG----------------"} +{"chrom":"13","start":95248349,"stop":95248351,"hgncId":"HGNC:20324","enstId":"ENST00000261296","exonNum":1,"exonCount":12,"alignment":"GGGGGGGGGGGSSGGG-GGGGGGGCGNSSNNDDDDSRGSSSSSSSSSSRSSGGGSGSSSSSS--------------------R-----------------"} diff --git a/src/cons/mod.rs b/src/cons/mod.rs index 53807085..fe561312 100644 --- a/src/cons/mod.rs +++ b/src/cons/mod.rs @@ -1,4 +1,3 @@ //! Handling of UCSC 100 vertebrate conservation data. pub mod cli; -pub mod pbs; diff --git a/src/cons/pbs.rs b/src/cons/pbs.rs deleted file mode 100644 index 51fa7a68..00000000 --- a/src/cons/pbs.rs +++ /dev/null @@ -1,3 +0,0 @@ -//! Data structures for (de-)serialization as generated by `prost-build`. - -include!(concat!(env!("OUT_DIR"), "/annonars.cons.v1.base.rs")); diff --git a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_all.snap b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_all.snap index 2d57cd76..8a56858a 100644 --- a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_all.snap +++ b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_all.snap @@ -2,54 +2,54 @@ source: src/dbsnp/cli/query.rs expression: "&out_data" --- -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"A","rs_id":80357446} -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"CA","rs_id":431825385} -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"T","rs_id":80357446} -{"chrom":"17","pos":41267746,"ref_allele":"CA","alt_allele":"C","rs_id":80357951} -{"chrom":"17","pos":41267747,"ref_allele":"A","alt_allele":"C","rs_id":80357327} -{"chrom":"17","pos":41267747,"ref_allele":"A","alt_allele":"G","rs_id":80357327} -{"chrom":"17","pos":41267747,"ref_allele":"A","alt_allele":"T","rs_id":80357327} -{"chrom":"17","pos":41267749,"ref_allele":"A","alt_allele":"G","rs_id":1298544053} -{"chrom":"17","pos":41267752,"ref_allele":"AT","alt_allele":"A","rs_id":80357943} -{"chrom":"17","pos":41267753,"ref_allele":"T","alt_allele":"C","rs_id":80357163} -{"chrom":"17","pos":41267753,"ref_allele":"T","alt_allele":"G","rs_id":80357163} -{"chrom":"17","pos":41267754,"ref_allele":"G","alt_allele":"A","rs_id":786202211} -{"chrom":"17","pos":41267754,"ref_allele":"GT","alt_allele":"G","rs_id":397508847} -{"chrom":"17","pos":41267755,"ref_allele":"T","alt_allele":"A","rs_id":80357276} -{"chrom":"17","pos":41267755,"ref_allele":"T","alt_allele":"C","rs_id":80357276} -{"chrom":"17","pos":41267756,"ref_allele":"G","alt_allele":"T","rs_id":1060502353} -{"chrom":"17","pos":41267757,"ref_allele":"G","alt_allele":"A","rs_id":1060504580} -{"chrom":"17","pos":41267758,"ref_allele":"TCA","alt_allele":"T","rs_id":80357972} -{"chrom":"17","pos":41267759,"ref_allele":"C","alt_allele":"T","rs_id":879255290} -{"chrom":"17","pos":41267760,"ref_allele":"A","alt_allele":"C","rs_id":886040898} -{"chrom":"17","pos":41267761,"ref_allele":"C","alt_allele":"A","rs_id":80357498} -{"chrom":"17","pos":41267761,"ref_allele":"C","alt_allele":"T","rs_id":80357498} -{"chrom":"17","pos":41267762,"ref_allele":"A","alt_allele":"C","rs_id":80357164} -{"chrom":"17","pos":41267762,"ref_allele":"A","alt_allele":"G","rs_id":80357164} -{"chrom":"17","pos":41267762,"ref_allele":"A","alt_allele":"T","rs_id":80357164} -{"chrom":"17","pos":41267763,"ref_allele":"C","alt_allele":"A","rs_id":1800062} -{"chrom":"17","pos":41267763,"ref_allele":"C","alt_allele":"T","rs_id":1800062} -{"chrom":"17","pos":41267763,"ref_allele":"CTT","alt_allele":"C","rs_id":80357949} -{"chrom":"17","pos":41267766,"ref_allele":"T","alt_allele":"A","rs_id":1293537445} -{"chrom":"17","pos":41267767,"ref_allele":"G","alt_allele":"C","rs_id":80356880} -{"chrom":"17","pos":41267767,"ref_allele":"G","alt_allele":"T","rs_id":80356880} -{"chrom":"17","pos":41267770,"ref_allele":"G","alt_allele":"T","rs_id":183557525} -{"chrom":"17","pos":41267771,"ref_allele":"A","alt_allele":"T","rs_id":905812561} -{"chrom":"17","pos":41267771,"ref_allele":"AGACAG","alt_allele":"A","rs_id":886039920} -{"chrom":"17","pos":41267771,"ref_allele":"AGACAGGTT","alt_allele":"A","rs_id":886040338} -{"chrom":"17","pos":41267773,"ref_allele":"A","alt_allele":"C","rs_id":1235706456} -{"chrom":"17","pos":41267774,"ref_allele":"C","alt_allele":"A","rs_id":879255284} -{"chrom":"17","pos":41267774,"ref_allele":"CA","alt_allele":"C","rs_id":886039922} -{"chrom":"17","pos":41267775,"ref_allele":"AG","alt_allele":"A","rs_id":80357750} -{"chrom":"17","pos":41267776,"ref_allele":"G","alt_allele":"A","rs_id":786203319} -{"chrom":"17","pos":41267777,"ref_allele":"G","alt_allele":"A","rs_id":1064793357} -{"chrom":"17","pos":41267779,"ref_allele":"T","alt_allele":"G","rs_id":876660844} -{"chrom":"17","pos":41267780,"ref_allele":"C","alt_allele":"G","rs_id":80357066} -{"chrom":"17","pos":41267783,"ref_allele":"TG","alt_allele":"T","rs_id":886040332} -{"chrom":"17","pos":41267784,"ref_allele":"G","alt_allele":"C","rs_id":80357000} -{"chrom":"17","pos":41267788,"ref_allele":"A","alt_allele":"T","rs_id":397509331} -{"chrom":"17","pos":41267790,"ref_allele":"C","alt_allele":"T","rs_id":1343667553} -{"chrom":"17","pos":41267791,"ref_allele":"T","alt_allele":"C","rs_id":773841328} -{"chrom":"17","pos":41267792,"ref_allele":"C","alt_allele":"A","rs_id":80357443} -{"chrom":"17","pos":41267792,"ref_allele":"CCA","alt_allele":"C","rs_id":80357728} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"A","rsId":80357446} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"CA","rsId":431825385} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"T","rsId":80357446} +{"chrom":"17","pos":41267746,"refAllele":"CA","altAllele":"C","rsId":80357951} +{"chrom":"17","pos":41267747,"refAllele":"A","altAllele":"C","rsId":80357327} +{"chrom":"17","pos":41267747,"refAllele":"A","altAllele":"G","rsId":80357327} +{"chrom":"17","pos":41267747,"refAllele":"A","altAllele":"T","rsId":80357327} +{"chrom":"17","pos":41267749,"refAllele":"A","altAllele":"G","rsId":1298544053} +{"chrom":"17","pos":41267752,"refAllele":"AT","altAllele":"A","rsId":80357943} +{"chrom":"17","pos":41267753,"refAllele":"T","altAllele":"C","rsId":80357163} +{"chrom":"17","pos":41267753,"refAllele":"T","altAllele":"G","rsId":80357163} +{"chrom":"17","pos":41267754,"refAllele":"G","altAllele":"A","rsId":786202211} +{"chrom":"17","pos":41267754,"refAllele":"GT","altAllele":"G","rsId":397508847} +{"chrom":"17","pos":41267755,"refAllele":"T","altAllele":"A","rsId":80357276} +{"chrom":"17","pos":41267755,"refAllele":"T","altAllele":"C","rsId":80357276} +{"chrom":"17","pos":41267756,"refAllele":"G","altAllele":"T","rsId":1060502353} +{"chrom":"17","pos":41267757,"refAllele":"G","altAllele":"A","rsId":1060504580} +{"chrom":"17","pos":41267758,"refAllele":"TCA","altAllele":"T","rsId":80357972} +{"chrom":"17","pos":41267759,"refAllele":"C","altAllele":"T","rsId":879255290} +{"chrom":"17","pos":41267760,"refAllele":"A","altAllele":"C","rsId":886040898} +{"chrom":"17","pos":41267761,"refAllele":"C","altAllele":"A","rsId":80357498} +{"chrom":"17","pos":41267761,"refAllele":"C","altAllele":"T","rsId":80357498} +{"chrom":"17","pos":41267762,"refAllele":"A","altAllele":"C","rsId":80357164} +{"chrom":"17","pos":41267762,"refAllele":"A","altAllele":"G","rsId":80357164} +{"chrom":"17","pos":41267762,"refAllele":"A","altAllele":"T","rsId":80357164} +{"chrom":"17","pos":41267763,"refAllele":"C","altAllele":"A","rsId":1800062} +{"chrom":"17","pos":41267763,"refAllele":"C","altAllele":"T","rsId":1800062} +{"chrom":"17","pos":41267763,"refAllele":"CTT","altAllele":"C","rsId":80357949} +{"chrom":"17","pos":41267766,"refAllele":"T","altAllele":"A","rsId":1293537445} +{"chrom":"17","pos":41267767,"refAllele":"G","altAllele":"C","rsId":80356880} +{"chrom":"17","pos":41267767,"refAllele":"G","altAllele":"T","rsId":80356880} +{"chrom":"17","pos":41267770,"refAllele":"G","altAllele":"T","rsId":183557525} +{"chrom":"17","pos":41267771,"refAllele":"A","altAllele":"T","rsId":905812561} +{"chrom":"17","pos":41267771,"refAllele":"AGACAG","altAllele":"A","rsId":886039920} +{"chrom":"17","pos":41267771,"refAllele":"AGACAGGTT","altAllele":"A","rsId":886040338} +{"chrom":"17","pos":41267773,"refAllele":"A","altAllele":"C","rsId":1235706456} +{"chrom":"17","pos":41267774,"refAllele":"C","altAllele":"A","rsId":879255284} 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+{"chrom":"17","pos":41267792,"refAllele":"CCA","altAllele":"C","rsId":80357728} diff --git a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_pos_multi.snap b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_pos_multi.snap index 793cef59..fd00e6f3 100644 --- a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_pos_multi.snap +++ b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_pos_multi.snap @@ -2,7 +2,7 @@ source: src/dbsnp/cli/query.rs expression: "&out_data" --- -{"chrom":"17","pos":41267747,"ref_allele":"A","alt_allele":"C","rs_id":80357327} -{"chrom":"17","pos":41267747,"ref_allele":"A","alt_allele":"G","rs_id":80357327} -{"chrom":"17","pos":41267747,"ref_allele":"A","alt_allele":"T","rs_id":80357327} +{"chrom":"17","pos":41267747,"refAllele":"A","altAllele":"C","rsId":80357327} +{"chrom":"17","pos":41267747,"refAllele":"A","altAllele":"G","rsId":80357327} 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a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_range_by_accession.snap +++ b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_range_by_accession.snap @@ -2,5 +2,5 @@ source: src/dbsnp/cli/query.rs expression: "&out_data" --- -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"CA","rs_id":431825385} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"CA","rsId":431825385} diff --git a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_range_find_all.snap b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_range_find_all.snap index 2d57cd76..8a56858a 100644 --- a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_range_find_all.snap +++ b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_range_find_all.snap @@ -2,54 +2,54 @@ source: src/dbsnp/cli/query.rs expression: "&out_data" --- -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"A","rs_id":80357446} -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"CA","rs_id":431825385} -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"T","rs_id":80357446} -{"chrom":"17","pos":41267746,"ref_allele":"CA","alt_allele":"C","rs_id":80357951} -{"chrom":"17","pos":41267747,"ref_allele":"A","alt_allele":"C","rs_id":80357327} -{"chrom":"17","pos":41267747,"ref_allele":"A","alt_allele":"G","rs_id":80357327} -{"chrom":"17","pos":41267747,"ref_allele":"A","alt_allele":"T","rs_id":80357327} -{"chrom":"17","pos":41267749,"ref_allele":"A","alt_allele":"G","rs_id":1298544053} -{"chrom":"17","pos":41267752,"ref_allele":"AT","alt_allele":"A","rs_id":80357943} -{"chrom":"17","pos":41267753,"ref_allele":"T","alt_allele":"C","rs_id":80357163} -{"chrom":"17","pos":41267753,"ref_allele":"T","alt_allele":"G","rs_id":80357163} -{"chrom":"17","pos":41267754,"ref_allele":"G","alt_allele":"A","rs_id":786202211} -{"chrom":"17","pos":41267754,"ref_allele":"GT","alt_allele":"G","rs_id":397508847} -{"chrom":"17","pos":41267755,"ref_allele":"T","alt_allele":"A","rs_id":80357276} -{"chrom":"17","pos":41267755,"ref_allele":"T","alt_allele":"C","rs_id":80357276} -{"chrom":"17","pos":41267756,"ref_allele":"G","alt_allele":"T","rs_id":1060502353} -{"chrom":"17","pos":41267757,"ref_allele":"G","alt_allele":"A","rs_id":1060504580} -{"chrom":"17","pos":41267758,"ref_allele":"TCA","alt_allele":"T","rs_id":80357972} -{"chrom":"17","pos":41267759,"ref_allele":"C","alt_allele":"T","rs_id":879255290} -{"chrom":"17","pos":41267760,"ref_allele":"A","alt_allele":"C","rs_id":886040898} -{"chrom":"17","pos":41267761,"ref_allele":"C","alt_allele":"A","rs_id":80357498} -{"chrom":"17","pos":41267761,"ref_allele":"C","alt_allele":"T","rs_id":80357498} -{"chrom":"17","pos":41267762,"ref_allele":"A","alt_allele":"C","rs_id":80357164} -{"chrom":"17","pos":41267762,"ref_allele":"A","alt_allele":"G","rs_id":80357164} -{"chrom":"17","pos":41267762,"ref_allele":"A","alt_allele":"T","rs_id":80357164} -{"chrom":"17","pos":41267763,"ref_allele":"C","alt_allele":"A","rs_id":1800062} -{"chrom":"17","pos":41267763,"ref_allele":"C","alt_allele":"T","rs_id":1800062} -{"chrom":"17","pos":41267763,"ref_allele":"CTT","alt_allele":"C","rs_id":80357949} -{"chrom":"17","pos":41267766,"ref_allele":"T","alt_allele":"A","rs_id":1293537445} -{"chrom":"17","pos":41267767,"ref_allele":"G","alt_allele":"C","rs_id":80356880} -{"chrom":"17","pos":41267767,"ref_allele":"G","alt_allele":"T","rs_id":80356880} -{"chrom":"17","pos":41267770,"ref_allele":"G","alt_allele":"T","rs_id":183557525} -{"chrom":"17","pos":41267771,"ref_allele":"A","alt_allele":"T","rs_id":905812561} -{"chrom":"17","pos":41267771,"ref_allele":"AGACAG","alt_allele":"A","rs_id":886039920} -{"chrom":"17","pos":41267771,"ref_allele":"AGACAGGTT","alt_allele":"A","rs_id":886040338} -{"chrom":"17","pos":41267773,"ref_allele":"A","alt_allele":"C","rs_id":1235706456} -{"chrom":"17","pos":41267774,"ref_allele":"C","alt_allele":"A","rs_id":879255284} -{"chrom":"17","pos":41267774,"ref_allele":"CA","alt_allele":"C","rs_id":886039922} -{"chrom":"17","pos":41267775,"ref_allele":"AG","alt_allele":"A","rs_id":80357750} -{"chrom":"17","pos":41267776,"ref_allele":"G","alt_allele":"A","rs_id":786203319} -{"chrom":"17","pos":41267777,"ref_allele":"G","alt_allele":"A","rs_id":1064793357} -{"chrom":"17","pos":41267779,"ref_allele":"T","alt_allele":"G","rs_id":876660844} -{"chrom":"17","pos":41267780,"ref_allele":"C","alt_allele":"G","rs_id":80357066} -{"chrom":"17","pos":41267783,"ref_allele":"TG","alt_allele":"T","rs_id":886040332} -{"chrom":"17","pos":41267784,"ref_allele":"G","alt_allele":"C","rs_id":80357000} -{"chrom":"17","pos":41267788,"ref_allele":"A","alt_allele":"T","rs_id":397509331} -{"chrom":"17","pos":41267790,"ref_allele":"C","alt_allele":"T","rs_id":1343667553} -{"chrom":"17","pos":41267791,"ref_allele":"T","alt_allele":"C","rs_id":773841328} -{"chrom":"17","pos":41267792,"ref_allele":"C","alt_allele":"A","rs_id":80357443} -{"chrom":"17","pos":41267792,"ref_allele":"CCA","alt_allele":"C","rs_id":80357728} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"A","rsId":80357446} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"CA","rsId":431825385} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"T","rsId":80357446} +{"chrom":"17","pos":41267746,"refAllele":"CA","altAllele":"C","rsId":80357951} +{"chrom":"17","pos":41267747,"refAllele":"A","altAllele":"C","rsId":80357327} +{"chrom":"17","pos":41267747,"refAllele":"A","altAllele":"G","rsId":80357327} +{"chrom":"17","pos":41267747,"refAllele":"A","altAllele":"T","rsId":80357327} +{"chrom":"17","pos":41267749,"refAllele":"A","altAllele":"G","rsId":1298544053} +{"chrom":"17","pos":41267752,"refAllele":"AT","altAllele":"A","rsId":80357943} +{"chrom":"17","pos":41267753,"refAllele":"T","altAllele":"C","rsId":80357163} +{"chrom":"17","pos":41267753,"refAllele":"T","altAllele":"G","rsId":80357163} +{"chrom":"17","pos":41267754,"refAllele":"G","altAllele":"A","rsId":786202211} +{"chrom":"17","pos":41267754,"refAllele":"GT","altAllele":"G","rsId":397508847} +{"chrom":"17","pos":41267755,"refAllele":"T","altAllele":"A","rsId":80357276} +{"chrom":"17","pos":41267755,"refAllele":"T","altAllele":"C","rsId":80357276} +{"chrom":"17","pos":41267756,"refAllele":"G","altAllele":"T","rsId":1060502353} +{"chrom":"17","pos":41267757,"refAllele":"G","altAllele":"A","rsId":1060504580} +{"chrom":"17","pos":41267758,"refAllele":"TCA","altAllele":"T","rsId":80357972} +{"chrom":"17","pos":41267759,"refAllele":"C","altAllele":"T","rsId":879255290} +{"chrom":"17","pos":41267760,"refAllele":"A","altAllele":"C","rsId":886040898} +{"chrom":"17","pos":41267761,"refAllele":"C","altAllele":"A","rsId":80357498} +{"chrom":"17","pos":41267761,"refAllele":"C","altAllele":"T","rsId":80357498} +{"chrom":"17","pos":41267762,"refAllele":"A","altAllele":"C","rsId":80357164} +{"chrom":"17","pos":41267762,"refAllele":"A","altAllele":"G","rsId":80357164} +{"chrom":"17","pos":41267762,"refAllele":"A","altAllele":"T","rsId":80357164} +{"chrom":"17","pos":41267763,"refAllele":"C","altAllele":"A","rsId":1800062} +{"chrom":"17","pos":41267763,"refAllele":"C","altAllele":"T","rsId":1800062} +{"chrom":"17","pos":41267763,"refAllele":"CTT","altAllele":"C","rsId":80357949} +{"chrom":"17","pos":41267766,"refAllele":"T","altAllele":"A","rsId":1293537445} +{"chrom":"17","pos":41267767,"refAllele":"G","altAllele":"C","rsId":80356880} +{"chrom":"17","pos":41267767,"refAllele":"G","altAllele":"T","rsId":80356880} +{"chrom":"17","pos":41267770,"refAllele":"G","altAllele":"T","rsId":183557525} +{"chrom":"17","pos":41267771,"refAllele":"A","altAllele":"T","rsId":905812561} +{"chrom":"17","pos":41267771,"refAllele":"AGACAG","altAllele":"A","rsId":886039920} +{"chrom":"17","pos":41267771,"refAllele":"AGACAGGTT","altAllele":"A","rsId":886040338} +{"chrom":"17","pos":41267773,"refAllele":"A","altAllele":"C","rsId":1235706456} +{"chrom":"17","pos":41267774,"refAllele":"C","altAllele":"A","rsId":879255284} +{"chrom":"17","pos":41267774,"refAllele":"CA","altAllele":"C","rsId":886039922} +{"chrom":"17","pos":41267775,"refAllele":"AG","altAllele":"A","rsId":80357750} +{"chrom":"17","pos":41267776,"refAllele":"G","altAllele":"A","rsId":786203319} +{"chrom":"17","pos":41267777,"refAllele":"G","altAllele":"A","rsId":1064793357} +{"chrom":"17","pos":41267779,"refAllele":"T","altAllele":"G","rsId":876660844} +{"chrom":"17","pos":41267780,"refAllele":"C","altAllele":"G","rsId":80357066} +{"chrom":"17","pos":41267783,"refAllele":"TG","altAllele":"T","rsId":886040332} +{"chrom":"17","pos":41267784,"refAllele":"G","altAllele":"C","rsId":80357000} +{"chrom":"17","pos":41267788,"refAllele":"A","altAllele":"T","rsId":397509331} +{"chrom":"17","pos":41267790,"refAllele":"C","altAllele":"T","rsId":1343667553} +{"chrom":"17","pos":41267791,"refAllele":"T","altAllele":"C","rsId":773841328} +{"chrom":"17","pos":41267792,"refAllele":"C","altAllele":"A","rsId":80357443} +{"chrom":"17","pos":41267792,"refAllele":"CCA","altAllele":"C","rsId":80357728} diff --git a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_range_find_first.snap b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_range_find_first.snap index a539a057..655742a1 100644 --- a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_range_find_first.snap +++ b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_range_find_first.snap @@ -2,8 +2,8 @@ source: src/dbsnp/cli/query.rs expression: "&out_data" --- -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"A","rs_id":80357446} -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"CA","rs_id":431825385} -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"T","rs_id":80357446} -{"chrom":"17","pos":41267746,"ref_allele":"CA","alt_allele":"C","rs_id":80357951} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"A","rsId":80357446} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"CA","rsId":431825385} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"T","rsId":80357446} +{"chrom":"17","pos":41267746,"refAllele":"CA","altAllele":"C","rsId":80357951} diff --git a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_var_single.snap b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_var_single.snap index 7acb9e09..066a5ad6 100644 --- a/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_var_single.snap +++ b/src/dbsnp/cli/snapshots/annonars__dbsnp__cli__query__test__smoke_query_var_single.snap @@ -2,5 +2,5 @@ source: src/dbsnp/cli/query.rs expression: "&out_data" --- -{"chrom":"17","pos":41267746,"ref_allele":"C","alt_allele":"CA","rs_id":431825385} +{"chrom":"17","pos":41267746,"refAllele":"C","altAllele":"CA","rsId":431825385} diff --git a/src/dbsnp/pbs.rs b/src/dbsnp/pbs.rs index 30fd0f43..8ffb4341 100644 --- a/src/dbsnp/pbs.rs +++ b/src/dbsnp/pbs.rs @@ -2,10 +2,9 @@ use std::str::FromStr; +pub use crate::pbs::dbsnp::Record; use noodles_vcf::record::info::field; -include!(concat!(env!("OUT_DIR"), "/annonars.dbsnp.v1.base.rs")); - impl Record { /// Creates a new `Record` from a VCF record and allele number. pub fn from_vcf_allele( diff --git a/src/functional/cli/import.rs b/src/functional/cli/import.rs index ab1e8d05..0575e02d 100644 --- a/src/functional/cli/import.rs +++ b/src/functional/cli/import.rs @@ -6,7 +6,7 @@ use clap::Parser; use noodles_gff as gff; use prost::Message; -use crate::pbs::annonars::functional::v1::refseq::{ +use crate::pbs::functional::refseq::{ Category as RefseqCategory, Record as RefseqRecord, RegulatoryClass as RefseqRegulatoryClass, }; use crate::{ diff --git a/src/functional/cli/query.rs b/src/functional/cli/query.rs index 9d77bb17..46996f05 100644 --- a/src/functional/cli/query.rs +++ b/src/functional/cli/query.rs @@ -97,7 +97,7 @@ pub fn open_rocksdb_from_args( fn print_record( out_writer: &mut Box, output_format: common::cli::OutputFormat, - value: &crate::pbs::annonars::functional::v1::refseq::Record, + value: &crate::pbs::functional::refseq::Record, ) -> Result<(), anyhow::Error> { match output_format { common::cli::OutputFormat::Jsonl => { @@ -113,17 +113,15 @@ pub fn query_for_accession( accession: &str, db: &rocksdb::DBWithThreadMode, cf_data: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { let raw_value = db.get_cf(cf_data, accession.as_bytes()).map_err(|e| { anyhow::anyhow!("error while querying for accession {:?}: {}", accession, e) })?; raw_value .map(|raw_value| { // Decode via prost. - crate::pbs::annonars::functional::v1::refseq::Record::decode(&mut std::io::Cursor::new( - &raw_value, - )) - .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) + crate::pbs::functional::refseq::Record::decode(&mut std::io::Cursor::new(&raw_value)) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) }) .transpose() } @@ -141,9 +139,9 @@ fn print_all( iter.seek(b""); while iter.valid() { if let Some(raw_value) = iter.value() { - let record = crate::pbs::annonars::functional::v1::refseq::Record::decode( - &mut std::io::Cursor::new(&raw_value), - ) + let record = crate::pbs::functional::refseq::Record::decode(&mut std::io::Cursor::new( + &raw_value, + )) .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; print_record(out_writer, out_format, &record)?; iter.next(); @@ -216,13 +214,13 @@ impl IntervalTrees { iter.seek(b""); while iter.valid() { if let Some(raw_value) = iter.value() { - let record = crate::pbs::annonars::functional::v1::refseq::Record::decode( + let record = crate::pbs::functional::refseq::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 crate::pbs::annonars::functional::v1::refseq::Record { + let crate::pbs::functional::refseq::Record { chromosome, start, stop, @@ -253,7 +251,7 @@ impl IntervalTrees { pub fn query( &self, range: &spdi::Range, - ) -> Result, anyhow::Error> { + ) -> Result, anyhow::Error> { 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) @@ -263,7 +261,7 @@ impl IntervalTrees { 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())? { - let record = crate::pbs::annonars::functional::v1::refseq::Record::decode( + let record = crate::pbs::functional::refseq::Record::decode( &mut std::io::Cursor::new(&raw_value), ) .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; diff --git a/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_by_accession_37.snap b/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_by_accession_37.snap index d9f2b919..83d7bc2d 100644 --- a/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_by_accession_37.snap +++ b/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_by_accession_37.snap @@ -2,5 +2,5 @@ source: src/functional/cli/query.rs expression: "&out_data" --- -{"chromosome":"1","start":1004592,"stop":1004706,"id":"id-GeneID:106783496-2","dbxref":"GeneID:106783496","category":5,"regulatory_class":null,"note":null,"experiment":null,"function":null} +{"chromosome":"1","start":1004592,"stop":1004706,"id":"id-GeneID:106783496-2","dbxref":"GeneID:106783496","category":"REGION"} diff --git a/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_by_accession_38.snap b/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_by_accession_38.snap index e0cc15cf..83f15df2 100644 --- a/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_by_accession_38.snap +++ b/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_by_accession_38.snap @@ -2,5 +2,5 @@ source: src/functional/cli/query.rs expression: "&out_data" --- -{"chromosome":"1","start":632109,"stop":632403,"id":"id-GeneID:121967041-2","dbxref":"GeneID:121967041","category":5,"regulatory_class":null,"note":null,"experiment":null,"function":null} +{"chromosome":"1","start":632109,"stop":632403,"id":"id-GeneID:121967041-2","dbxref":"GeneID:121967041","category":"REGION"} diff --git a/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_var_all_37.snap b/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_var_all_37.snap index 434fa70f..07bcee53 100644 --- a/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_var_all_37.snap +++ b/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_var_all_37.snap @@ -2,13259 +2,13259 @@ source: src/functional/cli/query.rs expression: "&out_data" --- -{"chromosome":"11","start":5225101,"stop":5228856,"id":"id-GeneID:105180392","dbxref":"GeneID:105180392","category":6,"regulatory_class":9,"note":null,"experiment":"EXISTENCE:fractionation evidence [ECO:0000100][PMID:8490185]","function":null} -{"chromosome":"11","start":5225101,"stop":5228856,"id":"id-GeneID:105180392-2","dbxref":"GeneID:105180392","category":5,"regulatory_class":null,"note":null,"experiment":null,"function":"regulatory_interactions: LOC110008579"} -{"chromosome":"11","start":5225328,"stop":5227598,"id":"id-GeneID:105180392-3","dbxref":"GeneID:105180392","category":6,"regulatory_class":1,"note":null,"experiment":"EXISTENCE:in vivo cleavage assay evidence [ECO:0001075][PMID:8490185]","function":null} -{"chromosome":"11","start":5226169,"stop":5226240,"id":"id-GeneID:105180392-4","dbxref":"GeneID:105180392","category":6,"regulatory_class":3,"note":null,"experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:11997516]","function":null} -{"chromosome":"11","start":5226196,"stop":5226211,"id":"id-GeneID:105180392-5","dbxref":"GeneID:105180392","category":4,"regulatory_class":null,"note":null,"experiment":"EXISTENCE:protein binding evidence [ECO:0000024][PMID:11997516]","function":"enhancer-blocking activity"} -{"chromosome":"11","start":5227420,"stop":5227449,"id":"id-GeneID:105180392-6","dbxref":"GeneID:105180392","category":4,"regulatory_class":null,"note":null,"experiment":"EXISTENCE:protein binding evidence [ECO:0000024][PMID:8490185]","function":null} -{"chromosome":"11","start":2019975,"stop":2024739,"id":"id-GeneID:105259599","dbxref":"GeneID:105259599","category":6,"regulatory_class":6,"note":null,"experiment":"EXISTENCE:mutant phenotype evidence [ECO:0000015][PMID:15314640, PMID:20007505]","function":"controls imprinted expression of the H19 and IGF2 genes"} -{"chromosome":"11","start":2021476,"stop":2021881,"id":"id-GeneID:105259599-10","dbxref":"GeneID:105259599","category":7,"regulatory_class":null,"note":null,"experiment":null,"function":null} -{"chromosome":"11","start":2021596,"stop":2021643,"id":"id-GeneID:105259599-11","dbxref":"GeneID:105259599","category":4,"regulatory_class":null,"note":null,"experiment":"EXISTENCE:chromatin immunoprecipitation evidence [ECO:0000226][PMID:12960026]","function":"binds the unmethylated maternal allele but not the methylated paternal allele"} -{"chromosome":"11","start":2021882,"stop":2022288,"id":"id-GeneID:105259599-12","dbxref":"GeneID:105259599","category":7,"regulatory_class":null,"note":null,"experiment":null,"function":null} -{"chromosome":"11","start":2022002,"stop":2022049,"id":"id-GeneID:105259599-13","dbxref":"GeneID:105259599","category":4,"regulatory_class":null,"note":null,"experiment":"EXISTENCE:chromatin immunoprecipitation evidence [ECO:0000226][PMID:12960026]","function":"binds 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cancer cells {active_cell/tissue: VCaP}"} +{"chromosome":"21","start":42940858,"stop":42940880,"id":"id-GeneID:117135106-4","dbxref":"GeneID:117135106","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:24109594]","function":"androgen-responsive activation of reporter gene expression when four copies are used in transiently transfected VCaP prostate cancer cells {active_cell/tissue: VCaP(+R1881 androgen)}"} +{"chromosome":"2","start":162931130,"stop":162932906,"id":"id-GeneID:117152610","dbxref":"GeneID:117152610","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:28799235]","function":"drives testosterone- and dihydrotestosterone-stimulated DPP4 expression in transfected COV434 granulosa cells {active_cell/tissue: COV434(+T or +DHT)}"} 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{active_cell/tissue: KG1a | U937 | Jurkat | C33A | immature myeloblast}"} +{"chromosome":"15","start":90358020,"stop":90359174,"id":"id-GeneID:117204000-2","dbxref":"GeneID:117204000","category":"REGION","function":"regulatory_interactions: ANPEP"} +{"chromosome":"15","start":90358020,"stop":90358508,"id":"id-GeneID:117204000-3","dbxref":"GeneID:117204000","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:7721782, PMID:10477683, PMID:9786929, PMID:9566892]","function":"drives ANPEP expression in transfected KG1a myeloblastic, U937 myelomonocitic, Jurkat T lymphoblastic, HL-60 myeloid and NIH3T3 fibroblastic cells {active_cell/tissue: KG1a | U937 | Jurkat | HL-60 | NIH3T3}"} +{"chromosome":"15","start":90358123,"stop":90358128,"id":"id-GeneID:117204000-4","dbxref":"GeneID:117204000","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:site-directed mutagenesis 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[ECO:0000049][PMID:9566892]","function":"positively regulates the -411 to +65 ANPEP distal promoter in transfected KG1a myeloblastic cells {active_cell/tissue: KG1a}"} +{"chromosome":"15","start":90349767,"stop":90351559,"id":"id-GeneID:117204001","dbxref":"GeneID:117204001","category":"REGION","function":"regulatory_interactions: ANPEP"} +{"chromosome":"15","start":90349928,"stop":90350209,"id":"id-GeneID:117204001-10","dbxref":"GeneID:117204001","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:10623580]","function":"ATBF1-mediated negative regulation of the -350 to -68 ANPEP proximal promoter in transfected Caco-2 intestinal cells {active_cell/tissue: Caco-2(+ATBF1-A)}"} 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the -296 CLEC4G promoter in transfected THP-1 monocytic leukemia cells, and is important for transactivation by PU.1 in cooperation with RUNX3 in NIH3T3 fibroblasts {active_cell/tissue: THP-1 | NIH3T3(+PU.1 and RUNX3)}"} +{"chromosome":"19","start":7797229,"stop":7797325,"id":"id-GeneID:117282006-6","dbxref":"GeneID:117282006","category":"REPEAT_REGION","experiment":"EXISTENCE:sequence similarity evidence [ECO:0000044][PMID:19111020]"} +{"chromosome":"19","start":7812298,"stop":7814052,"id":"id-GeneID:117307477","dbxref":"GeneID:117307477","category":"REGION","function":"regulatory_interactions: CD209"} +{"chromosome":"19","start":7812414,"stop":7814052,"id":"id-GeneID:117307477-10","dbxref":"GeneID:117307477","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:16051608]","function":"drives CD209 gene expression in transfected THP-1 monocytic leukemia, K562 erythroleukemia and Jurkat T cells {active_cell/tissue: THP-1 | K562 | Jurkat}"} +{"chromosome":"19","start":7812414,"stop":7813672,"id":"id-GeneID:117307477-11","dbxref":"GeneID:117307477","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:16051608]","function":"drives CD209 gene expression in transfected THP-1 monocytic leukemia cells at high activity, and in K562 erythroleukemia and Jurkat T cells at low activity {active_cell/tissue: THP-1 | K562 | Jurkat}"} +{"chromosome":"19","start":7812414,"stop":7812862,"id":"id-GeneID:117307477-12","dbxref":"GeneID:117307477","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:16051608, PMID:19386588, PMID:24389203]","function":"drives CD209 gene expression in transfected THP-1 monocytic leukemia cells at high activity, and in K562 erythroleukemia and Jurkat T cells at low activity; can be transactivated by RUNX1, RUNX3 or Myb in K562 cells, by PU.1 in THP-1 and 293T cells, or by PU.1 in cooperation with RUNX3 or Myb in NIH3T3 fibroblasts {active_cell/tissue: THP-1 | K562 | Jurkat | 293T(+PU.1) | NIH3T3(+PU.1 and RUNX3 or +PU.1 and Myb)}"} +{"chromosome":"19","start":7812416,"stop":7814052,"id":"id-GeneID:117307477-13","dbxref":"GeneID:117307477","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:31540687]","function":"drives CD209 gene expression in transfected TNF-alpha-induced HK-2 renal proximal tubular epithelial cells, and is positively regulated by RUNX1 {active_cell/tissue: HK-2}"} +{"chromosome":"19","start":7812452,"stop":7812457,"id":"id-GeneID:117307477-14","dbxref":"GeneID:117307477","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:site-directed mutagenesis evidence [ECO:0005528][PMID:12957386]","function":"positively regulates activity of the +251 CD209 promoter in transfected Jurkat T cells and KG-1 macrophages {active_cell/tissue: Jurkat | KG-1}"} +{"chromosome":"19","start":7812471,"stop":7812476,"id":"id-GeneID:117307477-15","dbxref":"GeneID:117307477","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:site-directed mutagenesis evidence [ECO:0005528][PMID:16051608]","function":"contributes to positive regulation of the -468 CD209 promoter in transfected THP-1 monocytic leukemia cells and in PU.1-transactivated NIH3T3 fibroblasts in cooperation with the -111 PU.1 binding region {active_cell/tissue: THP-1 | NIH3T3(+PU.1)}"} +{"chromosome":"19","start":7812482,"stop":7812516,"id":"id-GeneID:117307477-16","dbxref":"GeneID:117307477","category":"PROTEIN_BIND","experiment":"EXISTENCE:protein binding evidence [ECO:0000024][PMID:16051608]","function":"binds PU.1 in THP-1 and MDDC cells {active_cell/tissue: THP-1 | MDDC}"} 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+{"chromosome":"19","start":7812505,"stop":7812505,"id":"id-GeneID:117307477-19","dbxref":"GeneID:117307477","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:site-directed mutagenesis evidence [ECO:0005528][PMID:12957386]","function":"positively regulates activity of the +251 CD209 promoter in transfected Jurkat T cells and KG-1 macrophages {active_cell/tissue: Jurkat | KG-1}"} +{"chromosome":"19","start":7812298,"stop":7813725,"id":"id-GeneID:117307477-2","dbxref":"GeneID:117307477","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:27539513]","function":"drives CD209 gene expression in transfected LC5 embryonic lung and THP-1 monocytic leukemia cells, with higher activity for the XGAG haplotype compared to the XAGA haplotype {active_cell/tissue: LC-5 | THP-1}"} 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{active_cell/tissue: Jurkat | KG-1}"} +{"chromosome":"19","start":7812520,"stop":7812529,"id":"id-GeneID:117307477-22","dbxref":"GeneID:117307477","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:22675249]","function":"positively regulates activity of an 0.2 kb CD209 promoter in transfected 293T embryonic kidney, HaCaT skin and IL-4 + PMA-treated THP-1 monocytic leukemia cells {active_cell/tissue: 293T | HaCaT | THP-1(+IL-4 and PMA)}"} +{"chromosome":"19","start":7812523,"stop":7812527,"id":"id-GeneID:117307477-23","dbxref":"GeneID:117307477","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:site-directed mutagenesis evidence [ECO:0005528][PMID:12957386]","function":"positively regulates activity of the +251 CD209 promoter in transfected Jurkat T cells and KG-1 macrophages {active_cell/tissue: Jurkat | KG-1}"} 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and A375SM melanoma cells {active_cell/tissue: DM-4 | A375SM}"} +{"chromosome":"9","start":90340884,"stop":90340886,"id":"id-GeneID:117600004-25","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:site-directed mutagenesis evidence [ECO:0005528][PMID:20088826]","function":"important for FOXO1-mediated CTSL expression in transfected HEK293 embryonic kidney cells {active_cell/tissue: HEK293}"} +{"chromosome":"9","start":90340897,"stop":90341107,"id":"id-GeneID:117600004-26","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:11574156, PMID:17574778]","function":"drives VEGF-responsive CTSL expression in transfected U87MG glioblastoma cells {active_cell/tissue: U87MG}"} 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cells {active_cell/tissue: DM-4}"} +{"chromosome":"9","start":90339240,"stop":90339561,"id":"id-GeneID:117600004-3","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:11574156]","function":"positively regulates the -1825 CTSL promoter in transfected U87MG glioblastoma cells {active_cell/tissue: U87MG}"} +{"chromosome":"9","start":90340930,"stop":90340932,"id":"id-GeneID:117600004-30","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:site-directed mutagenesis evidence [ECO:0005528][PMID:11742542, PMID:17574778, PMID:18366346]","function":"positively regulates and confers VEGF responsiveness on the CTSL promoter in transfected DM-4 and A375SM melanoma cells and U87MG glioblastoma cells {active_cell/tissue: DM-4 | A375SM | U87MG}"} 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+{"chromosome":"9","start":90341312,"stop":90342351,"id":"id-GeneID:117600004-38","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:14636995]","function":"drives CTSL expression with modest activity in transfected HepG2 heptocarcinoma cells {active_cell/tissue: HepG2}"} +{"chromosome":"9","start":90341551,"stop":90341696,"id":"id-GeneID:117600004-39","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:14636995]","function":"negatively regulates the hCATL B CTSL promoter in transfected HepG2 heptocarcinoma cells {active_cell/tissue: HepG2}"} +{"chromosome":"9","start":90339458,"stop":90341079,"id":"id-GeneID:117600004-4","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:20088826]","function":"drives FOXO1-mediated CTSL expression in transfected HEK293 embryonic kidney cells {active_cell/tissue: HEK293}"} +{"chromosome":"9","start":90341697,"stop":90341930,"id":"id-GeneID:117600004-40","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:14636995]","function":"negatively regulates the hCATL B CTSL promoter in transfected HepG2 heptocarcinoma cells {active_cell/tissue: HepG2}"} +{"chromosome":"9","start":90341931,"stop":90342351,"id":"id-GeneID:117600004-41","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:14636995]","function":"drives CTSL expression with moderate activity in transformed HepG2 heptocarcinoma and U87MG glioblastoma cells, and with low activity in untransformed Chang liver cells {active_cell/tissue: HepG2 | U87MG | Chang liver}"} +{"chromosome":"9","start":90339562,"stop":90341107,"id":"id-GeneID:117600004-5","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:11574156, PMID:20536385]","function":"drives CTSL expression in transfected U87MG and U373MG glioblastoma cells {active_cell/tissue: U87MG | U373MG}"} +{"chromosome":"9","start":90339574,"stop":90341006,"id":"id-GeneID:117600004-6","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:22871890]","function":"drives CTSL expression in transfected PC12 rat chromaffin cells {active_cell/tissue: PC12}"} +{"chromosome":"9","start":90339615,"stop":90339644,"id":"id-GeneID:117600004-7","dbxref":"GeneID:117600004","category":"PROTEIN_BIND","experiment":"EXISTENCE:protein binding evidence [ECO:0000024][PMID:20088826]"} +{"chromosome":"9","start":90339629,"stop":90339631,"id":"id-GeneID:117600004-8","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"TRANSCRIPTIONAL_CIS_REGULATORY_REGION","experiment":"EXISTENCE:site-directed mutagenesis evidence [ECO:0005528][PMID:20088826]","function":"important for FOXO1-mediated CTSL expression in transfected HEK293 embryonic kidney cells {active_cell/tissue: HEK293}"} +{"chromosome":"9","start":90339776,"stop":90341107,"id":"id-GeneID:117600004-9","dbxref":"GeneID:117600004","category":"REGULATORY","regulatoryClass":"PROMOTER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:21700710]","function":"drives PPARgamma-induced CTSL expression with low-moderate activity in GW929-treated human monocyte-derived macrophages {active_cell/tissue: HMDM(+GW929)}"} +{"chromosome":"9","start":90346023,"stop":90347522,"id":"id-GeneID:117693187","dbxref":"GeneID:117693187","category":"REGULATORY","regulatoryClass":"SILENCER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:18366346]","function":"represses activity of the CTSL promoter in transfected A375SM melanoma cells {active_cell/tissue: A375SM}"} +{"chromosome":"9","start":90346023,"stop":90347522,"id":"id-GeneID:117693187-2","dbxref":"GeneID:117693187","category":"REGION","function":"regulatory_interactions: CTSL | LOC117600004"} diff --git a/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_var_range_37.snap b/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_var_range_37.snap index c4a5d633..e4925313 100644 --- a/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_var_range_37.snap +++ b/src/functional/cli/snapshots/annonars__functional__cli__query__test__smoke_query_var_range_37.snap @@ -2,6 +2,6 @@ source: src/functional/cli/query.rs expression: "&out_data" --- -{"chromosome":"1","start":3157509,"stop":3157803,"id":"id-GeneID:112577578","dbxref":"GeneID:112577578","category":6,"regulatory_class":2,"note":null,"experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:27701403]","function":"activates a minimal TATA promoter and a strong SV40 promoter by Sharpr-MPRA in K562 cells"} -{"chromosome":"1","start":3157509,"stop":3157803,"id":"id-GeneID:112577578-2","dbxref":"GeneID:112577578","category":5,"regulatory_class":null,"note":null,"experiment":null,"function":null} +{"chromosome":"1","start":3157509,"stop":3157803,"id":"id-GeneID:112577578","dbxref":"GeneID:112577578","category":"REGULATORY","regulatoryClass":"ENHANCER","experiment":"EXISTENCE:reporter gene assay evidence [ECO:0000049][PMID:27701403]","function":"activates a minimal TATA promoter and a strong SV40 promoter by Sharpr-MPRA in K562 cells"} +{"chromosome":"1","start":3157509,"stop":3157803,"id":"id-GeneID:112577578-2","dbxref":"GeneID:112577578","category":"REGION"} diff --git a/src/genes/cli/data.rs b/src/genes/cli/data.rs index 4136376c..69a1030d 100644 --- a/src/genes/cli/data.rs +++ b/src/genes/cli/data.rs @@ -1537,7 +1537,7 @@ pub mod shet { pub mod gtex { use serde::{Deserialize, Serialize}; - use crate::genes::pbs::{GtexTissue, GtexTissueDetailed}; + use crate::pbs::genes::{GtexTissue, GtexTissueDetailed}; /// GTEx V8 tissue types. #[derive(Debug, Clone, Serialize, Deserialize)] diff --git a/src/genes/cli/import.rs b/src/genes/cli/import.rs index 1d1d9032..4d2f03f4 100644 --- a/src/genes/cli/import.rs +++ b/src/genes/cli/import.rs @@ -13,7 +13,7 @@ use tracing::info; use crate::{ common::{self, version}, - genes::pbs, + pbs, }; use super::data::{ @@ -332,8 +332,8 @@ fn load_gtex(path: &str) -> Result, anyhow::Error> Ok(result) } -/// Convert from `data::*` records to `pbs::*` records. -fn convert_record(record: data::Record) -> pbs::Record { +/// Convert from `data::*` records to protobuf records. +fn convert_record(record: data::Record) -> pbs::genes::Record { let data::Record { acmg_sf, clingen, @@ -363,7 +363,7 @@ fn convert_record(record: data::Record) -> pbs::Record { variants_to_report, } = acmg_sf; - pbs::AcmgSecondaryFindingRecord { + pbs::genes::AcmgSecondaryFindingRecord { hgnc_id, ensembl_gene_id, ncbi_gene_id, @@ -380,7 +380,7 @@ fn convert_record(record: data::Record) -> pbs::Record { let clingen = clingen.map(|clingen| { let first = clingen[0].clone(); - let mut result = pbs::ClingenCurationRecord { + let mut result = pbs::genes::ClingenCurationRecord { gene_symbol: first.gene_symbol, hgnc_id: first.hgnc_id, gene_url: first.gene_url, @@ -390,7 +390,7 @@ fn convert_record(record: data::Record) -> pbs::Record { for record in clingen { result .disease_records - .push(pbs::ClingenCurationDiseaseRecord { + .push(pbs::genes::ClingenCurationDiseaseRecord { disease_label: record.disease_label.clone(), mondo_id: record.mondo_id.clone(), disease_url: record.disease_url.clone(), @@ -524,7 +524,7 @@ fn convert_record(record: data::Record) -> pbs::Record { zfin_zebrafish_phenotype_tag, } = dbnsfp; - pbs::DbnsfpRecord { + pbs::genes::DbnsfpRecord { gene_name, ensembl_gene, chr, @@ -656,7 +656,7 @@ fn convert_record(record: data::Record) -> pbs::Record { exac_oe_lof, } = gnomad_constraints; - pbs::GnomadConstraintsRecord { + pbs::genes::GnomadConstraintsRecord { ensembl_gene_id, entrez_id, gene_symbol, @@ -738,7 +738,7 @@ fn convert_record(record: data::Record) -> pbs::Record { mane_select, } = hgnc; - Some(pbs::HgncRecord { + Some(pbs::genes::HgncRecord { hgnc_id, symbol, name, @@ -772,7 +772,7 @@ fn convert_record(record: data::Record) -> pbs::Record { lsdb: lsdb .map(|lsdb| { lsdb.iter() - .map(|lsdb| pbs::HgncLsdb { + .map(|lsdb| pbs::genes::HgncLsdb { name: lsdb.name.clone(), url: lsdb.url.clone(), }) @@ -807,14 +807,14 @@ fn convert_record(record: data::Record) -> pbs::Record { summary, rif_entries, } = ncbi; - pbs::NcbiRecord { + pbs::genes::NcbiRecord { gene_id, summary, rif_entries: rif_entries .map(|rif_entries| { rif_entries .into_iter() - .map(|rif_entry| pbs::RifEntry { + .map(|rif_entry| pbs::genes::RifEntry { pmids: rif_entry.pmids.unwrap_or_default(), text: rif_entry.text, }) @@ -826,11 +826,11 @@ fn convert_record(record: data::Record) -> pbs::Record { let omim = omim.map(|omim| { let omim::Record { hgnc_id, diseases } = omim; - pbs::OmimRecord { + pbs::genes::OmimRecord { hgnc_id, omim_diseases: diseases .into_iter() - .map(|disease| pbs::OmimTerm { + .map(|disease| pbs::genes::OmimTerm { omim_id: disease.omim_id, label: disease.label, }) @@ -840,11 +840,11 @@ fn convert_record(record: data::Record) -> pbs::Record { let orpha = orpha.map(|orpha| { let orpha::Record { hgnc_id, diseases } = orpha; - pbs::OrphaRecord { + pbs::genes::OrphaRecord { hgnc_id, orpha_diseases: diseases .into_iter() - .map(|disease| pbs::OrphaTerm { + .map(|disease| pbs::genes::OrphaTerm { orpha_id: disease.orpha_id, label: disease.label, }) @@ -858,7 +858,7 @@ fn convert_record(record: data::Record) -> pbs::Record { p_haplo, p_triplo, } = rcnv; - pbs::RcnvRecord { + pbs::genes::RcnvRecord { hgnc_id, p_haplo, p_triplo, @@ -867,7 +867,7 @@ fn convert_record(record: data::Record) -> pbs::Record { let shet = shet.map(|shet| { let shet::Record { hgnc_id, s_het } = shet; - pbs::ShetRecord { hgnc_id, s_het } + pbs::genes::ShetRecord { hgnc_id, s_het } }); let gtex = gtex.map(|gtex| { @@ -885,14 +885,14 @@ fn convert_record(record: data::Record) -> pbs::Record { tissue_detailed, tpms, } = record; - pbs::GtexTissueRecord { + pbs::genes::GtexTissueRecord { tissue: tissue as i32, tissue_detailed: tissue_detailed as i32, tpms, } }) .collect::>(); - pbs::GtexRecord { + pbs::genes::GtexRecord { hgnc_id, ensembl_gene_id, ensembl_gene_version, @@ -900,7 +900,7 @@ fn convert_record(record: data::Record) -> pbs::Record { } }); - pbs::Record { + pbs::genes::Record { acmg_sf, clingen, dbnsfp, diff --git a/src/genes/cli/query.rs b/src/genes/cli/query.rs index 0d58359a..a4c3a4d9 100644 --- a/src/genes/cli/query.rs +++ b/src/genes/cli/query.rs @@ -4,7 +4,7 @@ use std::sync::Arc; use prost::Message; -use crate::{common, genes::pbs}; +use crate::{common, pbs::genes}; /// Command line arguments for `gene query` sub command. #[derive(clap::Parser, Debug, Clone)] @@ -63,7 +63,7 @@ pub fn open_rocksdb_from_args( fn print_record( out_writer: &mut Box, output_format: common::cli::OutputFormat, - value: &pbs::Record, + value: &genes::Record, ) -> Result<(), anyhow::Error> { match output_format { common::cli::OutputFormat::Jsonl => { @@ -79,13 +79,13 @@ pub fn query_for_gene( hgnc_id: &str, db: &rocksdb::DBWithThreadMode, cf_data: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { let raw_value = db .get_cf(cf_data, hgnc_id.as_bytes()) .map_err(|e| anyhow::anyhow!("error while querying for HGNC ID {}: {}", hgnc_id, e))?; raw_value .map(|raw_value| { - pbs::Record::decode(&mut std::io::Cursor::new(&raw_value)).map_err(|e| { + genes::Record::decode(&mut std::io::Cursor::new(&raw_value)).map_err(|e| { anyhow::anyhow!( "error while decoding gene record for HGNC ID {}: {}", hgnc_id, diff --git a/src/genes/mod.rs b/src/genes/mod.rs index f553b0fb..909c7e7b 100644 --- a/src/genes/mod.rs +++ b/src/genes/mod.rs @@ -1,4 +1,3 @@ //! Code for storing and querying gene-related information. pub mod cli; -pub mod pbs; diff --git a/src/genes/pbs.rs b/src/genes/pbs.rs deleted file mode 100644 index db951c5c..00000000 --- a/src/genes/pbs.rs +++ /dev/null @@ -1,3 +0,0 @@ -//! Data structures for (de-)serialization as generated by `prost-build`. - -include!(concat!(env!("OUT_DIR"), "/annonars.gene.v1.base.rs")); diff --git a/src/gnomad_mtdna/cli/import.rs b/src/gnomad_mtdna/cli/import.rs index 530d682f..619014b8 100644 --- a/src/gnomad_mtdna/cli/import.rs +++ b/src/gnomad_mtdna/cli/import.rs @@ -3,13 +3,13 @@ use std::sync::Arc; use clap::Parser; -use indicatif::ParallelProgressIterator; -use prost::Message; +use indicatif::ParallelProgressIterator as _; +use prost::Message as _; use rayon::prelude::{IntoParallelRefIterator, ParallelIterator}; use crate::{ common::{self}, - gnomad_pbs, + pbs, }; /// Command line arguments for `gnomad_mtdna import` sub command. @@ -145,7 +145,7 @@ fn process_window( for allele_no in 0..vcf_record.alternate_bases().len() { let key_buf: Vec = common::keys::Var::from_vcf_allele(&vcf_record, allele_no).into(); - let record = gnomad_pbs::mtdna::Record::from_vcf_allele( + let record = pbs::gnomad::mtdna::Record::from_vcf_allele( &vcf_record, allele_no, &details_options, @@ -168,13 +168,13 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> .import_fields_json .clone() .map(|v| { - serde_json::to_string(&serde_json::from_str::( + serde_json::to_string(&serde_json::from_str::( &v, )?) }) .or_else(|| { Some(serde_json::to_string( - &gnomad_pbs::mtdna::DetailsOptions::default(), + &pbs::gnomad::mtdna::DetailsOptions::default(), )) }) .transpose()?, @@ -231,7 +231,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> #[cfg(test)] mod test { - use crate::gnomad_pbs::mtdna::DetailsOptions; + use crate::pbs::gnomad::mtdna::DetailsOptions; use super::*; diff --git a/src/gnomad_mtdna/cli/query.rs b/src/gnomad_mtdna/cli/query.rs index 53da42d1..71187dfd 100644 --- a/src/gnomad_mtdna/cli/query.rs +++ b/src/gnomad_mtdna/cli/query.rs @@ -7,7 +7,7 @@ use prost::Message; use crate::{ common::{self, cli::extract_chrom, keys, spdi}, cons::cli::args::vars::ArgsQuery, - gnomad_pbs, + pbs, }; /// Command line arguments for `tsv query` sub command. @@ -85,7 +85,7 @@ pub fn open_rocksdb_from_args( fn print_record( out_writer: &mut Box, output_format: common::cli::OutputFormat, - value: &gnomad_pbs::mtdna::Record, + value: &pbs::gnomad::mtdna::Record, ) -> Result<(), anyhow::Error> { match output_format { common::cli::OutputFormat::Jsonl => { @@ -102,7 +102,7 @@ pub fn query_for_variant( meta: &Meta, db: &rocksdb::DBWithThreadMode, cf_data: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { // Split off the genome release (checked) and convert to key as used in database. let query = spdi::Var { sequence: extract_chrom::from_var(variant, Some(&meta.genome_release))?, @@ -118,7 +118,7 @@ pub fn query_for_variant( raw_value .map(|raw_value| { // Decode via prost. - gnomad_pbs::mtdna::Record::decode(&mut std::io::Cursor::new(&raw_value)) + pbs::gnomad::mtdna::Record::decode(&mut std::io::Cursor::new(&raw_value)) .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) }) .transpose() @@ -204,7 +204,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> } let record = - gnomad_pbs::mtdna::Record::decode(&mut std::io::Cursor::new(&raw_value)) + pbs::gnomad::mtdna::Record::decode(&mut std::io::Cursor::new(&raw_value)) .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; print_record(&mut out_writer, args.out_format, &record)?; iter.next(); diff --git a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_all.snap b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_all.snap index 86db986e..7004f585 100644 --- a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_all.snap +++ b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_all.snap @@ -2,8 +2,8 @@ source: src/gnomad_mtdna/cli/query.rs expression: "&out_data" --- 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diff --git a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_pos_single.snap b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_pos_single.snap index 1a2243b8..927b87e3 100644 --- a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_pos_single.snap +++ b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_pos_single.snap @@ -2,5 +2,5 @@ source: src/gnomad_mtdna/cli/query.rs expression: "&out_data" --- 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diff --git a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_all.snap b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_all.snap index 86db986e..7004f585 100644 --- a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_all.snap +++ b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_all.snap @@ -2,8 +2,8 @@ source: src/gnomad_mtdna/cli/query.rs expression: "&out_data" --- 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diff --git a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_first.snap b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_first.snap index f40c368f..93d95d63 100644 --- a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_first.snap +++ b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_first.snap @@ -2,5 +2,5 @@ source: src/gnomad_mtdna/cli/query.rs expression: "&out_data" --- 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diff --git a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_second.snap b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_second.snap index 5252f768..553ed1a7 100644 --- a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_second.snap +++ b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_range_find_second.snap @@ -2,5 +2,5 @@ source: src/gnomad_mtdna/cli/query.rs expression: "&out_data" --- 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diff --git a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_var_single.snap b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_var_single.snap index 1a2243b8..927b87e3 100644 --- a/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_var_single.snap +++ b/src/gnomad_mtdna/cli/snapshots/annonars__gnomad_mtdna__cli__query__test__smoke_query_var_single.snap @@ -2,5 +2,5 @@ source: src/gnomad_mtdna/cli/query.rs expression: "&out_data" --- 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diff --git a/src/gnomad_nuclear/cli/import.rs b/src/gnomad_nuclear/cli/import.rs index b8eeb1c1..285f3a76 100644 --- a/src/gnomad_nuclear/cli/import.rs +++ b/src/gnomad_nuclear/cli/import.rs @@ -10,7 +10,7 @@ use rayon::prelude::{IntoParallelRefIterator, ParallelIterator}; use crate::{ common::{self}, - gnomad_pbs::{self, gnomad2, gnomad3}, + pbs::gnomad::{gnomad2, gnomad3}, }; /// Select the type of gnomAD data to import. @@ -203,7 +203,7 @@ fn process_window( .as_ref() .expect("has been set earlier"), )?; - gnomad_pbs::gnomad2::Record::from_vcf_allele( + crate::pbs::gnomad::gnomad2::Record::from_vcf_allele( &vcf_record, allele_no, &details_options, @@ -216,7 +216,7 @@ fn process_window( .as_ref() .expect("has been set earlier"), )?; - gnomad_pbs::gnomad3::Record::from_vcf_allele( + crate::pbs::gnomad::gnomad3::Record::from_vcf_allele( &vcf_record, allele_no, &details_options, diff --git a/src/gnomad_nuclear/cli/query.rs b/src/gnomad_nuclear/cli/query.rs index 8f74e2d0..51b66850 100644 --- a/src/gnomad_nuclear/cli/query.rs +++ b/src/gnomad_nuclear/cli/query.rs @@ -2,12 +2,12 @@ use std::{io::Write, sync::Arc}; -use prost::Message; +use prost::Message as _; use crate::{ common::{self, cli::extract_chrom, keys, spdi}, cons::cli::args::vars::ArgsQuery, - gnomad_pbs, + pbs, }; /// Command line arguments for `tsv query` sub command. @@ -85,7 +85,7 @@ pub fn open_rocksdb_from_args( fn print_record( out_writer: &mut Box, output_format: common::cli::OutputFormat, - value: &gnomad_pbs::gnomad2::Record, + value: &pbs::gnomad::gnomad2::Record, ) -> Result<(), anyhow::Error> { match output_format { common::cli::OutputFormat::Jsonl => { @@ -102,7 +102,7 @@ pub fn query_for_variant( meta: &Meta, db: &rocksdb::DBWithThreadMode, cf_data: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { // Split off the genome release (checked) and convert to key as used in database. let query = spdi::Var { sequence: extract_chrom::from_var(variant, Some(&meta.genome_release))?, @@ -118,7 +118,7 @@ pub fn query_for_variant( raw_value .map(|raw_value| { // Decode via prost. - gnomad_pbs::gnomad2::Record::decode(&mut std::io::Cursor::new(&raw_value)) + pbs::gnomad::gnomad2::Record::decode(&mut std::io::Cursor::new(&raw_value)) .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) }) .transpose() @@ -204,7 +204,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> } let record = - gnomad_pbs::gnomad2::Record::decode(&mut std::io::Cursor::new(&raw_value)) + pbs::gnomad::gnomad2::Record::decode(&mut std::io::Cursor::new(&raw_value)) .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; print_record(&mut out_writer, args.out_format, &record)?; iter.next(); diff --git a/src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_all.snap b/src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_all.snap index 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diff --git a/src/gnomad_pbs/exac_cnv.rs b/src/gnomad_pbs/exac_cnv.rs deleted file mode 100644 index 5786f4b0..00000000 --- a/src/gnomad_pbs/exac_cnv.rs +++ /dev/null @@ -1,3 +0,0 @@ -//! Code for working with the ExAC r1 CNV data. - -include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.v1.exac_cnv.rs")); diff --git a/src/gnomad_pbs/gnomad_cnv4.rs b/src/gnomad_pbs/gnomad_cnv4.rs deleted file mode 100644 index 509722b9..00000000 --- a/src/gnomad_pbs/gnomad_cnv4.rs +++ /dev/null @@ -1,6 +0,0 @@ -//! Code for working with the gnomAD CNV v4.0 data. - -include!(concat!( - env!("OUT_DIR"), - "/annonars.gnomad.v1.gnomad_cnv4.rs" -)); diff --git a/src/gnomad_pbs/gnomad_sv2.rs b/src/gnomad_pbs/gnomad_sv2.rs deleted file mode 100644 index 3490957b..00000000 --- a/src/gnomad_pbs/gnomad_sv2.rs +++ /dev/null @@ -1,6 +0,0 @@ -//! Code for working with the gnomAD SV v2.1 data. - -include!(concat!( - env!("OUT_DIR"), - "/annonars.gnomad.v1.gnomad_sv2.rs" -)); diff --git a/src/gnomad_pbs/gnomad_sv4.rs b/src/gnomad_pbs/gnomad_sv4.rs deleted file mode 100644 index a814459a..00000000 --- a/src/gnomad_pbs/gnomad_sv4.rs +++ /dev/null @@ -1,6 +0,0 @@ -//! Code for working with the gnomAD SV v4.0 data. - -include!(concat!( - env!("OUT_DIR"), - "/annonars.gnomad.v1.gnomad_sv4.rs" -)); diff --git a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad2__test__record_from_vcf_allele_gnomad_exomes_grch37.snap b/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad2__test__record_from_vcf_allele_gnomad_exomes_grch37.snap deleted file mode 100644 index e90bcc18..00000000 --- a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad2__test__record_from_vcf_allele_gnomad_exomes_grch37.snap +++ /dev/null @@ -1,10293 +0,0 @@ ---- -source: src/gnomad_pbs/gnomad2.rs -expression: records ---- -- chrom: "1" - pos: 55505599 - ref_allele: C - alt_allele: G - filters: [] - vep: - - allele: G - consequence: missense_variant - impact: MODERATE - symbol: PCSK9 - gene: ENSG00000169174 - feature_type: Transcript - feature: ENST00000302118 - feature_biotype: protein_coding - exon: 1/12 - intron: ~ - hgvsc: "ENST00000302118.5:c.89C>G" - hgvsp: 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clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: "DE_NOVO_DONOR_PROB:0.146539915246404&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_POS:-119&INTRON_END:55509515&DE_NOVO_DONOR_MES_POS:-122&INTRON_START:55505718&EXON_END:55505717&EXON_START:55505221&DE_NOVO_DONOR_MES:-1.61109392005567" - - allele: G - consequence: missense_variant - impact: MODERATE - symbol: PCSK9 - gene: ENSG00000169174 - feature_type: Transcript - feature: ENST00000452118 - feature_biotype: protein_coding - exon: 1/6 - intron: ~ - hgvsc: "ENST00000452118.2:c.89C>G" - hgvsp: "ENSP00000401598.2:p.Ala30Gly" - cdna_position: "169" - cds_position: "89" - protein_position: "30" - amino_acids: A/G - codons: gCg/gGg - existing_variation: ~ - dbsnp_id: "1" - distance: ~ - strand: "1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: HGNC - hgnc_id: "20001" - canonical: false - tsl: ~ - 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- dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] -- chrom: "1" - pos: 55505615 - ref_allele: C - alt_allele: T - filters: [] - vep: - - allele: T - consequence: synonymous_variant - impact: LOW - symbol: PCSK9 - gene: ENSG00000169174 - feature_type: Transcript - feature: ENST00000302118 - feature_biotype: protein_coding - exon: 1/12 - intron: ~ - hgvsc: "ENST00000302118.5:c.105C>T" - hgvsp: "ENST00000302118.5:c.105C>T(p.=)" - cdna_position: "395" - cds_position: "105" - protein_position: "35" - amino_acids: D - codons: gaC/gaT - existing_variation: rs533474523 - dbsnp_id: "1" - distance: ~ - strand: "1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: HGNC - hgnc_id: "20001" - canonical: true - tsl: ~ - appris: ~ - ccds: CCDS603.1 - ensp: ENSP00000303208 - swissprot: Q8NBP7 - trembl: ~ - uniparc: UPI00001615E1 - gene_pheno: "1" - sift: ~ - polyphen: ~ - domains: - - id: PTHR10795 - source: hmmpanther - - id: PTHR10795 - source: hmmpanther - hgvs_offset: ~ - gmaf: 0.0002 - afr_maf: 0.0002414 - amr_maf: 0 - eas_maf: 0 - eur_maf: 0 - sas_maf: 0 - aa_maf: 0.001 - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: 0 - exac_afr_maf: 0.00001679 - exac_amr_maf: 0 - exac_eas_maf: 0.00007421 - exac_fin_maf: 0 - exac_nfe_maf: 0 - exac_oth_maf: 0 - exac_sas_maf: 0 - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: "DE_NOVO_DONOR_MES_POS:-106&INTRON_START:55505718&INTRON_END:55509515&EXON_START:55505221&DE_NOVO_DONOR_MES:-4.29805061924569&EXON_END:55505717&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_PROB:0.0706215314144107&DE_NOVO_DONOR_POS:-105" - - allele: T - consequence: synonymous_variant - impact: LOW - symbol: PCSK9 - gene: ENSG00000169174 - feature_type: Transcript - feature: ENST00000452118 - feature_biotype: protein_coding - exon: 1/6 - intron: ~ - hgvsc: "ENST00000452118.2:c.105C>T" - hgvsp: "ENST00000452118.2:c.105C>T(p.=)" - 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an_popmax: 31262 - nhomalt_popmax: 0 - nonpar: true - liftover_info: ~ - rf_info: - rf_tp_probability: 0.779496 - rf_positive_label: false - rf_negative_label: false - rf_label: ~ - rf_train: false - variant_info: - variant_type: snv - allele_type: snv - n_alt_alleles: 1 - was_mixed: false - has_star: false - quality_info: - fs: 0 - inbreeding_coeff: -0.0015 - mq: 54.15 - mq_rank_sum: ~ - qd: 32.98 - read_pos_rank_sum: ~ - vqsr_positive_train_site: false - vqsr_negative_train_site: true - base_q_rank_sum: ~ - clipping_rank_sum: ~ - sor: 1.091 - dp: 3965717 - vqslod: 3.32 - vqsr_culprit: MQ - segdup: true - lcr: false - decoy: false - transmitted_singleton: false - pab_max: ~ - age_info: - age_hist_hom_bin_freq: [] - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: [] - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 3 - dp_hist_alt_n_larger: 1 - dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] - diff --git a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad2__test__record_from_vcf_allele_gnomad_exomes_grch38.snap b/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad2__test__record_from_vcf_allele_gnomad_exomes_grch38.snap deleted file mode 100644 index 86e2ce56..00000000 --- a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad2__test__record_from_vcf_allele_gnomad_exomes_grch38.snap +++ /dev/null @@ -1,5912 +0,0 @@ ---- -source: src/gnomad_pbs/gnomad2.rs -expression: records ---- -- chrom: chr1 - pos: 138653 - ref_allele: C - alt_allele: G - filters: [] - vep: - - allele: G - consequence: synonymous_variant - impact: LOW - symbol: AL627309.1 - gene: ENSG00000237683 - feature_type: Transcript - feature: ENST00000423372 - feature_biotype: protein_coding - exon: 1/2 - intron: ~ - hgvsc: "ENST00000423372.3:c.657G>C" - hgvsp: "ENST00000423372.3:c.657G>C(p.=)" - cdna_position: "727" - cds_position: "657" - protein_position: "219" - amino_acids: G - codons: ggG/ggC - existing_variation: ~ - dbsnp_id: "1" - distance: ~ - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: Clone_based_ensembl_gene - hgnc_id: ~ - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ENSP00000473460 - swissprot: ~ - trembl: R4GN28&B7Z7W4 - uniparc: UPI0002C88512 - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - eur_maf: ~ - sas_maf: ~ - aa_maf: ~ - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: G - consequence: downstream_gene_variant - impact: MODIFIER - symbol: CICP27 - gene: ENSG00000233750 - feature_type: Transcript - feature: ENST00000442987 - feature_biotype: processed_pseudogene - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - existing_variation: ~ - dbsnp_id: "1" - distance: "3817" - strand: "1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: HGNC - hgnc_id: "48835" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - eur_maf: ~ - sas_maf: ~ - aa_maf: ~ - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: G - consequence: downstream_gene_variant - impact: MODIFIER - symbol: RP11-34P13.13 - gene: ENSG00000241860 - feature_type: Transcript - feature: ENST00000484859 - feature_biotype: antisense - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - existing_variation: ~ - dbsnp_id: "1" - distance: "2821" - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: Clone_based_vega_gene - hgnc_id: ~ - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - eur_maf: ~ - sas_maf: ~ - aa_maf: ~ - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - 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reverse_complemented_alleles: false - swapped_alleles: false - original_alleles: [] - original_contig: "1" - original_start: "138654" - rf_info: - rf_tp_probability: 0.0797253 - rf_positive_label: false - rf_negative_label: false - rf_label: ~ - rf_train: false - variant_info: - variant_type: snv - allele_type: snv - n_alt_alleles: 1 - was_mixed: false - has_star: false - quality_info: - fs: 0.508 - inbreeding_coeff: -0.0431 - mq: 36.86 - mq_rank_sum: 0.482 - qd: 5.59 - read_pos_rank_sum: 0.516 - vqsr_positive_train_site: false - vqsr_negative_train_site: false - base_q_rank_sum: 3.84 - clipping_rank_sum: -0.328 - sor: 0.638 - dp: 4938132 - vqslod: 0.585 - vqsr_culprit: QD - segdup: true - lcr: false - decoy: false - transmitted_singleton: false - pab_max: 1 - age_info: - age_hist_hom_bin_freq: [] - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: [] - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 15028 - dp_hist_alt_n_larger: 2 - dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] -- chrom: chr1 - pos: 138667 - ref_allele: G - alt_allele: C - filters: [] - vep: - - allele: C - consequence: missense_variant - impact: MODERATE - symbol: AL627309.1 - gene: ENSG00000237683 - feature_type: Transcript - feature: ENST00000423372 - feature_biotype: protein_coding - exon: 1/2 - intron: ~ - hgvsc: "ENST00000423372.3:c.643C>G" - hgvsp: "ENSP00000473460.1:p.Leu215Val" - cdna_position: "713" - cds_position: "643" - protein_position: "215" - amino_acids: L/V - codons: Ctt/Gtt - existing_variation: ~ - dbsnp_id: "1" - distance: ~ - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: Clone_based_ensembl_gene - hgnc_id: ~ - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ENSP00000473460 - swissprot: ~ - trembl: R4GN28&B7Z7W4 - uniparc: UPI0002C88512 - gene_pheno: ~ - sift: - prediction: tolerated - score: 0.09 - polyphen: - prediction: possibly_damaging - score: 0.801 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appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - eur_maf: ~ - sas_maf: ~ - aa_maf: ~ - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: RP11-34P13.13 - gene: ENSG00000241860 - feature_type: Transcript - feature: ENST00000484859 - feature_biotype: antisense - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - existing_variation: ~ - dbsnp_id: "1" - distance: "2807" - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: Clone_based_vega_gene - hgnc_id: ~ - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - eur_maf: ~ - sas_maf: ~ - aa_maf: ~ - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: RP11-34P13.13 - gene: ENSG00000241860 - feature_type: Transcript - feature: ENST00000490997 - feature_biotype: antisense - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - existing_variation: ~ - dbsnp_id: "1" - distance: "4141" - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: Clone_based_vega_gene - hgnc_id: ~ - canonical: false - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - eur_maf: ~ - sas_maf: ~ - aa_maf: ~ - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: RP11-34P13.14 - gene: ENSG00000239906 - feature_type: Transcript - feature: ENST00000493797 - feature_biotype: 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RP11-34P13.15 - gene: ENSG00000268903 - feature_type: Transcript - feature: ENST00000494149 - feature_biotype: processed_pseudogene - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - existing_variation: ~ - dbsnp_id: "1" - distance: "2772" - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: Clone_based_vega_gene - hgnc_id: ~ - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - eur_maf: ~ - sas_maf: ~ - aa_maf: ~ - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: upstream_gene_variant - impact: MODIFIER - symbol: RP11-34P13.16 - gene: ENSG00000269981 - feature_type: Transcript - feature: ENST00000595919 - feature_biotype: processed_pseudogene - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - existing_variation: ~ - dbsnp_id: "1" - distance: "702" - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: Clone_based_vega_gene - hgnc_id: ~ - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - eur_maf: ~ - sas_maf: ~ - aa_maf: ~ - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: 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af: 0 - xy: - ac: 1 - an: 27368 - nhomalt: 0 - af: 0.000036539 - raw: - ac: 1 - an: 109674 - nhomalt: 0 - af: 0.00000911793 - popmax: sas - af_popmax: 0.000163079 - ac_popmax: 1 - an_popmax: 6132 - nhomalt_popmax: 0 - nonpar: false - liftover_info: - reverse_complemented_alleles: false - swapped_alleles: false - original_alleles: [] - original_contig: "1" - original_start: "138667" - rf_info: - rf_tp_probability: 0.0108928 - rf_positive_label: false - rf_negative_label: false - rf_label: ~ - rf_train: false - variant_info: - variant_type: snv - allele_type: snv - n_alt_alleles: 1 - was_mixed: false - has_star: false - quality_info: - fs: 18.822 - inbreeding_coeff: -0.0435 - mq: 34.94 - mq_rank_sum: -1.023 - qd: 4.06 - read_pos_rank_sum: -0.527 - vqsr_positive_train_site: false - vqsr_negative_train_site: false - base_q_rank_sum: -0.581 - clipping_rank_sum: 0.03 - sor: 0.09 - dp: 4968225 - vqslod: -13.81 - vqsr_culprit: FS - segdup: true - lcr: false - decoy: false - transmitted_singleton: false - pab_max: 0.000000000185456 - age_info: - age_hist_hom_bin_freq: [] - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: [] - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 15028 - dp_hist_alt_n_larger: 1 - dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] - diff --git a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad2__test__record_from_vcf_allele_gnomad_genomes_grch37.snap b/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad2__test__record_from_vcf_allele_gnomad_genomes_grch37.snap deleted file mode 100644 index 742f9abf..00000000 --- a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad2__test__record_from_vcf_allele_gnomad_genomes_grch37.snap +++ /dev/null @@ -1,4395 +0,0 @@ ---- -source: src/gnomad_pbs/gnomad2.rs -expression: records ---- -- chrom: "1" - pos: 55505599 - ref_allele: C - alt_allele: G - filters: [] - vep: - - allele: G - consequence: missense_variant - impact: MODERATE - symbol: PCSK9 - gene: ENSG00000169174 - feature_type: Transcript - feature: ENST00000302118 - feature_biotype: protein_coding - exon: 1/12 - intron: ~ - hgvsc: "ENST00000302118.5:c.89C>G" - hgvsp: "ENSP00000303208.5:p.Ala30Gly" - cdna_position: "379" - cds_position: "89" - protein_position: "30" - amino_acids: A/G - codons: gCg/gGg - existing_variation: ~ - dbsnp_id: "1" - distance: ~ - strand: "1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: HGNC - hgnc_id: "20001" - canonical: true - tsl: ~ - appris: ~ - ccds: CCDS603.1 - ensp: ENSP00000303208 - swissprot: Q8NBP7 - trembl: ~ - uniparc: UPI00001615E1 - gene_pheno: "1" - sift: - prediction: deleterious_low_confidence - score: 0.03 - polyphen: - prediction: possibly_damaging - score: 0.583 - domains: - - id: SignalP-noTM - source: Cleavage_site_(Signalp) - - id: PTHR10795 - source: hmmpanther - - id: PTHR10795 - source: hmmpanther - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - eur_maf: ~ - sas_maf: ~ - aa_maf: ~ - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: "MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_MES:-1.61109392005567&DE_NOVO_DONOR_MES_POS:-122&EXON_END:55505717&INTRON_START:55505718&DE_NOVO_DONOR_PROB:0.146539915246404&INTRON_END:55509515&DE_NOVO_DONOR_POS:-119&EXON_START:55505221" - - allele: G - consequence: missense_variant - impact: MODERATE - symbol: PCSK9 - gene: ENSG00000169174 - feature_type: Transcript - feature: ENST00000452118 - feature_biotype: protein_coding - exon: 1/6 - intron: ~ - hgvsc: "ENST00000452118.2:c.89C>G" - hgvsp: "ENSP00000401598.2:p.Ala30Gly" - cdna_position: "169" - cds_position: "89" - protein_position: "30" - amino_acids: A/G - codons: gCg/gGg - existing_variation: ~ - dbsnp_id: "1" - distance: ~ - strand: "1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: HGNC - hgnc_id: "20001" - canonical: false - tsl: ~ - appris: ~ - ccds: ~ - ensp: ENSP00000401598 - swissprot: ~ - trembl: B4DEZ9 - uniparc: UPI00017A6F55 - gene_pheno: "1" - sift: - prediction: deleterious_low_confidence - score: 0.02 - polyphen: - prediction: possibly_damaging - score: 0.655 - domains: - - id: SignalP-noTM - source: Cleavage_site_(Signalp) - - id: PTHR10795 - source: hmmpanther - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - eur_maf: ~ - sas_maf: ~ - aa_maf: ~ - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: "DE_NOVO_DONOR_MES_POS:-122&DE_NOVO_DONOR_MES:-1.61109392005567&MUTANT_DONOR_MES:8.16693067332728&INTRON_END:55509515&DE_NOVO_DONOR_POS:-119&EXON_END:55505717&DE_NOVO_DONOR_PROB:0.146539915246404&INTRON_START:55505718&EXON_START:55505431" - - allele: G - consequence: upstream_gene_variant - impact: MODIFIER - symbol: PCSK9 - gene: ENSG00000169174 - feature_type: Transcript - feature: ENST00000543384 - feature_biotype: protein_coding - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - existing_variation: ~ - dbsnp_id: "1" - distance: "296" - strand: "1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: HGNC - hgnc_id: "20001" - canonical: false - tsl: ~ - appris: ~ - ccds: ~ - ensp: ENSP00000441859 - swissprot: ~ - trembl: F5GWF0 - uniparc: UPI000206501F - gene_pheno: "1" - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: ~ - afr_maf: ~ - amr_maf: ~ - eas_maf: ~ - 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ac_popmax: 1 - an_popmax: 11088 - nhomalt_popmax: 0 - nonpar: false - liftover_info: ~ - rf_info: - rf_tp_probability: 0.77474 - rf_positive_label: false - rf_negative_label: false - rf_label: ~ - rf_train: false - variant_info: - variant_type: snv - allele_type: snv - n_alt_alleles: 1 - was_mixed: false - has_star: false - quality_info: - fs: 1.515 - inbreeding_coeff: 0.0198 - mq: 59.95 - mq_rank_sum: -1.385 - qd: 12.71 - read_pos_rank_sum: 0.308 - vqsr_positive_train_site: false - vqsr_negative_train_site: true - base_q_rank_sum: 2.21 - clipping_rank_sum: 1.33 - sor: 1.022 - dp: 696568 - vqslod: -2.305 - vqsr_culprit: MQ - segdup: false - lcr: false - decoy: false - transmitted_singleton: false - pab_max: 1 - age_info: - age_hist_hom_bin_freq: [] - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: [] - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 2 - dp_hist_alt_n_larger: 0 - dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] -- chrom: "1" - pos: 55516888 - ref_allele: G - alt_allele: GA - filters: [] - vep: - - allele: A - consequence: intron_variant - impact: MODIFIER - symbol: PCSK9 - gene: ENSG00000169174 - feature_type: Transcript - feature: ENST00000302118 - feature_biotype: protein_coding - exon: ~ - intron: 3/11 - hgvsc: "ENST00000302118.5:c.524-1063_524-1062insA" - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - existing_variation: rs527413419 - dbsnp_id: "1" - distance: ~ - strand: "1" - flags: ~ - variant_class: insertion - minimised: "1" - symbol_source: HGNC - hgnc_id: "20001" - canonical: true - tsl: ~ - appris: ~ - ccds: CCDS603.1 - ensp: ENSP00000303208 - swissprot: Q8NBP7 - trembl: ~ - uniparc: UPI00001615E1 - gene_pheno: "1" - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: 0.0032 - afr_maf: ~ - amr_maf: 0.0113 - eas_maf: 0.0014 - eur_maf: 0 - sas_maf: 0 - aa_maf: 0 - ea_maf: ~ - exac_maf: ~ - 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~ - trembl: B4DEZ9 - uniparc: UPI00017A6F55 - gene_pheno: "1" - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - gmaf: 0.0032 - afr_maf: ~ - amr_maf: 0.0113 - eas_maf: 0.0014 - eur_maf: 0 - sas_maf: 0 - aa_maf: 0 - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: ~ - exac_afr_maf: ~ - exac_amr_maf: ~ - exac_eas_maf: ~ - exac_fin_maf: ~ - exac_nfe_maf: ~ - exac_oth_maf: ~ - exac_sas_maf: ~ - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: HC - lof_filter: ~ - lof_flags: ~ - lof_info: "GERP_DIST:364.1444&BP_DIST:304&PERCENTILE:0.885113268608414&DIST_FROM_LAST_EXON:210&50_BP_RULE:PASS&PHYLOCSF_TOO_SHORT" - - allele: A - consequence: non_coding_transcript_exon_variant&non_coding_transcript_variant - impact: MODIFIER - symbol: PCSK9 - gene: ENSG00000169174 - feature_type: Transcript - feature: ENST00000490692 - feature_biotype: processed_transcript - exon: 1/8 - intron: ~ - hgvsc: "ENST00000490692.1:n.282_283insA" 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ac: 0 - an: 1516 - nhomalt: 0 - af: 0 - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - - population: nfe_seu - counts: - overall: - ac: 0 - an: 106 - nhomalt: 0 - af: 0 - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - - population: nfe_swe - counts: - overall: ~ - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - - population: oth - counts: - overall: - ac: 1 - an: 1010 - nhomalt: 0 - af: 0.000990099 - xx: - ac: 0 - an: 544 - nhomalt: 0 - af: 0 - xy: - ac: 1 - an: 466 - nhomalt: 0 - af: 0.00214592 - faf95: ~ - faf99: ~ - - population: sas - counts: - overall: ~ - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - by_sex: - overall: - ac: 154 - an: 26576 - nhomalt: 0 - af: 0.0057947 - xx: - ac: 66 - an: 12578 - nhomalt: 0 - af: 0.00524726 - xy: - ac: 88 - an: 13998 - nhomalt: 0 - af: 0.00628661 - raw: - ac: 154 - an: 26608 - nhomalt: 0 - af: 0.00578773 - popmax: afr - af_popmax: 0.0177986 - ac_popmax: 152 - an_popmax: 8540 - nhomalt_popmax: 0 - nonpar: false - liftover_info: ~ - rf_info: - rf_tp_probability: 0.952127 - rf_positive_label: true - rf_negative_label: false - rf_label: TP - rf_train: true - variant_info: - variant_type: indel - allele_type: ins - n_alt_alleles: 1 - was_mixed: false - has_star: false - quality_info: - fs: 0.52 - inbreeding_coeff: -0.0043 - mq: 60 - mq_rank_sum: -0.017 - qd: 15.91 - read_pos_rank_sum: 0.122 - vqsr_positive_train_site: true - vqsr_negative_train_site: false - base_q_rank_sum: -0.161 - clipping_rank_sum: -0.129 - sor: 0.654 - dp: 660105 - vqslod: 4.41 - vqsr_culprit: FS - segdup: false - lcr: false - decoy: false - transmitted_singleton: false - pab_max: 1 - age_info: - age_hist_hom_bin_freq: [] - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: [] - age_hist_het_n_smaller: 64 - age_hist_het_n_larger: 2 - depth_info: - dp_hist_all_n_larger: 1 - dp_hist_alt_n_larger: 0 - dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] -- chrom: X - pos: 69902634 - ref_allele: C - alt_allele: T - filters: [] - vep: - - allele: T - consequence: missense_variant - impact: MODERATE - symbol: TEX11 - gene: ENSG00000120498 - feature_type: Transcript - feature: ENST00000344304 - feature_biotype: protein_coding - exon: 13/29 - intron: ~ - hgvsc: "ENST00000344304.3:c.1091G>A" - hgvsp: "ENSP00000340995.3:p.Arg364His" - cdna_position: "1091" - cds_position: "1091" - protein_position: "364" - amino_acids: R/H - codons: cGt/cAt - existing_variation: rs201471690 - dbsnp_id: "1" - distance: ~ - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: HGNC - hgnc_id: "11733" - canonical: false - tsl: ~ - appris: ~ - ccds: CCDS35323.1 - ensp: ENSP00000340995 - swissprot: Q8IYF3 - trembl: ~ - uniparc: UPI000013CA89 - gene_pheno: "1" - sift: - prediction: tolerated - score: 1 - polyphen: - prediction: benign - score: 0.007 - domains: - - id: PTHR22904 - source: hmmpanther - - id: PTHR22904 - source: hmmpanther - - id: PF08631 - source: Pfam_domain - hgvs_offset: ~ - gmaf: 0.0005 - afr_maf: 0 - amr_maf: 0.0008 - eas_maf: 0 - eur_maf: 0 - sas_maf: 0.001 - aa_maf: 0 - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: 0 - exac_afr_maf: 0.00003295 - exac_amr_maf: 0.0001237 - exac_eas_maf: 0.00002495 - exac_fin_maf: 0 - exac_nfe_maf: 0 - exac_oth_maf: 0.00002306 - exac_sas_maf: 0 - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: "EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108&MUTANT_DONOR_MES:6.38837132164763&DE_NOVO_DONOR_PROB:0.0218748740634797&INTRON_END:69902523&INTRON_START:69898740" - - allele: T - consequence: missense_variant - impact: MODERATE - symbol: TEX11 - gene: ENSG00000120498 - feature_type: Transcript - feature: ENST00000374320 - feature_biotype: protein_coding - exon: 3/19 - intron: ~ - hgvsc: "ENST00000374320.2:c.116G>A" - hgvsp: "ENSP00000363440.2:p.Arg39His" - cdna_position: "338" - cds_position: "116" - protein_position: "39" - amino_acids: R/H - codons: cGt/cAt - existing_variation: rs201471690 - dbsnp_id: "1" - distance: ~ - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: HGNC - hgnc_id: "11733" - canonical: false - tsl: ~ - appris: ~ - ccds: ~ - ensp: ENSP00000363440 - swissprot: Q8IYF3 - trembl: ~ - uniparc: UPI00004A2D6C - gene_pheno: "1" - sift: - prediction: tolerated - score: 1 - polyphen: - prediction: benign - score: 0.007 - domains: - - id: PTHR22904 - source: hmmpanther - - id: PTHR22904 - source: hmmpanther - - id: PF08631 - source: Pfam_domain - hgvs_offset: ~ - gmaf: 0.0005 - afr_maf: 0 - amr_maf: 0.0008 - eas_maf: 0 - eur_maf: 0 - sas_maf: 0.001 - aa_maf: 0 - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: 0 - exac_afr_maf: 0.00003295 - exac_amr_maf: 0.0001237 - exac_eas_maf: 0.00002495 - exac_fin_maf: 0 - exac_nfe_maf: 0 - exac_oth_maf: 0.00002306 - exac_sas_maf: 0 - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: "INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763&INTRON_START:69898740&EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108" - - allele: T - consequence: missense_variant - impact: MODERATE - symbol: TEX11 - gene: ENSG00000120498 - feature_type: Transcript - feature: ENST00000374333 - feature_biotype: protein_coding - exon: 14/30 - intron: ~ - hgvsc: "ENST00000374333.2:c.1046G>A" - hgvsp: "ENSP00000363453.2:p.Arg349His" - cdna_position: "1145" - cds_position: "1046" - protein_position: "349" - amino_acids: R/H - codons: cGt/cAt - existing_variation: rs201471690 - dbsnp_id: "1" - distance: ~ - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: HGNC - hgnc_id: "11733" - canonical: false - tsl: ~ - appris: ~ - ccds: CCDS43968.1 - ensp: ENSP00000363453 - swissprot: Q8IYF3 - trembl: ~ - uniparc: UPI00002122F2 - gene_pheno: "1" - sift: - prediction: tolerated - score: 1 - polyphen: - prediction: benign - score: 0.003 - domains: - - id: PTHR22904 - source: hmmpanther - - id: PTHR22904 - source: hmmpanther - - id: PF08631 - source: Pfam_domain - hgvs_offset: ~ - gmaf: 0.0005 - afr_maf: 0 - amr_maf: 0.0008 - eas_maf: 0 - eur_maf: 0 - sas_maf: 0.001 - aa_maf: 0 - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: 0 - exac_afr_maf: 0.00003295 - exac_amr_maf: 0.0001237 - exac_eas_maf: 0.00002495 - exac_fin_maf: 0 - exac_nfe_maf: 0 - exac_oth_maf: 0.00002306 - exac_sas_maf: 0 - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: "DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108&EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&INTRON_START:69898740&INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763" - - allele: T - consequence: missense_variant - impact: MODERATE - symbol: TEX11 - gene: ENSG00000120498 - feature_type: Transcript - feature: ENST00000395889 - feature_biotype: protein_coding - exon: 15/31 - intron: ~ - hgvsc: "ENST00000395889.2:c.1091G>A" - hgvsp: "ENSP00000379226.2:p.Arg364His" - cdna_position: "1247" - cds_position: "1091" - protein_position: "364" - amino_acids: R/H - codons: cGt/cAt - existing_variation: rs201471690 - dbsnp_id: "1" - distance: ~ - strand: "-1" - flags: ~ - variant_class: SNV - minimised: "1" - symbol_source: HGNC - hgnc_id: "11733" - canonical: true - tsl: ~ - appris: ~ - ccds: CCDS35323.1 - ensp: ENSP00000379226 - swissprot: Q8IYF3 - trembl: ~ - uniparc: UPI000013CA89 - gene_pheno: "1" - sift: - prediction: tolerated - score: 1 - polyphen: - prediction: benign - score: 0.007 - domains: - - id: PTHR22904 - source: hmmpanther - - id: PTHR22904 - source: hmmpanther - - id: PF08631 - source: Pfam_domain - hgvs_offset: ~ - gmaf: 0.0005 - afr_maf: 0 - amr_maf: 0.0008 - eas_maf: 0 - eur_maf: 0 - sas_maf: 0.001 - aa_maf: 0 - ea_maf: ~ - exac_maf: ~ - exac_adj_maf: 0 - exac_afr_maf: 0.00003295 - exac_amr_maf: 0.0001237 - exac_eas_maf: 0.00002495 - exac_fin_maf: 0 - exac_nfe_maf: 0 - exac_oth_maf: 0.00002306 - exac_sas_maf: 0 - clin_sig: ~ - somatic: ~ - pheno: ~ - pubmed: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: "INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763&INTRON_START:69898740&EXON_END:69902675&EXON_START:69902524&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108" - allele_counts: - - cohort: ~ - by_population: - - population: 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xy: ~ - faf95: ~ - faf99: ~ - - population: fin - counts: - overall: - ac: 0 - an: 2574 - nhomalt: 0 - af: 0 - xx: - ac: 0 - an: 1844 - nhomalt: 0 - af: 0 - xy: - ac: 0 - an: 730 - nhomalt: 0 - af: 0 - faf95: ~ - faf99: ~ - - population: nfe - counts: - overall: - ac: 0 - an: 10810 - nhomalt: 0 - af: 0 - xx: - ac: 0 - an: 6806 - nhomalt: 0 - af: 0 - xy: - ac: 0 - an: 4004 - nhomalt: 0 - af: 0 - faf95: 0 - faf99: 0 - - population: nfe_bgr - counts: - overall: ~ - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - - population: nfe_est - counts: - overall: - ac: 0 - an: 3312 - nhomalt: 0 - af: 0 - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - - population: nfe_nwe - counts: - overall: - ac: 0 - an: 5938 - nhomalt: 0 - af: 0 - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - - population: nfe_onf - counts: - overall: - ac: 0 - an: 1486 - nhomalt: 0 - af: 0 - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - - population: nfe_seu - counts: - overall: - ac: 0 - an: 74 - nhomalt: 0 - af: 0 - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - - population: nfe_swe - counts: - overall: ~ - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - - population: oth - counts: - overall: - ac: 0 - an: 797 - nhomalt: 0 - af: 0 - xx: - ac: 0 - an: 562 - nhomalt: 0 - af: 0 - xy: - ac: 0 - an: 235 - nhomalt: 0 - af: 0 - faf95: ~ - faf99: ~ - - population: sas - counts: - overall: ~ - xx: ~ - xy: ~ - faf95: ~ - faf99: ~ - by_sex: - overall: - ac: 1 - an: 21857 - nhomalt: 0 - af: 0.0000457519 - xx: - ac: 1 - an: 13926 - nhomalt: 0 - af: 0.0000718081 - xy: - ac: 0 - an: 7931 - nhomalt: 0 - af: 0 - raw: - ac: 1 - an: 22675 - nhomalt: 0 - af: 0.0000441014 - popmax: afr - af_popmax: 0.000170039 - ac_popmax: 1 - an_popmax: 5881 - nhomalt_popmax: 0 - - cohort: controls - by_population: - - population: afr - counts: - overall: - ac: 0 - an: 1779 - nhomalt: 0 - af: 0 - xx: - ac: 0 - an: 1166 - nhomalt: 0 - af: 0 - xy: - ac: 0 - an: 613 - nhomalt: 0 - af: 0 - faf95: 0 - faf99: 0 - - population: amr - counts: - overall: - ac: 0 - an: 177 - nhomalt: 0 - af: 0 - xx: 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faf99: ~ - by_sex: - overall: - ac: 1 - an: 18848 - nhomalt: 0 - af: 0.000053056 - xx: - ac: 1 - an: 12590 - nhomalt: 0 - af: 0.0000794281 - xy: - ac: 0 - an: 6258 - nhomalt: 0 - af: 0 - raw: - ac: 1 - an: 19603 - nhomalt: 0 - af: 0.0000510126 - popmax: afr - af_popmax: 0.0001734 - ac_popmax: 1 - an_popmax: 5767 - nhomalt_popmax: 0 - nonpar: true - liftover_info: ~ - rf_info: - rf_tp_probability: 0.208912 - rf_positive_label: false - rf_negative_label: false - rf_label: ~ - rf_train: false - variant_info: - variant_type: snv - allele_type: snv - n_alt_alleles: 1 - was_mixed: false - has_star: false - quality_info: - fs: 3.617 - inbreeding_coeff: -0.0007 - mq: 60 - mq_rank_sum: 0.344 - qd: 4.62 - read_pos_rank_sum: 1.23 - vqsr_positive_train_site: false - vqsr_negative_train_site: false - base_q_rank_sum: 1.87 - clipping_rank_sum: 1.62 - sor: 1.358 - dp: 464079 - vqslod: 13.71 - vqsr_culprit: MQ - segdup: false - lcr: false - decoy: false - transmitted_singleton: false - pab_max: 0.0871586 - age_info: - age_hist_hom_bin_freq: [] - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: [] - age_hist_het_n_smaller: 1 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 0 - dp_hist_alt_n_larger: 0 - dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] - diff --git a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad3__test__record_from_vcf_allele_gnomad_genomes_grch38.snap b/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad3__test__record_from_vcf_allele_gnomad_genomes_grch38.snap deleted file mode 100644 index 2d88d526..00000000 --- a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__gnomad3__test__record_from_vcf_allele_gnomad_genomes_grch38.snap +++ /dev/null @@ -1,11778 +0,0 @@ ---- -source: src/gnomad_pbs/gnomad3.rs -assertion_line: 422 -expression: records ---- -- chrom: chr1 - pos: 15971 - ref_allele: G - alt_allele: C - filters: [] - vep: - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: DDX11L1 - gene: ENSG00000223972 - feature_type: Transcript - feature: ENST00000450305 - feature_biotype: transcribed_unprocessed_pseudogene - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "2301" - strand: "1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:37102" - canonical: ~ - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: DDX11L1 - gene: ENSG00000223972 - feature_type: Transcript - feature: ENST00000456328 - feature_biotype: processed_transcript - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "1562" - strand: "1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:37102" - canonical: true - tsl: 1 - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: intron_variant&non_coding_transcript_variant - impact: MODIFIER - symbol: WASH7P - gene: ENSG00000227232 - feature_type: Transcript - feature: ENST00000488147 - feature_biotype: unprocessed_pseudogene - exon: ~ - intron: 8/10 - hgvsc: "ENST00000488147.1:n.1068-24C>G" - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: "-1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:38034" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: MIR6859-1 - gene: ENSG00000278267 - feature_type: Transcript - feature: ENST00000619216 - feature_biotype: miRNA - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "1398" - strand: "-1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:50039" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: intron_variant&non_coding_transcript_variant - impact: MODIFIER - symbol: WASH7P - gene: "653635" - feature_type: Transcript - feature: NR_024540.1 - feature_biotype: transcribed_pseudogene - exon: ~ - intron: 8/10 - hgvsc: "NR_024540.1:n.1081-24C>G" - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: "-1" - variant_class: SNV - minimised: ~ - symbol_source: EntrezGene - hgnc_id: "HGNC:38034" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: DDX11L1 - gene: "100287102" - feature_type: Transcript - feature: NR_046018.2 - feature_biotype: transcribed_pseudogene - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "1562" - strand: "1" - variant_class: SNV - minimised: ~ - symbol_source: EntrezGene - hgnc_id: "HGNC:37102" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: MIR6859-1 - gene: "102466751" - feature_type: Transcript - feature: NR_106918.1 - feature_biotype: miRNA - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "1398" - strand: "-1" - variant_class: SNV - minimised: ~ - symbol_source: EntrezGene - hgnc_id: "HGNC:50039" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: regulatory_region_variant - impact: MODIFIER - symbol: "" - gene: "" - feature_type: RegulatoryFeature - feature: ENSR00000344266 - feature_biotype: CTCF_binding_site - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: ~ - variant_class: SNV - minimised: ~ - symbol_source: ~ - hgnc_id: ~ - canonical: ~ - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - 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lof_info: ~ - - allele: A - consequence: intron_variant&non_coding_transcript_variant - impact: MODIFIER - symbol: WASH7P - gene: ENSG00000227232 - feature_type: Transcript - feature: ENST00000488147 - feature_biotype: unprocessed_pseudogene - exon: ~ - intron: 8/10 - hgvsc: "ENST00000488147.1:n.1068-26C>T" - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: "-1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:38034" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: A - consequence: downstream_gene_variant - impact: MODIFIER - symbol: MIR6859-1 - gene: ENSG00000278267 - feature_type: Transcript - feature: 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nhomalt_popmax: ~ - nonpar: false - effect_info: - primate_ai_score: ~ - revel_score: ~ - splice_ai_max_ds: ~ - splice_ai_consequence: ~ - cadd_raw: ~ - cadd_phred: 5.483 - variant_info: - variant_type: multi-snv - allele_type: snv - n_alt_alleles: 3 - was_mixed: false - monoallelic: false - var_dp: 3 - quality_info: - as_fs: 5.44066 - inbreeding_coeff: -0.0000296831 - as_mq: 45.042 - mq_rank_sum: -0.355 - as_mq_rank_sum: -0.717 - as_qd: 4.3829 - read_pos_rank_sum: -0.536 - as_read_pos_rank_sum: -0.536 - as_sor: 1.10954 - positive_train_site: false - negative_train_site: true - as_vqslod: -2.257 - as_culprit: AS_QD - segdup: false - lcr: false - transmitted_singleton: false - as_pab_max: 1 - as_qual_approx: 1179 - as_sb_table: "158" - age_info: - age_hist_hom_bin_freq: [] - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: [] - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 559 - dp_hist_alt_n_larger: 0 - dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] -- chrom: chr1 - pos: 15973 - ref_allele: G - alt_allele: C - filters: [] - vep: - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: DDX11L1 - gene: ENSG00000223972 - feature_type: Transcript - feature: ENST00000450305 - feature_biotype: transcribed_unprocessed_pseudogene - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "2303" - strand: "1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:37102" - canonical: ~ - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: DDX11L1 - gene: ENSG00000223972 - feature_type: Transcript - feature: ENST00000456328 - feature_biotype: processed_transcript - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "1564" - strand: "1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:37102" - canonical: true - tsl: 1 - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: intron_variant&non_coding_transcript_variant - impact: MODIFIER - symbol: WASH7P - gene: ENSG00000227232 - feature_type: Transcript - feature: ENST00000488147 - feature_biotype: unprocessed_pseudogene - exon: ~ - intron: 8/10 - hgvsc: "ENST00000488147.1:n.1068-26C>G" - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: "-1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:38034" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: MIR6859-1 - gene: ENSG00000278267 - feature_type: Transcript - feature: ENST00000619216 - feature_biotype: miRNA - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "1396" - strand: "-1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:50039" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: intron_variant&non_coding_transcript_variant - impact: MODIFIER - symbol: WASH7P - gene: "653635" - feature_type: Transcript - feature: NR_024540.1 - feature_biotype: transcribed_pseudogene - exon: ~ - intron: 8/10 - hgvsc: "NR_024540.1:n.1081-26C>G" - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: "-1" - variant_class: SNV - minimised: ~ - symbol_source: EntrezGene - hgnc_id: "HGNC:38034" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: DDX11L1 - gene: "100287102" - feature_type: Transcript - feature: NR_046018.2 - feature_biotype: transcribed_pseudogene - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "1564" - strand: "1" - variant_class: SNV - minimised: ~ - symbol_source: EntrezGene - hgnc_id: "HGNC:37102" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: downstream_gene_variant - impact: MODIFIER - symbol: MIR6859-1 - gene: "102466751" - feature_type: Transcript - feature: NR_106918.1 - feature_biotype: miRNA - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "1396" - strand: "-1" - variant_class: SNV - minimised: ~ - symbol_source: EntrezGene - hgnc_id: "HGNC:50039" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: C - consequence: regulatory_region_variant - impact: MODIFIER - symbol: "" - gene: "" - feature_type: RegulatoryFeature - feature: ENSR00000344266 - feature_biotype: CTCF_binding_site - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: ~ - variant_class: SNV - 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AS_MQRankSum - segdup: false - lcr: false - transmitted_singleton: false - as_pab_max: 0.850554 - as_qual_approx: 1986 - as_sb_table: "66" - age_info: - age_hist_hom_bin_freq: [] - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: [] - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 561 - dp_hist_alt_n_larger: 0 - dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] -- chrom: chr1 - pos: 15975 - ref_allele: A - alt_allele: G - filters: [] - vep: - - allele: G - consequence: downstream_gene_variant - impact: MODIFIER - symbol: DDX11L1 - gene: ENSG00000223972 - feature_type: Transcript - feature: ENST00000450305 - feature_biotype: transcribed_unprocessed_pseudogene - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: "2305" - strand: "1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: 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motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: G - consequence: intron_variant&non_coding_transcript_variant - impact: MODIFIER - symbol: WASH7P - gene: ENSG00000227232 - feature_type: Transcript - feature: ENST00000488147 - feature_biotype: unprocessed_pseudogene - exon: ~ - intron: 8/10 - hgvsc: "ENST00000488147.1:n.1068-28T>C" - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: "-1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:38034" - canonical: true - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - - allele: G - consequence: downstream_gene_variant - impact: MODIFIER - symbol: MIR6859-1 - gene: 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was_mixed: false - monoallelic: false - var_dp: 1 - quality_info: - as_fs: 1.29277 - inbreeding_coeff: -0.0000149012 - as_mq: 44.7114 - mq_rank_sum: 1.611 - as_mq_rank_sum: 1.611 - as_qd: 5.3617 - read_pos_rank_sum: -1.396 - as_read_pos_rank_sum: -1.396 - as_sor: 0.963111 - positive_train_site: false - negative_train_site: true - as_vqslod: -2.989 - as_culprit: AS_QD - segdup: false - lcr: false - transmitted_singleton: false - as_pab_max: 0.404873 - as_qual_approx: 252 - as_sb_table: "21" - age_info: - age_hist_hom_bin_freq: [] - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: [] - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 561 - dp_hist_alt_n_larger: 0 - dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] -- chrom: chr1 - pos: 15977 - ref_allele: G - alt_allele: A - filters: [] - vep: - - allele: A - consequence: downstream_gene_variant - impact: MODIFIER - symbol: DDX11L1 - gene: ENSG00000223972 - 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af_popmax: ~ - ac_popmax: ~ - an_popmax: ~ - nhomalt_popmax: ~ - nonpar: false - effect_info: - primate_ai_score: ~ - revel_score: ~ - splice_ai_max_ds: ~ - splice_ai_consequence: ~ - cadd_raw: ~ - cadd_phred: 4.644 - variant_info: - variant_type: multi-snv - allele_type: snv - n_alt_alleles: 2 - was_mixed: false - monoallelic: false - var_dp: 2 - quality_info: - as_fs: 1.34551 - inbreeding_coeff: -0.00000739098 - as_mq: 46.237 - mq_rank_sum: -0.067 - as_mq_rank_sum: 3.027 - as_qd: 3.17544 - read_pos_rank_sum: -1.001 - as_read_pos_rank_sum: -1.001 - as_sor: 0.367725 - positive_train_site: false - negative_train_site: true - as_vqslod: -2.5822 - as_culprit: AS_QD - segdup: false - lcr: false - transmitted_singleton: false - as_pab_max: 0.6875 - as_qual_approx: 181 - as_sb_table: "34" - age_info: - age_hist_hom_bin_freq: [] - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: [] - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 561 - dp_hist_alt_n_larger: 0 - dp_hist_all_bin_freq: [] - dp_hist_alt_bin_freq: [] - diff --git a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__vep_gnomad2__test__vep_from_string_indel.snap b/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__vep_gnomad2__test__vep_from_string_indel.snap deleted file mode 100644 index 99976290..00000000 --- a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__vep_gnomad2__test__vep_from_string_indel.snap +++ /dev/null @@ -1,73 +0,0 @@ ---- -source: src/gnomad_pbs/vep_gnomad2.rs -expression: vep ---- -allele: A -consequence: frameshift_variant -impact: HIGH -symbol: PCSK9 -gene: ENSG00000169174 -feature_type: Transcript -feature: ENST00000452118 -feature_biotype: protein_coding -exon: 4/6 -intron: ~ -hgvsc: "ENST00000452118.2:c.547_548insA" -hgvsp: "ENSP00000401598.2:p.Gly183GlufsTer23" -cdna_position: 627-628 -cds_position: 547-548 -protein_position: "183" -amino_acids: G/EX -codons: ggc/gAgc -existing_variation: rs527413419 -dbsnp_id: "1" -distance: ~ -strand: "1" -flags: ~ -variant_class: insertion -minimised: "1" -symbol_source: HGNC -hgnc_id: "20001" -canonical: false -tsl: ~ -appris: ~ -ccds: ~ -ensp: ENSP00000401598 -swissprot: ~ -trembl: B4DEZ9 -uniparc: UPI00017A6F55 -gene_pheno: "1" -sift: ~ -polyphen: ~ -domains: [] -hgvs_offset: ~ -gmaf: 0.0032 -afr_maf: ~ -amr_maf: 0.0113 -eas_maf: 0.0014 -eur_maf: 0 -sas_maf: 0 -aa_maf: 0 -ea_maf: ~ -exac_maf: ~ -exac_adj_maf: ~ -exac_afr_maf: ~ -exac_amr_maf: ~ -exac_eas_maf: ~ -exac_fin_maf: ~ -exac_nfe_maf: ~ -exac_oth_maf: ~ -exac_sas_maf: ~ -clin_sig: ~ -somatic: ~ -pheno: ~ -pubmed: ~ -motif_name: ~ -motif_pos: ~ -high_inf_pos: ~ -motif_score_change: ~ -lof: HC -lof_filter: ~ -lof_flags: ~ -lof_info: "GERP_DIST:364.1444&BP_DIST:304&PERCENTILE:0.885113268608414&DIST_FROM_LAST_EXON:210&50_BP_RULE:PASS&PHYLOCSF_TOO_SHORT" - diff --git a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__vep_gnomad2__test__vep_from_string_snv.snap b/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__vep_gnomad2__test__vep_from_string_snv.snap deleted file mode 100644 index 660d3888..00000000 --- a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__vep_gnomad2__test__vep_from_string_snv.snap +++ /dev/null @@ -1,83 +0,0 @@ ---- -source: src/gnomad_pbs/vep_gnomad2.rs -expression: vep ---- -allele: G -consequence: missense_variant -impact: MODERATE -symbol: PCSK9 -gene: ENSG00000169174 -feature_type: Transcript -feature: ENST00000302118 -feature_biotype: protein_coding -exon: 1/12 -intron: ~ -hgvsc: "ENST00000302118.5:c.89C>G" -hgvsp: "ENSP00000303208.5:p.Ala30Gly" -cdna_position: "379" -cds_position: "89" -protein_position: "30" -amino_acids: A/G -codons: gCg/gGg -existing_variation: ~ -dbsnp_id: "1" -distance: ~ -strand: "1" -flags: ~ -variant_class: SNV -minimised: "1" -symbol_source: HGNC -hgnc_id: "20001" -canonical: true -tsl: ~ -appris: ~ -ccds: CCDS603.1 -ensp: ENSP00000303208 -swissprot: Q8NBP7 -trembl: ~ -uniparc: UPI00001615E1 -gene_pheno: "1" -sift: - prediction: deleterious_low_confidence - score: 0.03 -polyphen: - prediction: possibly_damaging - score: 0.583 -domains: - - id: SignalP-noTM - source: Cleavage_site_(Signalp) - - id: PTHR10795 - source: hmmpanther - - id: PTHR10795 - source: hmmpanther -hgvs_offset: ~ -gmaf: ~ -afr_maf: ~ -amr_maf: ~ -eas_maf: ~ -eur_maf: ~ -sas_maf: ~ -aa_maf: ~ -ea_maf: ~ -exac_maf: ~ -exac_adj_maf: ~ -exac_afr_maf: ~ -exac_amr_maf: ~ -exac_eas_maf: ~ -exac_fin_maf: ~ -exac_nfe_maf: ~ -exac_oth_maf: ~ -exac_sas_maf: ~ -clin_sig: ~ -somatic: ~ -pheno: ~ -pubmed: ~ -motif_name: ~ -motif_pos: ~ -high_inf_pos: ~ -motif_score_change: ~ -lof: ~ -lof_filter: ~ -lof_flags: ~ -lof_info: "DE_NOVO_DONOR_PROB:0.146539915246404&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_POS:-119&INTRON_END:55509515&DE_NOVO_DONOR_MES_POS:-122&INTRON_START:55505718&EXON_END:55505717&EXON_START:55505221&DE_NOVO_DONOR_MES:-1.61109392005567" - diff --git a/src/gnomad_sv/cli/import/exac_cnv.rs b/src/gnomad_sv/cli/import/exac_cnv.rs index cec402ff..dbe5c104 100644 --- a/src/gnomad_sv/cli/import/exac_cnv.rs +++ b/src/gnomad_sv/cli/import/exac_cnv.rs @@ -10,8 +10,8 @@ use std::{ use byteorder::ByteOrder as _; use prost::Message as _; -pub use crate::gnomad_pbs::exac_cnv::CnvType; -use crate::gnomad_pbs::exac_cnv::{Population, Record}; +pub use crate::pbs::gnomad::exac_cnv::CnvType; +use crate::pbs::gnomad::exac_cnv::{Population, Record}; /// The to be imported section. #[derive(Clone, Copy, Debug, Default, Eq, PartialEq)] diff --git a/src/gnomad_sv/cli/import/gnomad_cnv4.rs b/src/gnomad_sv/cli/import/gnomad_cnv4.rs index a83a59ac..f09ca80b 100644 --- a/src/gnomad_sv/cli/import/gnomad_cnv4.rs +++ b/src/gnomad_sv/cli/import/gnomad_cnv4.rs @@ -4,13 +4,13 @@ use std::{str::FromStr, sync::Arc}; use crate::{ common::noodles::{get_f32, get_i32, get_string, get_vec_str}, - gnomad_pbs::exac_cnv::CnvType, - gnomad_pbs::gnomad_cnv4::{ + pbs::gnomad::exac_cnv::CnvType, + pbs::gnomad::gnomad_cnv4::{ CarrierCounts, CarrierCountsBySex, Population, PopulationAlleleCounts, Record, }, }; -use prost::Message; +use prost::Message as _; impl FromStr for CnvType { type Err = anyhow::Error; diff --git a/src/gnomad_sv/cli/import/gnomad_sv2.rs b/src/gnomad_sv/cli/import/gnomad_sv2.rs index 1252dc30..70fb8866 100644 --- a/src/gnomad_sv/cli/import/gnomad_sv2.rs +++ b/src/gnomad_sv/cli/import/gnomad_sv2.rs @@ -7,7 +7,7 @@ use std::{str::FromStr, sync::Arc}; use crate::{ common::noodles::{get_f32, get_i32, get_string}, - gnomad_pbs::gnomad_sv2::{ + pbs::gnomad::gnomad_sv2::{ AlleleCounts, AlleleCountsBySex, CohortAlleleCounts, CpxType, Filter, Population, PopulationAlleleCounts, Record, SvType, }, diff --git a/src/gnomad_sv/cli/import/gnomad_sv4.rs b/src/gnomad_sv/cli/import/gnomad_sv4.rs index 76758a84..2d569415 100644 --- a/src/gnomad_sv/cli/import/gnomad_sv4.rs +++ b/src/gnomad_sv/cli/import/gnomad_sv4.rs @@ -10,8 +10,8 @@ use crate::{ self, noodles::{get_f32, get_i32, get_string}, }, - gnomad_pbs::gnomad_sv2::CpxType, - gnomad_pbs::gnomad_sv4::{ + pbs::gnomad::gnomad_sv2::CpxType, + pbs::gnomad::gnomad_sv4::{ AlleleCounts, AlleleCountsBySex, CohortAlleleCounts, Filter, Population, PopulationAlleleCounts, Record, SvType, }, diff --git a/src/gnomad_sv/cli/query.rs b/src/gnomad_sv/cli/query.rs index 9ad714c1..96445535 100644 --- a/src/gnomad_sv/cli/query.rs +++ b/src/gnomad_sv/cli/query.rs @@ -115,13 +115,13 @@ pub fn open_rocksdb_from_args( #[serde(rename_all = "snake_case")] pub enum Record { /// ExAC SV record. - ExacCnv(crate::gnomad_pbs::exac_cnv::Record), + ExacCnv(crate::pbs::gnomad::exac_cnv::Record), /// gnomAD-SV v2 record. - GnomadSv2(crate::gnomad_pbs::gnomad_sv2::Record), + GnomadSv2(crate::pbs::gnomad::gnomad_sv2::Record), /// gnomAD-CNV v4 record. - GnomadCnv4(crate::gnomad_pbs::gnomad_cnv4::Record), + GnomadCnv4(crate::pbs::gnomad::gnomad_cnv4::Record), /// gnomAD-SV v4 record. - GnomadSv4(crate::gnomad_pbs::gnomad_sv4::Record), + GnomadSv4(crate::pbs::gnomad::gnomad_sv4::Record), } /// The necessary data for the tree construction. @@ -201,16 +201,16 @@ fn decode_record(data: &[u8], meta: &Meta) -> Result { meta.gnomad_version.as_str(), ) { ("grch37", "exomes", "1.0") => Record::ExacCnv( - crate::gnomad_pbs::exac_cnv::Record::decode(&mut std::io::Cursor::new(&data))?, + crate::pbs::gnomad::exac_cnv::Record::decode(&mut std::io::Cursor::new(&data))?, ), ("grch37", "genomes", "2.1") => Record::GnomadSv2( - crate::gnomad_pbs::gnomad_sv2::Record::decode(&mut std::io::Cursor::new(&data))?, + crate::pbs::gnomad::gnomad_sv2::Record::decode(&mut std::io::Cursor::new(&data))?, ), ("grch38", "exomes", "4.0") => Record::GnomadCnv4( - crate::gnomad_pbs::gnomad_cnv4::Record::decode(&mut std::io::Cursor::new(&data))?, + crate::pbs::gnomad::gnomad_cnv4::Record::decode(&mut std::io::Cursor::new(&data))?, ), ("grch38", "genomes", "4.0") => Record::GnomadSv4( - crate::gnomad_pbs::gnomad_sv4::Record::decode(&mut std::io::Cursor::new(&data))?, + crate::pbs::gnomad::gnomad_sv4::Record::decode(&mut std::io::Cursor::new(&data))?, ), _ => { anyhow::bail!( 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 index 11eb32ac..690da690 100644 --- 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 @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d46d9ca44889ed3027732042dd760efac47908fdb4838247297d942c1dd6f567 -size 218 +oid sha256:c9378d2b126d4612054f1302cecf20e5fb3e161c80e4b75222ca6200b70e1dca +size 202 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-cnv4-some.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-cnv4-some.snap index 5ef78e82..de6c9344 100644 --- a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-cnv4-some.snap +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-cnv4-some.snap @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:6c288dcf2e0d26732160a8ea1d50c101d38ff9f3d554187bb9572635ea6005da -size 10975 +oid sha256:5f7c5a61e05426c38a500b79cee505452889082c9764500c1aad22d74b0e788c +size 9100 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv2-some.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv2-some.snap index 6d5d5075..cdcc0314 100644 --- a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv2-some.snap +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv2-some.snap @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:39a6b6528c99c0035fa0c625385453d20f746c658ff60901d8f7caf70996eb4d -size 16515 +oid sha256:45c9decd1fc2f9f63d98f013bc972a1fec676b5b4359047484e099fe977b3153 +size 4547 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv4-some.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv4-some.snap index efd92a38..68599d61 100644 --- a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv4-some.snap +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_range@gnomad-sv4-some.snap @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 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a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_accession@gnomad-sv2.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_accession@gnomad-sv2.snap index d03fff0c..64165f67 100644 --- a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_accession@gnomad-sv2.snap +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_accession@gnomad-sv2.snap @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:72e6fe7edd6b7d42c8c6120115711037e976cb3e0500c107c5d3cc93e8153753 -size 9533 +oid sha256:97f89c321d8046faae9ecfc009c58715dcdb0f38e1b1cc6ee1815b8079ab5665 +size 8265 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_accession@gnomad-sv4.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_accession@gnomad-sv4.snap index d1ee8b2e..137e2f67 100644 --- a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_accession@gnomad-sv4.snap +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_accession@gnomad-sv4.snap @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:159b060e61613440d04ee6564df0bdd27bbece00503329176d1912a435cb8796 -size 21282 +oid sha256:4efa0f87ce53355ecca7982fe04c5757784cf85f80d374c5ac9b01ce90d654d1 +size 3287 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@exac-cnv.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@exac-cnv.snap index 89a3b426..9ebd526d 100644 --- a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@exac-cnv.snap +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@exac-cnv.snap @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:61acda8fdcbe485f990091311c2ad34d567d14e5c8044dbf8d2ef948454122c2 -size 1564 +oid sha256:1a740095618d0d3e4d7e363ffae571de7c5ec8bf1e67d065f58a97368828f7be +size 1497 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 fa006f78..ed2f7105 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 sha256:6fcea22ca14cc0e97baf57c598fbaebd6b6a40ac92cd7b17f000e1b907c8ec57 -size 106643 +oid sha256:0e639c658158e608d8f7e8a6b7df908982931be9746b8a35ca5922c8cfd4e860 +size 80903 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-sv2.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-sv2.snap index b2bb2e1a..1054216e 100644 --- a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-sv2.snap +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-sv2.snap @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:3882cf6f5c656999df9ce59947034c4e9471ab00536e59084d7c1b1d30d28c02 -size 418698 +oid sha256:8d0d066a4116ce8707bdc2e143dd79182838d70d61cca8145d94dc43d6a67252 +size 278646 diff --git a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-sv4.snap b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-sv4.snap index 49d4edb7..ed90f445 100644 --- a/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-sv4.snap +++ b/src/gnomad_sv/cli/snapshots/annonars__gnomad_sv__cli__query__test__smoke_query_var_all@gnomad-sv4.snap @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:090bf1c3f85ab838cc74bf18edd432286b2791dd6834ecd484e922cc7212c56b -size 11137349 +oid sha256:21f47b08fcc74ab46c236ad1e60563fbd89f6248e2c3aa80ae4069234c3290d6 +size 1697327 diff --git a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_all.snap b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_all.snap index 0ae0243f..e608da12 100644 --- a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_all.snap +++ b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_all.snap @@ -2,8 +2,8 @@ source: src/helixmtdb/cli/query.rs expression: "&out_data" --- -{"chrom":"chrM","pos":5,"ref_allele":"A","alt_allele":"C","num_total":196554,"num_het":0,"num_hom":1,"feature_type":"non_coding","gene_name":"MT-CRb"} -{"chrom":"chrM","pos":10,"ref_allele":"T","alt_allele":"C","num_total":196554,"num_het":1,"num_hom":7,"feature_type":"non_coding","gene_name":"MT-CRb"} -{"chrom":"chrM","pos":11,"ref_allele":"C","alt_allele":"T","num_total":196554,"num_het":1,"num_hom":0,"feature_type":"non_coding","gene_name":"MT-CRb"} -{"chrom":"chrM","pos":12,"ref_allele":"T","alt_allele":"C","num_total":196554,"num_het":0,"num_hom":1,"feature_type":"non_coding","gene_name":"MT-CRb"} +{"chrom":"chrM","pos":5,"refAllele":"A","altAllele":"C","numTotal":196554,"numHom":1,"featureType":"non_coding","geneName":"MT-CRb"} +{"chrom":"chrM","pos":10,"refAllele":"T","altAllele":"C","numTotal":196554,"numHet":1,"numHom":7,"featureType":"non_coding","geneName":"MT-CRb"} +{"chrom":"chrM","pos":11,"refAllele":"C","altAllele":"T","numTotal":196554,"numHet":1,"featureType":"non_coding","geneName":"MT-CRb"} +{"chrom":"chrM","pos":12,"refAllele":"T","altAllele":"C","numTotal":196554,"numHom":1,"featureType":"non_coding","geneName":"MT-CRb"} diff --git a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_pos_single.snap b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_pos_single.snap index 9b5e2cd6..303ca4af 100644 --- a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_pos_single.snap +++ b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_pos_single.snap @@ -2,5 +2,5 @@ source: src/helixmtdb/cli/query.rs expression: "&out_data" --- -{"chrom":"chrM","pos":11,"ref_allele":"C","alt_allele":"T","num_total":196554,"num_het":1,"num_hom":0,"feature_type":"non_coding","gene_name":"MT-CRb"} +{"chrom":"chrM","pos":11,"refAllele":"C","altAllele":"T","numTotal":196554,"numHet":1,"featureType":"non_coding","geneName":"MT-CRb"} diff --git a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_all.snap b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_all.snap index 0ae0243f..e608da12 100644 --- a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_all.snap +++ b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_all.snap @@ -2,8 +2,8 @@ source: src/helixmtdb/cli/query.rs expression: "&out_data" --- -{"chrom":"chrM","pos":5,"ref_allele":"A","alt_allele":"C","num_total":196554,"num_het":0,"num_hom":1,"feature_type":"non_coding","gene_name":"MT-CRb"} -{"chrom":"chrM","pos":10,"ref_allele":"T","alt_allele":"C","num_total":196554,"num_het":1,"num_hom":7,"feature_type":"non_coding","gene_name":"MT-CRb"} -{"chrom":"chrM","pos":11,"ref_allele":"C","alt_allele":"T","num_total":196554,"num_het":1,"num_hom":0,"feature_type":"non_coding","gene_name":"MT-CRb"} -{"chrom":"chrM","pos":12,"ref_allele":"T","alt_allele":"C","num_total":196554,"num_het":0,"num_hom":1,"feature_type":"non_coding","gene_name":"MT-CRb"} +{"chrom":"chrM","pos":5,"refAllele":"A","altAllele":"C","numTotal":196554,"numHom":1,"featureType":"non_coding","geneName":"MT-CRb"} +{"chrom":"chrM","pos":10,"refAllele":"T","altAllele":"C","numTotal":196554,"numHet":1,"numHom":7,"featureType":"non_coding","geneName":"MT-CRb"} +{"chrom":"chrM","pos":11,"refAllele":"C","altAllele":"T","numTotal":196554,"numHet":1,"featureType":"non_coding","geneName":"MT-CRb"} +{"chrom":"chrM","pos":12,"refAllele":"T","altAllele":"C","numTotal":196554,"numHom":1,"featureType":"non_coding","geneName":"MT-CRb"} diff --git a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_first.snap b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_first.snap index 2f033f9a..234039e1 100644 --- a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_first.snap +++ b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_first.snap @@ -2,5 +2,5 @@ source: src/helixmtdb/cli/query.rs expression: "&out_data" --- -{"chrom":"chrM","pos":5,"ref_allele":"A","alt_allele":"C","num_total":196554,"num_het":0,"num_hom":1,"feature_type":"non_coding","gene_name":"MT-CRb"} +{"chrom":"chrM","pos":5,"refAllele":"A","altAllele":"C","numTotal":196554,"numHom":1,"featureType":"non_coding","geneName":"MT-CRb"} diff --git a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_second.snap b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_second.snap index 1f52a34a..382cf62b 100644 --- a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_second.snap +++ b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_range_find_second.snap @@ -2,5 +2,5 @@ source: src/helixmtdb/cli/query.rs expression: "&out_data" --- -{"chrom":"chrM","pos":10,"ref_allele":"T","alt_allele":"C","num_total":196554,"num_het":1,"num_hom":7,"feature_type":"non_coding","gene_name":"MT-CRb"} +{"chrom":"chrM","pos":10,"refAllele":"T","altAllele":"C","numTotal":196554,"numHet":1,"numHom":7,"featureType":"non_coding","geneName":"MT-CRb"} diff --git a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_var_single.snap b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_var_single.snap index 9b5e2cd6..303ca4af 100644 --- a/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_var_single.snap +++ b/src/helixmtdb/cli/snapshots/annonars__helixmtdb__cli__query__test__smoke_query_var_single.snap @@ -2,5 +2,5 @@ source: src/helixmtdb/cli/query.rs expression: "&out_data" --- -{"chrom":"chrM","pos":11,"ref_allele":"C","alt_allele":"T","num_total":196554,"num_het":1,"num_hom":0,"feature_type":"non_coding","gene_name":"MT-CRb"} +{"chrom":"chrM","pos":11,"refAllele":"C","altAllele":"T","numTotal":196554,"numHet":1,"featureType":"non_coding","geneName":"MT-CRb"} diff --git a/src/helixmtdb/pbs.rs b/src/helixmtdb/pbs.rs index 2a170707..67184487 100644 --- a/src/helixmtdb/pbs.rs +++ b/src/helixmtdb/pbs.rs @@ -2,10 +2,9 @@ use std::str::FromStr; +pub use crate::pbs::helixmtdb::Record; use noodles_vcf::record::info::field; -include!(concat!(env!("OUT_DIR"), "/annonars.helixmtdb.v1.base.rs")); - impl Record { /// Creates a new `Record` from a VCF record and allele number. pub fn from_vcf_allele( diff --git a/src/lib.rs b/src/lib.rs index 279e7bc1..6858601a 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -16,7 +16,6 @@ pub mod functional; pub mod genes; pub mod gnomad_mtdna; pub mod gnomad_nuclear; -pub mod gnomad_pbs; pub mod gnomad_sv; pub mod helixmtdb; pub mod pbs; diff --git a/src/pbs/annonars/clinvar/mod.rs b/src/pbs/annonars/clinvar/mod.rs deleted file mode 100644 index 5af7023d..00000000 --- a/src/pbs/annonars/clinvar/mod.rs +++ /dev/null @@ -1,3 +0,0 @@ -//! Code generate for protobufs by `prost-build`. - -pub mod v1; diff --git a/src/pbs/annonars/clinvar/v1/minimal.rs b/src/pbs/annonars/clinvar/v1/minimal.rs deleted file mode 100644 index 852bf89a..00000000 --- a/src/pbs/annonars/clinvar/v1/minimal.rs +++ /dev/null @@ -1,3 +0,0 @@ -//! Code generate for protobufs by `prost-build`. - -include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.v1.minimal.rs")); diff --git a/src/pbs/annonars/clinvar/v1/mod.rs b/src/pbs/annonars/clinvar/v1/mod.rs deleted file mode 100644 index a68a9abc..00000000 --- a/src/pbs/annonars/clinvar/v1/mod.rs +++ /dev/null @@ -1,5 +0,0 @@ -//! Code generate for protobufs by `prost-build`. - -pub mod minimal; -pub mod per_gene; -pub mod sv; diff --git a/src/pbs/annonars/clinvar/v1/per_gene.rs b/src/pbs/annonars/clinvar/v1/per_gene.rs deleted file mode 100644 index a2ee007f..00000000 --- a/src/pbs/annonars/clinvar/v1/per_gene.rs +++ /dev/null @@ -1,3 +0,0 @@ -//! Code generate for protobufs by `prost-build`. - -include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.v1.per_gene.rs")); diff --git a/src/pbs/annonars/clinvar/v1/sv.rs b/src/pbs/annonars/clinvar/v1/sv.rs deleted file mode 100644 index e29f7e9b..00000000 --- a/src/pbs/annonars/clinvar/v1/sv.rs +++ /dev/null @@ -1,3 +0,0 @@ -//! Code generate for protobufs by `prost-build`. - -include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.v1.sv.rs")); diff --git a/src/pbs/annonars/functional/mod.rs b/src/pbs/annonars/functional/mod.rs deleted file mode 100644 index 5af7023d..00000000 --- a/src/pbs/annonars/functional/mod.rs +++ /dev/null @@ -1,3 +0,0 @@ -//! Code generate for protobufs by `prost-build`. - -pub mod v1; diff --git a/src/pbs/annonars/functional/v1/mod.rs b/src/pbs/annonars/functional/v1/mod.rs deleted file mode 100644 index 352d9f62..00000000 --- a/src/pbs/annonars/functional/v1/mod.rs +++ /dev/null @@ -1,3 +0,0 @@ -//! Code generate for protobufs by `prost-build`. - -pub mod refseq; diff --git a/src/pbs/annonars/functional/v1/refseq.rs b/src/pbs/annonars/functional/v1/refseq.rs deleted file mode 100644 index cc3e21ea..00000000 --- a/src/pbs/annonars/functional/v1/refseq.rs +++ /dev/null @@ -1,6 +0,0 @@ -//! Code generate for protobufs by `prost-build`. - -include!(concat!( - env!("OUT_DIR"), - "/annonars.functional.v1.refseq.rs" -)); diff --git a/src/pbs/annonars/mod.rs b/src/pbs/annonars/mod.rs deleted file mode 100644 index c4059fa5..00000000 --- a/src/pbs/annonars/mod.rs +++ /dev/null @@ -1,4 +0,0 @@ -//! Code generate for protobufs by `prost-build`. - -pub mod clinvar; -pub mod functional; diff --git a/src/pbs/clinvar.rs b/src/pbs/clinvar.rs new file mode 100644 index 00000000..0cb86ea6 --- /dev/null +++ b/src/pbs/clinvar.rs @@ -0,0 +1,25 @@ +//! Code generate for protobufs by `prost-build`. + +/// Code generate for protobufs by `prost-build`. +pub mod minimal { + include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.minimal.rs")); + include!(concat!( + env!("OUT_DIR"), + "/annonars.clinvar.minimal.serde.rs" + )); +} + +/// Code generate for protobufs by `prost-build`. +pub mod per_gene { + include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.per_gene.rs")); + include!(concat!( + env!("OUT_DIR"), + "/annonars.clinvar.per_gene.serde.rs" + )); +} + +/// Code generate for protobufs by `prost-build`. +pub mod sv { + include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.sv.rs")); + include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.sv.serde.rs")); +} diff --git a/src/pbs/cons.rs b/src/pbs/cons.rs new file mode 100644 index 00000000..65574b82 --- /dev/null +++ b/src/pbs/cons.rs @@ -0,0 +1,4 @@ +//! Code generate for protobufs by `prost-build`. + +include!(concat!(env!("OUT_DIR"), "/annonars.cons.base.rs")); +include!(concat!(env!("OUT_DIR"), "/annonars.cons.base.serde.rs")); diff --git a/src/pbs/dbsnp.rs b/src/pbs/dbsnp.rs new file mode 100644 index 00000000..aa72dba7 --- /dev/null +++ b/src/pbs/dbsnp.rs @@ -0,0 +1,4 @@ +//! Code generate for protobufs by `prost-build`. + +include!(concat!(env!("OUT_DIR"), "/annonars.dbsnp.base.rs")); +include!(concat!(env!("OUT_DIR"), "/annonars.dbsnp.base.serde.rs")); diff --git a/src/pbs/functional.rs b/src/pbs/functional.rs new file mode 100644 index 00000000..e94ceba4 --- /dev/null +++ b/src/pbs/functional.rs @@ -0,0 +1,10 @@ +//! Code generate for protobufs by `prost-build`. + +/// Code generate for protobufs by `prost-build`. +pub mod refseq { + include!(concat!(env!("OUT_DIR"), "/annonars.functional.refseq.rs")); + include!(concat!( + env!("OUT_DIR"), + "/annonars.functional.refseq.serde.rs" + )); +} diff --git a/src/pbs/genes.rs b/src/pbs/genes.rs new file mode 100644 index 00000000..209ff4fa --- /dev/null +++ b/src/pbs/genes.rs @@ -0,0 +1,4 @@ +//! Code generate for protobufs by `prost-build`. + +include!(concat!(env!("OUT_DIR"), "/annonars.genes.base.rs")); +include!(concat!(env!("OUT_DIR"), "/annonars.genes.base.serde.rs")); diff --git a/src/pbs/gnomad/exac_cnv.rs b/src/pbs/gnomad/exac_cnv.rs new file mode 100644 index 00000000..815c9549 --- /dev/null +++ b/src/pbs/gnomad/exac_cnv.rs @@ -0,0 +1,7 @@ +//! Code generate for protobufs by `prost-build`. + +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.exac_cnv.rs")); +include!(concat!( + env!("OUT_DIR"), + "/annonars.gnomad.exac_cnv.serde.rs" +)); diff --git a/src/gnomad_pbs/gnomad2.rs b/src/pbs/gnomad/gnomad2.rs similarity index 99% rename from src/gnomad_pbs/gnomad2.rs rename to src/pbs/gnomad/gnomad2.rs index e17dba2d..79feb8e4 100644 --- a/src/gnomad_pbs/gnomad2.rs +++ b/src/pbs/gnomad/gnomad2.rs @@ -1,4 +1,4 @@ -//! Protocolbuffers for gnomAD v2 nuclear data structures. +//! Code generate for protobufs by `prost-build`. use std::str::FromStr; @@ -6,7 +6,11 @@ use noodles_vcf::record::info::field; use crate::common; -include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.v1.gnomad2.rs")); +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.gnomad2.rs")); +include!(concat!( + env!("OUT_DIR"), + "/annonars.gnomad.gnomad2.serde.rs" +)); /// The cohorts that are available in the gnomAD-exomes/genomes VCFs. pub static COHORTS: &[&str] = &["controls", "non_cancer", "non_neuro", "non_topmed"]; diff --git a/src/gnomad_pbs/gnomad3.rs b/src/pbs/gnomad/gnomad3.rs similarity index 98% rename from src/gnomad_pbs/gnomad3.rs rename to src/pbs/gnomad/gnomad3.rs index 05f15573..e783fe7f 100644 --- a/src/gnomad_pbs/gnomad3.rs +++ b/src/pbs/gnomad/gnomad3.rs @@ -1,4 +1,4 @@ -//! Protocolbuffers for gnomAD v3 nuclear data structures. +//! Code generate for protobufs by `prost-build`. use std::str::FromStr; @@ -6,7 +6,11 @@ use noodles_vcf::record::info::field; use crate::common; -include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.v1.gnomad3.rs")); +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.gnomad3.rs")); +include!(concat!( + env!("OUT_DIR"), + "/annonars.gnomad.gnomad3.serde.rs" +)); /// The cohorts that are available in the gnomAD-exomes/genomes VCFs. pub static COHORTS: &[&str] = &[ diff --git a/src/pbs/gnomad/gnomad_cnv4.rs b/src/pbs/gnomad/gnomad_cnv4.rs new file mode 100644 index 00000000..53aeb633 --- /dev/null +++ b/src/pbs/gnomad/gnomad_cnv4.rs @@ -0,0 +1,7 @@ +//! Code generate for protobufs by `prost-build`. + +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.gnomad_cnv4.rs")); +include!(concat!( + env!("OUT_DIR"), + "/annonars.gnomad.gnomad_cnv4.serde.rs" +)); diff --git a/src/pbs/gnomad/gnomad_sv2.rs b/src/pbs/gnomad/gnomad_sv2.rs new file mode 100644 index 00000000..64de42e2 --- /dev/null +++ b/src/pbs/gnomad/gnomad_sv2.rs @@ -0,0 +1,7 @@ +//! Code generate for protobufs by `prost-build`. + +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.gnomad_sv2.rs")); +include!(concat!( + env!("OUT_DIR"), + "/annonars.gnomad.gnomad_sv2.serde.rs" +)); diff --git a/src/pbs/gnomad/gnomad_sv4.rs b/src/pbs/gnomad/gnomad_sv4.rs new file mode 100644 index 00000000..d954b294 --- /dev/null +++ b/src/pbs/gnomad/gnomad_sv4.rs @@ -0,0 +1,7 @@ +//! Code generate for protobufs by `prost-build`. + +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.gnomad_sv4.rs")); +include!(concat!( + env!("OUT_DIR"), + "/annonars.gnomad.gnomad_sv4.serde.rs" +)); diff --git a/src/gnomad_pbs/mod.rs b/src/pbs/gnomad/mod.rs similarity index 75% rename from src/gnomad_pbs/mod.rs rename to src/pbs/gnomad/mod.rs index 0cf13d91..a24f4f1b 100644 --- a/src/gnomad_pbs/mod.rs +++ b/src/pbs/gnomad/mod.rs @@ -1,4 +1,4 @@ -//! Protocolbuffers related code for gnomAD mtDNA and nuclear. +//! Code generate for protobufs by `prost-build`. pub mod exac_cnv; pub mod gnomad2; diff --git a/src/gnomad_pbs/mtdna.rs b/src/pbs/gnomad/mtdna.rs similarity index 98% rename from src/gnomad_pbs/mtdna.rs rename to src/pbs/gnomad/mtdna.rs index 1b1141e5..7c2a4e08 100644 --- a/src/gnomad_pbs/mtdna.rs +++ b/src/pbs/gnomad/mtdna.rs @@ -1,4 +1,4 @@ -//! Protocolbuffers for gnomAD nuclear data structures. +//! Code generate for protobufs by `prost-build`. use std::str::FromStr; @@ -7,7 +7,8 @@ use noodles_vcf::record::info::field; use super::vep_gnomad3::Vep; use crate::common; -include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.v1.mtdna.rs")); +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.mtdna.rs")); +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.mtdna.serde.rs")); /// Options struct that allows to specify which details fields are to be extracted from /// gnomAD-mtDNA VCF records. diff --git a/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__gnomad2__test__record_from_vcf_allele_gnomad_exomes_grch37.snap b/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__gnomad2__test__record_from_vcf_allele_gnomad_exomes_grch37.snap new file mode 100644 index 00000000..2300abb2 --- /dev/null +++ b/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__gnomad2__test__record_from_vcf_allele_gnomad_exomes_grch37.snap @@ -0,0 +1,5251 @@ +--- +source: src/pbs/gnomad/gnomad2.rs +expression: records +--- +- chrom: "1" + pos: 55505599 + refAllele: C + altAllele: G + vep: + - allele: G + consequence: missense_variant + impact: MODERATE + symbol: PCSK9 + gene: ENSG00000169174 + featureType: Transcript + feature: ENST00000302118 + featureBiotype: protein_coding + exon: 1/12 + hgvsc: "ENST00000302118.5:c.89C>G" + hgvsp: "ENSP00000303208.5:p.Ala30Gly" + cdnaPosition: "379" + cdsPosition: "89" + proteinPosition: "30" + aminoAcids: A/G + codons: gCg/gGg + dbsnpId: "1" + strand: "1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "20001" + canonical: true + ccds: CCDS603.1 + ensp: ENSP00000303208 + swissprot: Q8NBP7 + uniparc: UPI00001615E1 + genePheno: "1" + sift: + prediction: deleterious_low_confidence + score: 0.03 + polyphen: + prediction: possibly_damaging + score: 0.583 + domains: + - id: SignalP-noTM + source: Cleavage_site_(Signalp) + - id: PTHR10795 + source: hmmpanther + - id: PTHR10795 + source: hmmpanther + lofInfo: "DE_NOVO_DONOR_PROB:0.146539915246404&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_POS:-119&INTRON_END:55509515&DE_NOVO_DONOR_MES_POS:-122&INTRON_START:55505718&EXON_END:55505717&EXON_START:55505221&DE_NOVO_DONOR_MES:-1.61109392005567" + - allele: G + consequence: missense_variant + impact: MODERATE + symbol: PCSK9 + gene: ENSG00000169174 + featureType: Transcript + feature: ENST00000452118 + featureBiotype: protein_coding + exon: 1/6 + hgvsc: "ENST00000452118.2:c.89C>G" + hgvsp: "ENSP00000401598.2:p.Ala30Gly" + cdnaPosition: "169" + cdsPosition: "89" + proteinPosition: "30" + aminoAcids: A/G + codons: gCg/gGg + dbsnpId: "1" + strand: "1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "20001" + ensp: ENSP00000401598 + trembl: B4DEZ9 + uniparc: UPI00017A6F55 + genePheno: "1" + sift: + prediction: deleterious_low_confidence + score: 0.02 + polyphen: + prediction: possibly_damaging + score: 0.655 + domains: + - id: SignalP-noTM + source: Cleavage_site_(Signalp) + - id: PTHR10795 + source: hmmpanther + lofInfo: "DE_NOVO_DONOR_MES_POS:-122&INTRON_START:55505718&INTRON_END:55509515&EXON_START:55505431&DE_NOVO_DONOR_MES:-1.61109392005567&EXON_END:55505717&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_PROB:0.146539915246404&DE_NOVO_DONOR_POS:-119" + - allele: G + consequence: upstream_gene_variant + impact: MODIFIER + symbol: PCSK9 + gene: ENSG00000169174 + featureType: Transcript + feature: ENST00000543384 + featureBiotype: protein_coding + dbsnpId: "1" + distance: "296" + strand: "1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "20001" + ensp: ENSP00000441859 + trembl: F5GWF0 + uniparc: UPI000206501F + genePheno: "1" + - allele: G + consequence: regulatory_region_variant + impact: MODIFIER + featureType: RegulatoryFeature + feature: ENSR00001037993 + featureBiotype: promoter + dbsnpId: "1" + variantClass: SNV + minimised: "1" + alleleCounts: + - byPopulation: + - population: afr + counts: + overall: + an: 10278 + xx: + an: 6396 + xy: + an: 3882 + faf95: 0 + faf99: 0 + - population: amr + counts: + overall: + an: 26912 + xx: + an: 15498 + xy: + an: 11414 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 8820 + xx: + an: 4180 + xy: + an: 4640 + - population: eas + counts: + overall: + an: 13152 + xx: + an: 6510 + xy: + an: 6642 + faf95: 0 + faf99: 0 + - 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allele: T + consequence: missense_variant + impact: MODERATE + symbol: TEX11 + gene: ENSG00000120498 + featureType: Transcript + feature: ENST00000344304 + featureBiotype: protein_coding + exon: 13/29 + hgvsc: "ENST00000344304.3:c.1168C>A" + hgvsp: "ENSP00000340995.3:p.Leu390Ile" + cdnaPosition: "1168" + cdsPosition: "1168" + proteinPosition: "390" + aminoAcids: L/I + codons: Ctt/Att + dbsnpId: "1" + strand: "-1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "11733" + ccds: CCDS35323.1 + ensp: ENSP00000340995 + swissprot: Q8IYF3 + uniparc: UPI000013CA89 + genePheno: "1" + sift: + prediction: tolerated + score: 0.17 + polyphen: + prediction: benign + score: 0.105 + domains: + - id: seg + source: Low_complexity_(Seg) + - id: PTHR22904 + source: hmmpanther + - id: PTHR22904 + source: hmmpanther + - id: PF08631 + source: Pfam_domain + - allele: T + consequence: missense_variant + impact: MODERATE + symbol: TEX11 + gene: ENSG00000120498 + featureType: Transcript + feature: ENST00000374320 + featureBiotype: protein_coding + exon: 3/19 + hgvsc: "ENST00000374320.2:c.193C>A" + hgvsp: "ENSP00000363440.2:p.Leu65Ile" + cdnaPosition: "415" + cdsPosition: "193" + proteinPosition: "65" + aminoAcids: L/I + codons: Ctt/Att + dbsnpId: "1" + strand: "-1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "11733" + ensp: ENSP00000363440 + swissprot: Q8IYF3 + uniparc: UPI00004A2D6C + genePheno: "1" + sift: + prediction: tolerated + score: 0.12 + polyphen: + prediction: benign + score: 0.105 + domains: + - id: seg + source: Low_complexity_(Seg) + - id: PTHR22904 + source: hmmpanther + - id: PTHR22904 + source: hmmpanther + - id: PF08631 + source: Pfam_domain + - allele: T + consequence: missense_variant + impact: MODERATE + symbol: TEX11 + gene: ENSG00000120498 + featureType: Transcript + feature: ENST00000374333 + featureBiotype: protein_coding + exon: 14/30 + hgvsc: "ENST00000374333.2:c.1123C>A" + hgvsp: "ENSP00000363453.2:p.Leu375Ile" + cdnaPosition: "1222" + cdsPosition: "1123" + proteinPosition: "375" + aminoAcids: L/I + codons: Ctt/Att + dbsnpId: "1" + strand: "-1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "11733" + ccds: CCDS43968.1 + ensp: ENSP00000363453 + swissprot: Q8IYF3 + uniparc: UPI00002122F2 + genePheno: "1" + sift: + prediction: tolerated + score: 0.18 + polyphen: + prediction: benign + score: 0.416 + domains: + - id: seg + source: Low_complexity_(Seg) + - id: PTHR22904 + source: hmmpanther + - id: PTHR22904 + source: hmmpanther + - id: PF08631 + source: Pfam_domain + - 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allele: G + consequence: downstream_gene_variant + impact: MODIFIER + symbol: RP11-34P13.13 + gene: ENSG00000241860 + featureType: Transcript + feature: ENST00000490997 + featureBiotype: antisense + dbsnpId: "1" + distance: "4155" + strand: "-1" + variantClass: SNV + minimised: "1" + symbolSource: Clone_based_vega_gene + - allele: G + consequence: downstream_gene_variant + impact: MODIFIER + symbol: RP11-34P13.14 + gene: ENSG00000239906 + featureType: Transcript + feature: ENST00000493797 + featureBiotype: antisense + dbsnpId: "1" + distance: "1137" + strand: "-1" + variantClass: SNV + minimised: "1" + symbolSource: Clone_based_vega_gene + canonical: true + - allele: G + consequence: upstream_gene_variant + impact: MODIFIER + symbol: RP11-34P13.15 + gene: ENSG00000268903 + featureType: Transcript + feature: ENST00000494149 + featureBiotype: processed_pseudogene + dbsnpId: "1" + distance: "2758" + strand: "-1" + variantClass: SNV + minimised: "1" + symbolSource: Clone_based_vega_gene + canonical: true + - 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allele: G + consequence: missense_variant + impact: MODERATE + symbol: PCSK9 + gene: ENSG00000169174 + featureType: Transcript + feature: ENST00000302118 + featureBiotype: protein_coding + exon: 1/12 + hgvsc: "ENST00000302118.5:c.89C>G" + hgvsp: "ENSP00000303208.5:p.Ala30Gly" + cdnaPosition: "379" + cdsPosition: "89" + proteinPosition: "30" + aminoAcids: A/G + codons: gCg/gGg + dbsnpId: "1" + strand: "1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "20001" + canonical: true + ccds: CCDS603.1 + ensp: ENSP00000303208 + swissprot: Q8NBP7 + uniparc: UPI00001615E1 + genePheno: "1" + sift: + prediction: deleterious_low_confidence + score: 0.03 + polyphen: + prediction: possibly_damaging + score: 0.583 + domains: + - id: SignalP-noTM + source: Cleavage_site_(Signalp) + - id: PTHR10795 + source: hmmpanther + - id: PTHR10795 + source: hmmpanther + lofInfo: "MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_MES:-1.61109392005567&DE_NOVO_DONOR_MES_POS:-122&EXON_END:55505717&INTRON_START:55505718&DE_NOVO_DONOR_PROB:0.146539915246404&INTRON_END:55509515&DE_NOVO_DONOR_POS:-119&EXON_START:55505221" + - allele: G + consequence: missense_variant + impact: MODERATE + symbol: PCSK9 + gene: ENSG00000169174 + featureType: Transcript + feature: ENST00000452118 + featureBiotype: protein_coding + exon: 1/6 + hgvsc: "ENST00000452118.2:c.89C>G" + hgvsp: "ENSP00000401598.2:p.Ala30Gly" + cdnaPosition: "169" + cdsPosition: "89" + proteinPosition: "30" + aminoAcids: A/G + codons: gCg/gGg + dbsnpId: "1" + strand: "1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "20001" + ensp: ENSP00000401598 + trembl: B4DEZ9 + uniparc: UPI00017A6F55 + genePheno: "1" + sift: + prediction: deleterious_low_confidence + score: 0.02 + polyphen: + prediction: possibly_damaging + score: 0.655 + domains: + - id: SignalP-noTM + source: Cleavage_site_(Signalp) + - id: PTHR10795 + source: hmmpanther + lofInfo: "DE_NOVO_DONOR_MES_POS:-122&DE_NOVO_DONOR_MES:-1.61109392005567&MUTANT_DONOR_MES:8.16693067332728&INTRON_END:55509515&DE_NOVO_DONOR_POS:-119&EXON_END:55505717&DE_NOVO_DONOR_PROB:0.146539915246404&INTRON_START:55505718&EXON_START:55505431" + - allele: G + consequence: upstream_gene_variant + impact: MODIFIER + symbol: PCSK9 + gene: ENSG00000169174 + featureType: Transcript + feature: ENST00000543384 + featureBiotype: protein_coding + dbsnpId: "1" + distance: "296" + strand: "1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "20001" + ensp: ENSP00000441859 + trembl: F5GWF0 + uniparc: UPI000206501F + genePheno: "1" + - allele: G + consequence: regulatory_region_variant + impact: MODIFIER + featureType: RegulatoryFeature + feature: ENSR00001037993 + featureBiotype: promoter + dbsnpId: "1" + variantClass: SNV + minimised: "1" + alleleCounts: + - byPopulation: + - population: afr + counts: + overall: + an: 8706 + xx: + an: 3678 + xy: + an: 5028 + faf95: 0 + faf99: 0 + - population: amr + counts: + overall: + an: 848 + xx: + an: 414 + xy: + an: 434 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 290 + xx: + an: 80 + xy: + an: 210 + - population: eas + counts: + overall: + an: 1558 + xx: + an: 538 + xy: + an: 1020 + faf95: 0 + faf99: 0 + - population: eas_jpn + counts: {} + - population: eas_oea + counts: {} + - population: eas_kor + counts: {} + - population: fin + counts: + overall: + an: 3476 + xx: + an: 1846 + xy: + an: 1630 + - population: nfe + counts: + overall: + ac: 1 + an: 15428 + af: 0.0000648172 + xx: + ac: 1 + an: 6806 + af: 0.000146929 + xy: + an: 8622 + faf95: 0 + faf99: 0 + - population: nfe_bgr + counts: {} + - population: nfe_est + counts: + overall: + an: 4592 + - population: nfe_nwe + counts: + overall: + an: 8594 + - population: nfe_onf + counts: + overall: + an: 2136 + - population: nfe_seu + counts: + overall: + ac: 1 + an: 106 + af: 0.00943396 + - population: nfe_swe + counts: {} + - population: oth + counts: + overall: + an: 1086 + xx: + an: 560 + xy: + an: 526 + - population: sas + counts: {} + bySex: + overall: + ac: 1 + an: 31392 + af: 0.0000318552 + xx: + ac: 1 + an: 13922 + af: 0.0000718288 + xy: + an: 17470 + raw: + ac: 1 + an: 31416 + af: 0.0000318309 + popmax: nfe + afPopmax: 0.0000648172 + acPopmax: 1 + anPopmax: 15428 + nhomaltPopmax: 0 + - cohort: controls + byPopulation: + - population: afr + counts: + overall: + an: 2570 + xx: + an: 1164 + xy: + an: 1406 + faf95: 0 + faf99: 0 + - population: amr + counts: + overall: + an: 246 + xx: + an: 120 + xy: + an: 126 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 38 + xx: + an: 24 + xy: + an: 14 + - population: eas + counts: + overall: + an: 914 + xx: + an: 342 + xy: + an: 572 + faf95: 0 + faf99: 0 + - population: eas_jpn + counts: {} + - population: eas_oea + counts: {} + - population: eas_kor + counts: {} + - population: fin + counts: + overall: + an: 1162 + xx: + an: 556 + xy: + an: 606 + - population: nfe + counts: + overall: + ac: 1 + an: 5518 + af: 0.000181225 + xx: + ac: 1 + an: 2576 + af: 0.000388199 + xy: + an: 2942 + faf95: 0 + faf99: 0 + - population: nfe_bgr + counts: {} + - population: nfe_est + counts: + overall: + an: 4104 + - population: nfe_nwe + counts: + overall: + an: 920 + - population: nfe_onf + counts: + overall: + an: 438 + - population: nfe_seu + counts: + overall: + ac: 1 + an: 56 + af: 0.0178571 + - population: nfe_swe + counts: {} + - population: oth + counts: + overall: + an: 424 + xx: + an: 226 + xy: + an: 198 + - population: sas + counts: {} + bySex: + overall: + ac: 1 + an: 10872 + af: 0.0000919794 + xx: + ac: 1 + an: 5008 + af: 0.000199681 + xy: + an: 5864 + raw: + ac: 1 + an: 10884 + af: 0.000091878 + popmax: nfe + afPopmax: 0.000181225 + acPopmax: 1 + anPopmax: 5518 + nhomaltPopmax: 0 + - cohort: non_cancer + byPopulation: + - population: afr + counts: {} + faf95: 0 + faf99: 0 + - population: amr + counts: {} + faf95: 0 + faf99: 0 + - population: asj + counts: {} + - population: eas + counts: {} + faf95: 0 + faf99: 0 + - population: eas_jpn + counts: {} + - population: eas_oea + counts: {} + - population: eas_kor + counts: {} + - population: fin + counts: {} + - population: nfe + counts: {} + faf95: 0 + faf99: 0 + - population: nfe_bgr + counts: {} + - population: nfe_est + counts: {} + - population: nfe_nwe + counts: {} + - population: nfe_onf + counts: {} + - population: nfe_seu + counts: {} + - population: nfe_swe + counts: {} + - population: oth + counts: {} + - population: sas + counts: {} + bySex: {} + - cohort: non_neuro + byPopulation: + - population: afr + counts: + overall: + an: 3384 + xx: + an: 1778 + xy: + an: 1606 + faf95: 0 + faf99: 0 + - population: amr + counts: + overall: + an: 554 + xx: + an: 310 + xy: + an: 244 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 246 + xx: + an: 60 + xy: + an: 186 + - population: eas + counts: + overall: + an: 1558 + xx: + an: 538 + xy: + an: 1020 + faf95: 0 + faf99: 0 + - population: eas_jpn + counts: {} + - population: eas_oea + counts: {} + - population: eas_kor + counts: {} + - population: fin + counts: + overall: + an: 1164 + xx: + an: 558 + xy: + an: 606 + - population: nfe + counts: + overall: + ac: 1 + an: 13618 + af: 0.0000734322 + xx: + ac: 1 + an: 5982 + af: 0.000167168 + xy: + an: 7636 + faf95: 0 + faf99: 0 + - population: nfe_bgr + counts: {} + - population: nfe_est + counts: + overall: + an: 4146 + - 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population: eas_jpn + counts: {} + - population: eas_oea + counts: {} + - population: eas_kor + counts: {} + - population: fin + counts: + overall: + an: 3476 + xx: + an: 1846 + xy: + an: 1630 + - population: nfe + counts: + overall: + ac: 1 + an: 11088 + af: 0.0000901876 + xx: + ac: 1 + an: 5610 + af: 0.000178253 + xy: + an: 5478 + faf95: 0 + faf99: 0 + - population: nfe_bgr + counts: {} + - population: nfe_est + counts: + overall: + an: 4570 + - population: nfe_nwe + counts: + overall: + an: 4898 + - population: nfe_onf + counts: + overall: + an: 1514 + - population: nfe_seu + counts: + overall: + ac: 1 + an: 106 + af: 0.00943396 + - population: nfe_swe + counts: {} + - population: oth + counts: + overall: + an: 1010 + xx: + an: 544 + xy: + an: 466 + - population: sas + counts: {} + bySex: + overall: + ac: 1 + an: 26586 + af: 0.0000376138 + xx: + ac: 1 + an: 12586 + af: 0.0000794534 + xy: + an: 14000 + raw: + ac: 1 + an: 26608 + af: 0.0000375827 + popmax: nfe + afPopmax: 0.0000901876 + acPopmax: 1 + anPopmax: 11088 + nhomaltPopmax: 0 + rfInfo: + rfTpProbability: 0.77474 + variantInfo: + variantType: snv + alleleType: snv + nAltAlleles: 1 + qualityInfo: + fs: 1.515 + inbreedingCoeff: 0.0198 + mq: 59.95 + mqRankSum: -1.385 + qd: 12.71 + readPosRankSum: 0.308 + vqsrNegativeTrainSite: true + baseQRankSum: 2.21 + clippingRankSum: 1.33 + sor: 1.022 + dp: 696568 + vqslod: -2.305 + vqsrCulprit: MQ + pabMax: 1 + ageInfo: + ageHistHomNSmaller: 0 + ageHistHomNLarger: 0 + ageHistHetNSmaller: 0 + ageHistHetNLarger: 0 + depthInfo: + dpHistAllNLarger: 2 + dpHistAltNLarger: 0 +- chrom: "1" + pos: 55516888 + refAllele: G + altAllele: GA + vep: + - allele: A + consequence: intron_variant + impact: MODIFIER + symbol: PCSK9 + gene: ENSG00000169174 + featureType: Transcript + feature: ENST00000302118 + featureBiotype: protein_coding + intron: 3/11 + hgvsc: "ENST00000302118.5:c.524-1063_524-1062insA" + existingVariation: rs527413419 + dbsnpId: "1" + strand: "1" + variantClass: insertion + minimised: "1" + symbolSource: HGNC + hgncId: "20001" + canonical: true + ccds: CCDS603.1 + ensp: ENSP00000303208 + swissprot: Q8NBP7 + uniparc: UPI00001615E1 + genePheno: "1" + gmaf: 0.0032 + amrMaf: 0.0113 + easMaf: 0.0014 + eurMaf: 0 + sasMaf: 0 + aaMaf: 0 + - allele: A + consequence: frameshift_variant + impact: HIGH + symbol: PCSK9 + gene: ENSG00000169174 + featureType: Transcript + feature: ENST00000452118 + featureBiotype: protein_coding + exon: 4/6 + hgvsc: "ENST00000452118.2:c.547_548insA" + hgvsp: "ENSP00000401598.2:p.Gly183GlufsTer23" + cdnaPosition: 627-628 + cdsPosition: 547-548 + proteinPosition: "183" + aminoAcids: G/EX + codons: ggc/gAgc + existingVariation: rs527413419 + dbsnpId: "1" + strand: "1" + variantClass: insertion + minimised: "1" + symbolSource: HGNC + hgncId: "20001" + ensp: ENSP00000401598 + trembl: B4DEZ9 + uniparc: UPI00017A6F55 + genePheno: "1" + gmaf: 0.0032 + amrMaf: 0.0113 + easMaf: 0.0014 + eurMaf: 0 + sasMaf: 0 + aaMaf: 0 + lof: HC + lofInfo: "GERP_DIST:364.1444&BP_DIST:304&PERCENTILE:0.885113268608414&DIST_FROM_LAST_EXON:210&50_BP_RULE:PASS&PHYLOCSF_TOO_SHORT" + - allele: A + consequence: non_coding_transcript_exon_variant&non_coding_transcript_variant + impact: MODIFIER + symbol: PCSK9 + gene: ENSG00000169174 + featureType: Transcript + feature: ENST00000490692 + featureBiotype: processed_transcript + exon: 1/8 + hgvsc: "ENST00000490692.1:n.282_283insA" + cdnaPosition: 282-283 + existingVariation: rs527413419 + dbsnpId: "1" + strand: "1" + variantClass: insertion + minimised: "1" + symbolSource: HGNC + hgncId: "20001" + genePheno: "1" + gmaf: 0.0032 + amrMaf: 0.0113 + easMaf: 0.0014 + eurMaf: 0 + sasMaf: 0 + aaMaf: 0 + - allele: A + consequence: intron_variant + impact: MODIFIER + symbol: PCSK9 + gene: ENSG00000169174 + featureType: Transcript + feature: ENST00000543384 + featureBiotype: protein_coding + intron: 1/9 + hgvsc: "ENST00000543384.1:c.-77-1063_-77-1062insA" + existingVariation: rs527413419 + dbsnpId: "1" + strand: "1" + variantClass: insertion + minimised: "1" + symbolSource: HGNC + hgncId: "20001" + ensp: ENSP00000441859 + trembl: F5GWF0 + uniparc: UPI000206501F + genePheno: "1" + gmaf: 0.0032 + amrMaf: 0.0113 + easMaf: 0.0014 + eurMaf: 0 + sasMaf: 0 + aaMaf: 0 + alleleCounts: + - 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cohort: non_topmed + byPopulation: + - population: afr + counts: + overall: + ac: 152 + an: 8540 + af: 0.0177986 + xx: + ac: 66 + an: 3606 + af: 0.0183028 + xy: + ac: 86 + an: 4934 + af: 0.0174301 + faf95: 0.0154185 + faf99: 0.0154183 + - population: amr + counts: + overall: + an: 810 + xx: + an: 394 + xy: + an: 416 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 138 + xx: + an: 62 + xy: + an: 76 + - population: eas + counts: + overall: + an: 1522 + xx: + an: 520 + xy: + an: 1002 + faf95: 0 + faf99: 0 + - population: eas_jpn + counts: {} + - population: eas_oea + counts: {} + - population: eas_kor + counts: {} + - population: fin + counts: + overall: + an: 3476 + xx: + an: 1846 + xy: + an: 1630 + - population: nfe + counts: + overall: + ac: 1 + an: 11080 + af: 0.0000902527 + xx: + an: 5606 + xy: + ac: 1 + an: 5474 + af: 0.000182682 + faf95: 0 + faf99: 0 + - population: nfe_bgr + counts: {} + - population: nfe_est + counts: + overall: + an: 4562 + - population: nfe_nwe + counts: + overall: + ac: 1 + an: 4896 + af: 0.000204248 + - population: nfe_onf + counts: + overall: + an: 1516 + - population: nfe_seu + counts: + overall: + an: 106 + - population: nfe_swe + counts: {} + - population: oth + counts: + overall: + ac: 1 + an: 1010 + af: 0.000990099 + xx: + an: 544 + xy: + ac: 1 + an: 466 + af: 0.00214592 + - population: sas + counts: {} + bySex: + overall: + ac: 154 + an: 26576 + af: 0.0057947 + xx: + ac: 66 + an: 12578 + af: 0.00524726 + xy: + ac: 88 + an: 13998 + af: 0.00628661 + raw: + ac: 154 + an: 26608 + af: 0.00578773 + popmax: afr + afPopmax: 0.0177986 + acPopmax: 152 + anPopmax: 8540 + nhomaltPopmax: 0 + rfInfo: + rfTpProbability: 0.952127 + rfPositiveLabel: true + rfLabel: TP + rfTrain: true + variantInfo: + variantType: indel + alleleType: ins + nAltAlleles: 1 + qualityInfo: + fs: 0.52 + inbreedingCoeff: -0.0043 + mq: 60 + mqRankSum: -0.017 + qd: 15.91 + readPosRankSum: 0.122 + vqsrPositiveTrainSite: true + baseQRankSum: -0.161 + clippingRankSum: -0.129 + sor: 0.654 + dp: 660105 + vqslod: 4.41 + vqsrCulprit: FS + pabMax: 1 + ageInfo: + ageHistHomNSmaller: 0 + ageHistHomNLarger: 0 + ageHistHetNSmaller: 64 + ageHistHetNLarger: 2 + depthInfo: + dpHistAllNLarger: 1 + dpHistAltNLarger: 0 +- chrom: X + pos: 69902634 + refAllele: C + altAllele: T + vep: + - allele: T + consequence: missense_variant + impact: MODERATE + symbol: TEX11 + gene: ENSG00000120498 + featureType: Transcript + feature: ENST00000344304 + featureBiotype: protein_coding + exon: 13/29 + hgvsc: "ENST00000344304.3:c.1091G>A" + hgvsp: "ENSP00000340995.3:p.Arg364His" + cdnaPosition: "1091" + cdsPosition: "1091" + proteinPosition: "364" + aminoAcids: R/H + codons: cGt/cAt + existingVariation: rs201471690 + dbsnpId: "1" + strand: "-1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "11733" + ccds: CCDS35323.1 + ensp: ENSP00000340995 + swissprot: Q8IYF3 + uniparc: UPI000013CA89 + genePheno: "1" + sift: + prediction: tolerated + score: 1 + polyphen: + prediction: benign + score: 0.007 + domains: + - id: PTHR22904 + source: hmmpanther + - id: PTHR22904 + source: hmmpanther + - id: PF08631 + source: Pfam_domain + gmaf: 0.0005 + afrMaf: 0 + amrMaf: 0.0008 + easMaf: 0 + eurMaf: 0 + sasMaf: 0.001 + aaMaf: 0 + exacAdjMaf: 0 + exacAfrMaf: 0.00003295 + exacAmrMaf: 0.0001237 + exacEasMaf: 0.00002495 + exacFinMaf: 0 + exacNfeMaf: 0 + exacOthMaf: 0.00002306 + exacSasMaf: 0 + lofInfo: "EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108&MUTANT_DONOR_MES:6.38837132164763&DE_NOVO_DONOR_PROB:0.0218748740634797&INTRON_END:69902523&INTRON_START:69898740" + - allele: T + consequence: missense_variant + impact: MODERATE + symbol: TEX11 + gene: ENSG00000120498 + featureType: Transcript + feature: ENST00000374320 + featureBiotype: protein_coding + exon: 3/19 + hgvsc: "ENST00000374320.2:c.116G>A" + hgvsp: "ENSP00000363440.2:p.Arg39His" + cdnaPosition: "338" + cdsPosition: "116" + proteinPosition: "39" + aminoAcids: R/H + codons: cGt/cAt + existingVariation: rs201471690 + dbsnpId: "1" + strand: "-1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "11733" + ensp: ENSP00000363440 + swissprot: Q8IYF3 + uniparc: UPI00004A2D6C + genePheno: "1" + sift: + prediction: tolerated + score: 1 + polyphen: + prediction: benign + score: 0.007 + domains: + - id: PTHR22904 + source: hmmpanther + - id: PTHR22904 + source: hmmpanther + - id: PF08631 + source: Pfam_domain + gmaf: 0.0005 + afrMaf: 0 + amrMaf: 0.0008 + easMaf: 0 + eurMaf: 0 + sasMaf: 0.001 + aaMaf: 0 + exacAdjMaf: 0 + exacAfrMaf: 0.00003295 + exacAmrMaf: 0.0001237 + exacEasMaf: 0.00002495 + exacFinMaf: 0 + exacNfeMaf: 0 + exacOthMaf: 0.00002306 + exacSasMaf: 0 + lofInfo: "INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763&INTRON_START:69898740&EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108" + - allele: T + consequence: missense_variant + impact: MODERATE + symbol: TEX11 + gene: ENSG00000120498 + featureType: Transcript + feature: ENST00000374333 + featureBiotype: protein_coding + exon: 14/30 + hgvsc: "ENST00000374333.2:c.1046G>A" + hgvsp: "ENSP00000363453.2:p.Arg349His" + cdnaPosition: "1145" + cdsPosition: "1046" + proteinPosition: "349" + aminoAcids: R/H + codons: cGt/cAt + existingVariation: rs201471690 + dbsnpId: "1" + strand: "-1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "11733" + ccds: CCDS43968.1 + ensp: ENSP00000363453 + swissprot: Q8IYF3 + uniparc: UPI00002122F2 + genePheno: "1" + sift: + prediction: tolerated + score: 1 + polyphen: + prediction: benign + score: 0.003 + domains: + - id: PTHR22904 + source: hmmpanther + - id: PTHR22904 + source: hmmpanther + - id: PF08631 + source: Pfam_domain + gmaf: 0.0005 + afrMaf: 0 + amrMaf: 0.0008 + easMaf: 0 + eurMaf: 0 + sasMaf: 0.001 + aaMaf: 0 + exacAdjMaf: 0 + exacAfrMaf: 0.00003295 + exacAmrMaf: 0.0001237 + exacEasMaf: 0.00002495 + exacFinMaf: 0 + exacNfeMaf: 0 + exacOthMaf: 0.00002306 + exacSasMaf: 0 + lofInfo: "DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108&EXON_START:69902524&EXON_END:69902675&DE_NOVO_DONOR_MES:0.0381663094165419&INTRON_START:69898740&INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763" + - allele: T + consequence: missense_variant + impact: MODERATE + symbol: TEX11 + gene: ENSG00000120498 + featureType: Transcript + feature: ENST00000395889 + featureBiotype: protein_coding + exon: 15/31 + hgvsc: "ENST00000395889.2:c.1091G>A" + hgvsp: "ENSP00000379226.2:p.Arg364His" + cdnaPosition: "1247" + cdsPosition: "1091" + proteinPosition: "364" + aminoAcids: R/H + codons: cGt/cAt + existingVariation: rs201471690 + dbsnpId: "1" + strand: "-1" + variantClass: SNV + minimised: "1" + symbolSource: HGNC + hgncId: "11733" + canonical: true + ccds: CCDS35323.1 + ensp: ENSP00000379226 + swissprot: Q8IYF3 + uniparc: UPI000013CA89 + genePheno: "1" + sift: + prediction: tolerated + score: 1 + polyphen: + prediction: benign + score: 0.007 + domains: + - id: PTHR22904 + source: hmmpanther + - id: PTHR22904 + source: hmmpanther + - id: PF08631 + source: Pfam_domain + gmaf: 0.0005 + afrMaf: 0 + amrMaf: 0.0008 + easMaf: 0 + eurMaf: 0 + sasMaf: 0.001 + aaMaf: 0 + exacAdjMaf: 0 + exacAfrMaf: 0.00003295 + exacAmrMaf: 0.0001237 + exacEasMaf: 0.00002495 + exacFinMaf: 0 + exacNfeMaf: 0 + exacOthMaf: 0.00002306 + exacSasMaf: 0 + lofInfo: "INTRON_END:69902523&DE_NOVO_DONOR_PROB:0.0218748740634797&MUTANT_DONOR_MES:6.38837132164763&INTRON_START:69898740&EXON_END:69902675&EXON_START:69902524&DE_NOVO_DONOR_MES:0.0381663094165419&DE_NOVO_DONOR_POS:-108&DE_NOVO_DONOR_MES_POS:-108" + alleleCounts: + - 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allele: C + consequence: downstream_gene_variant + impact: MODIFIER + symbol: DDX11L1 + gene: ENSG00000223972 + featureType: Transcript + feature: ENST00000450305 + featureBiotype: transcribed_unprocessed_pseudogene + dbsnpId: "1" + distance: "2301" + strand: "1" + variantClass: SNV + symbolSource: HGNC + hgncId: "HGNC:37102" + - allele: C + consequence: downstream_gene_variant + impact: MODIFIER + symbol: DDX11L1 + gene: ENSG00000223972 + featureType: Transcript + feature: ENST00000456328 + featureBiotype: processed_transcript + dbsnpId: "1" + distance: "1562" + strand: "1" + variantClass: SNV + symbolSource: HGNC + hgncId: "HGNC:37102" + canonical: true + tsl: 1 + - allele: C + consequence: intron_variant&non_coding_transcript_variant + impact: MODIFIER + symbol: WASH7P + gene: ENSG00000227232 + featureType: Transcript + feature: ENST00000488147 + featureBiotype: unprocessed_pseudogene + intron: 8/10 + hgvsc: "ENST00000488147.1:n.1068-24C>G" + dbsnpId: "1" + strand: "-1" + variantClass: SNV + symbolSource: HGNC + hgncId: "HGNC:38034" + canonical: true + - 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allele: A + consequence: downstream_gene_variant + impact: MODIFIER + symbol: MIR6859-1 + gene: ENSG00000278267 + featureType: Transcript + feature: ENST00000619216 + featureBiotype: miRNA + dbsnpId: "1" + distance: "1392" + strand: "-1" + variantClass: SNV + symbolSource: HGNC + hgncId: "HGNC:50039" + canonical: true + - allele: A + consequence: intron_variant&non_coding_transcript_variant + impact: MODIFIER + symbol: WASH7P + gene: "653635" + featureType: Transcript + feature: NR_024540.1 + featureBiotype: transcribed_pseudogene + intron: 8/10 + hgvsc: "NR_024540.1:n.1081-30C>T" + dbsnpId: "1" + strand: "-1" + variantClass: SNV + symbolSource: EntrezGene + hgncId: "HGNC:38034" + canonical: true + - allele: A + consequence: downstream_gene_variant + impact: MODIFIER + symbol: DDX11L1 + gene: "100287102" + featureType: Transcript + feature: NR_046018.2 + featureBiotype: transcribed_pseudogene + dbsnpId: "1" + distance: "1568" + strand: "1" + variantClass: SNV + symbolSource: EntrezGene + hgncId: "HGNC:37102" + canonical: true + - allele: A + consequence: downstream_gene_variant + impact: MODIFIER + symbol: MIR6859-1 + gene: "102466751" + featureType: Transcript + feature: NR_106918.1 + featureBiotype: miRNA + dbsnpId: "1" + distance: "1392" + strand: "-1" + variantClass: SNV + symbolSource: EntrezGene + hgncId: "HGNC:50039" + canonical: true + - allele: A + consequence: regulatory_region_variant + impact: MODIFIER + featureType: RegulatoryFeature + feature: ENSR00000344266 + featureBiotype: CTCF_binding_site + dbsnpId: "1" + variantClass: SNV + alleleCounts: + - byPopulation: + - population: afr + counts: + overall: + an: 37134 + xx: + an: 19924 + xy: + an: 17210 + faf95: 0 + faf99: 0 + - population: ami + counts: + overall: + an: 634 + xx: + an: 316 + xy: + an: 318 + - population: amr + counts: + overall: + an: 9746 + xx: + an: 4366 + xy: + an: 5380 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 2302 + xx: + an: 1258 + xy: + an: 1044 + - population: eas + counts: + overall: + an: 4670 + xx: + an: 2072 + xy: + an: 2598 + faf95: 0 + faf99: 0 + - population: fin + counts: + overall: + an: 5472 + xx: + an: 1494 + xy: + an: 3978 + - population: mid + counts: + overall: + an: 240 + xx: + an: 136 + xy: + an: 104 + - population: nfe + counts: + overall: + an: 46698 + xx: + an: 27388 + xy: + an: 19310 + faf95: 0 + faf99: 0 + - population: oth + counts: + overall: + an: 1404 + xx: + an: 710 + xy: + an: 694 + - population: sas + counts: + overall: + an: 3138 + xx: + an: 766 + xy: + an: 2372 + faf95: 0 + faf99: 0 + bySex: + overall: + an: 111438 + xx: + an: 58430 + xy: + an: 53008 + raw: + ac: 1 + an: 134888 + af: 0.00000741356 + - cohort: controls_and_biobanks + byPopulation: + - population: afr + counts: + overall: + an: 8112 + xx: + an: 4210 + xy: + an: 3902 + faf95: 0 + faf99: 0 + - population: ami + counts: + overall: + an: 30 + xx: + an: 12 + xy: + an: 18 + - population: amr + counts: + overall: + an: 3296 + xx: + an: 1750 + xy: + an: 1546 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 88 + xx: + an: 56 + xy: + an: 32 + - population: eas + counts: + overall: + an: 2238 + xx: + an: 954 + xy: + an: 1284 + faf95: 0 + faf99: 0 + - population: fin + counts: + overall: + an: 2706 + xx: + an: 326 + xy: + an: 2380 + - population: mid + counts: + overall: + an: 190 + xx: + an: 110 + xy: + an: 80 + - population: nfe + counts: + overall: + an: 4744 + xx: + an: 2312 + xy: + an: 2432 + faf95: 0 + faf99: 0 + - population: oth + counts: + overall: + an: 558 + xx: + an: 288 + xy: + an: 270 + - population: sas + counts: + overall: + an: 2158 + xx: + an: 610 + xy: + an: 1548 + faf95: 0 + faf99: 0 + bySex: + overall: + an: 24120 + xx: + an: 10628 + xy: + an: 13492 + raw: + an: 28832 + - cohort: non_cancer + byPopulation: + - population: afr + counts: + overall: + an: 36838 + xx: + an: 19782 + xy: + an: 17056 + faf95: 0 + faf99: 0 + - population: ami + counts: + overall: + an: 634 + xx: + an: 316 + xy: + an: 318 + - population: amr + counts: + overall: + an: 9628 + xx: + an: 4336 + xy: + an: 5292 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 2188 + xx: + an: 1170 + xy: + an: 1018 + - population: eas + counts: + overall: + an: 4456 + xx: + an: 1982 + xy: + an: 2474 + faf95: 0 + faf99: 0 + - population: fin + counts: + overall: + an: 5472 + xx: + an: 1494 + xy: + an: 3978 + - population: mid + counts: + overall: + an: 230 + xx: + an: 132 + xy: + an: 98 + - population: nfe + counts: + overall: + an: 44500 + xx: + an: 26552 + xy: + an: 17948 + faf95: 0 + faf99: 0 + - population: oth + counts: + overall: + an: 1356 + xx: + an: 692 + xy: + an: 664 + - population: sas + counts: + overall: + an: 3110 + xx: + an: 750 + xy: + an: 2360 + faf95: 0 + faf99: 0 + bySex: + overall: + an: 108412 + xx: + an: 57206 + xy: + an: 51206 + raw: + ac: 1 + an: 131384 + af: 0.00000761128 + - cohort: non_neuro + byPopulation: + - population: afr + counts: + overall: + an: 29240 + xx: + an: 16914 + xy: + an: 12326 + faf95: 0 + faf99: 0 + - population: ami + counts: + overall: + an: 604 + xx: + an: 290 + xy: + an: 314 + - population: amr + counts: + overall: + an: 9492 + xx: + an: 4262 + xy: + an: 5230 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 2252 + xx: + an: 1236 + xy: + an: 1016 + - population: eas + counts: + overall: + an: 4670 + xx: + an: 2072 + xy: + an: 2598 + faf95: 0 + faf99: 0 + - population: fin + counts: + overall: + an: 3450 + xx: + an: 420 + xy: + an: 3030 + - population: mid + counts: + overall: + an: 238 + xx: + an: 136 + xy: + an: 102 + - population: nfe + counts: + overall: + an: 44134 + xx: + an: 26354 + xy: + an: 17780 + faf95: 0 + faf99: 0 + - population: oth + counts: + overall: + an: 1340 + xx: + an: 682 + xy: + an: 658 + - population: sas + counts: + overall: + an: 3138 + xx: + an: 766 + xy: + an: 2372 + faf95: 0 + faf99: 0 + bySex: + overall: + an: 98558 + xx: + an: 53132 + xy: + an: 45426 + raw: + an: 119214 + - cohort: non_topmed + byPopulation: + - population: afr + counts: + overall: + an: 21974 + xx: + an: 10564 + xy: + an: 11410 + faf95: 0 + faf99: 0 + - population: ami + counts: + overall: + an: 60 + xx: + an: 38 + xy: + an: 22 + - population: amr + counts: + overall: + an: 8228 + xx: + an: 3444 + xy: + an: 4784 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 658 + xx: + an: 184 + xy: + an: 474 + - population: eas + counts: + overall: + an: 3330 + xx: + an: 1258 + xy: + an: 2072 + faf95: 0 + faf99: 0 + - population: fin + counts: + overall: + an: 5402 + xx: + an: 1450 + xy: + an: 3952 + - population: mid + counts: + overall: + an: 208 + xx: + an: 118 + xy: + an: 90 + - population: nfe + counts: + overall: + an: 13668 + xx: + an: 5924 + xy: + an: 7744 + faf95: 0 + faf99: 0 + - population: oth + counts: + overall: + an: 992 + xx: + an: 466 + xy: + an: 526 + - population: sas + counts: + overall: + an: 3124 + xx: + an: 764 + xy: + an: 2360 + faf95: 0 + faf99: 0 + bySex: + overall: + an: 57644 + xx: + an: 24210 + xy: + an: 33434 + raw: + ac: 1 + an: 70540 + af: 0.0000141764 + - cohort: non_v2 + byPopulation: + - population: afr + counts: + overall: + an: 25636 + xx: + an: 14188 + xy: + an: 11448 + faf95: 0 + faf99: 0 + - population: ami + counts: + overall: + an: 634 + xx: + an: 316 + xy: + an: 318 + - population: amr + counts: + overall: + an: 8738 + xx: + an: 3858 + xy: + an: 4880 + faf95: 0 + faf99: 0 + - population: asj + counts: + overall: + an: 2056 + xx: + an: 1146 + xy: + an: 910 + - population: eas + counts: + overall: + an: 2532 + xx: + an: 1198 + xy: + an: 1334 + faf95: 0 + faf99: 0 + - population: fin + counts: + overall: + an: 3498 + xx: + an: 616 + xy: + an: 2882 + - population: mid + counts: + overall: + an: 232 + xx: + an: 134 + xy: + an: 98 + - population: nfe + counts: + overall: + an: 36264 + xx: + an: 22592 + xy: + an: 13672 + faf95: 0 + faf99: 0 + - population: oth + counts: + overall: + an: 1256 + xx: + an: 640 + xy: + an: 616 + - population: sas + counts: + overall: + an: 2404 + xx: + an: 468 + xy: + an: 1936 + faf95: 0 + faf99: 0 + bySex: + overall: + an: 83250 + xx: + an: 45156 + xy: + an: 38094 + raw: + an: 100826 + effectInfo: + caddPhred: 4.644 + variantInfo: + variantType: multi-snv + alleleType: snv + nAltAlleles: 2 + varDp: 2 + qualityInfo: + asFs: 1.34551 + inbreedingCoeff: -0.00000739098 + asMq: 46.237 + mqRankSum: -0.067 + asMqRankSum: 3.027 + asQd: 3.17544 + readPosRankSum: -1.001 + asReadPosRankSum: -1.001 + asSor: 0.367725 + negativeTrainSite: true + asVqslod: -2.5822 + asCulprit: AS_QD + asPabMax: 0.6875 + asQualApprox: 181 + asSbTable: "34" + ageInfo: + ageHistHomNSmaller: 0 + ageHistHomNLarger: 0 + ageHistHetNSmaller: 0 + ageHistHetNLarger: 0 + depthInfo: + dpHistAllNLarger: 561 + dpHistAltNLarger: 0 + diff --git a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__mtdna__test__record_from_vcf_allele.snap b/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__mtdna__test__record_from_vcf_allele.snap similarity index 79% rename from src/gnomad_pbs/snapshots/annonars__gnomad_pbs__mtdna__test__record_from_vcf_allele.snap rename to src/pbs/gnomad/snapshots/annonars__pbs__gnomad__mtdna__test__record_from_vcf_allele.snap index 31e76274..a4121e06 100644 --- a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__mtdna__test__record_from_vcf_allele.snap +++ b/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__mtdna__test__record_from_vcf_allele.snap @@ -1,75 +1,30 @@ --- -source: src/gnomad_pbs/mtdna.rs +source: src/pbs/gnomad/mtdna.rs expression: records --- - chrom: MT pos: 3 - ref_allele: T - alt_allele: C - variant_collapsed: T3C - excluded_ac: 0 + refAllele: T + altAllele: C + variantCollapsed: T3C an: 56434 - ac_hom: 19 - ac_het: 1 - af_hom: 0.000336676 - af_het: 0.0000177198 - filters: [] - mitotip_score: ~ - mitotip_trna_prediction: ~ - pon_mt_trna_prediction: ~ - pon_ml_probability_of_pathogenicity: ~ + acHom: 19 + acHet: 1 + afHom: 0.000336676 + afHet: 0.0000177198 vep: - allele: C consequence: intergenic_variant impact: MODIFIER - symbol: "" - gene: "" - feature_type: Intergenic - feature: "" - feature_biotype: "" - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: ~ - variant_class: SNV - minimised: ~ - symbol_source: ~ - hgnc_id: ~ - canonical: ~ - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - quality_info: - dp_mean: 2522.87 - mq_mean: 60 - tlod_mean: 6805.54 - heteroplasmy_info: - heteroplasmy_below_min_het_threshold_hist: + featureType: Intergenic + dbsnpId: "1" + variantClass: SNV + qualityInfo: + dpMean: 2522.87 + mqMean: 60 + tlodMean: 6805.54 + heteroplasmyInfo: + heteroplasmyBelowMinHetThresholdHist: - 0 - 0 - 0 @@ -80,7 +35,7 @@ expression: records - 0 - 0 - 0 - hl_hist: + hlHist: - 0 - 0 - 0 @@ -91,10 +46,9 @@ expression: records - 0 - 1 - 19 - common_low_heteroplasmy: false - max_hl: 0.997 - filter_histograms: - base_qual_hist: + maxHl: 0.997 + filterHistograms: + baseQualHist: - 0 - 0 - 0 @@ -105,7 +59,7 @@ expression: records - 0 - 0 - 0 - position_hist: + positionHist: - 0 - 0 - 0 @@ -116,7 +70,7 @@ expression: records - 0 - 0 - 0 - strand_bias_hist: + strandBiasHist: - 0 - 0 - 0 @@ -127,7 +81,7 @@ expression: records - 0 - 0 - 0 - weak_evidence_hist: + weakEvidenceHist: - 0 - 0 - 0 @@ -138,7 +92,7 @@ expression: records - 0 - 0 - 0 - contamination_hist: + contaminationHist: - 0 - 0 - 0 @@ -149,8 +103,8 @@ expression: records - 0 - 0 - 0 - population_info: - pop_an: + populationInfo: + popAn: - 14347 - 392 - 5718 @@ -161,7 +115,7 @@ expression: records - 826 - 1493 - 20 - pop_ac_het: + popAcHet: - 0 - 0 - 0 @@ -172,7 +126,7 @@ expression: records - 0 - 0 - 0 - pop_ac_hom: + popAcHom: - 0 - 0 - 0 @@ -183,7 +137,7 @@ expression: records - 0 - 0 - 0 - pop_af_hom: + popAfHom: - 0 - 0 - 0 @@ -194,7 +148,7 @@ expression: records - 0 - 0 - 0 - pop_af_het: + popAfHet: - 0 - 0 - 0 @@ -205,7 +159,7 @@ expression: records - 0 - 0 - 0 - pop_hl_hist: + popHlHist: - 0 - 0 - 0 @@ -306,9 +260,8 @@ expression: records - 0 - 0 - 0 - haplogroup_info: - hap_defining_variant: false - hap_an: + haplogroupInfo: + hapAn: - 2680 - 1537 - 868 @@ -338,7 +291,7 @@ expression: records - 546 - 12 - 89 - hap_ac_het: + hapAcHet: - 0 - 0 - 0 @@ -368,7 +321,7 @@ expression: records - 0 - 0 - 0 - hap_ac_hom: + hapAcHom: - 0 - 0 - 0 @@ -398,7 +351,7 @@ expression: records - 0 - 0 - 0 - hap_af_het: + hapAfHet: - 0 - 0 - 0 @@ -428,7 +381,7 @@ expression: records - 0 - 0 - 0 - hap_af_hom: + hapAfHom: - 0 - 0 - 0 @@ -458,7 +411,7 @@ expression: records - 0 - 0 - 0 - hap_hl_hist: + hapHlHist: - 0 - 0 - 0 @@ -749,7 +702,7 @@ expression: records - 0 - 0 - 0 - hap_faf_hom: + hapFafHom: - 0 - 0 - 0 @@ -779,11 +732,11 @@ expression: records - 0 - 0 - 0 - hapmax_af_hom: T - hapmax_af_het: T - faf_hapmax_hom: 0.00351633 - age_info: - age_hist_hom_bin_freq: + hapmaxAfHom: T + hapmaxAfHet: T + fafHapmaxHom: 0.00351633 + ageInfo: + ageHistHomBinFreq: - 0 - 1 - 0 @@ -794,9 +747,9 @@ expression: records - 2 - 0 - 0 - age_hist_hom_n_smaller: 3 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: + ageHistHomNSmaller: 3 + ageHistHomNLarger: 0 + ageHistHetBinFreq: - 0 - 0 - 0 @@ -807,12 +760,12 @@ expression: records - 0 - 0 - 0 - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 35782 - dp_hist_alt_n_larger: 11 - dp_hist_all_bin_freq: + ageHistHetNSmaller: 0 + ageHistHetNLarger: 0 + depthInfo: + dpHistAllNLarger: 35782 + dpHistAltNLarger: 11 + dpHistAllBinFreq: - 0 - 1 - 217 @@ -823,7 +776,7 @@ expression: records - 3324 - 3791 - 4184 - dp_hist_alt_bin_freq: + dpHistAltBinFreq: - 0 - 0 - 0 @@ -836,73 +789,26 @@ expression: records - 0 - chrom: MT pos: 6 - ref_allele: C - alt_allele: CCTCAA - variant_collapsed: C6CCTCAA - excluded_ac: 1 + refAllele: C + altAllele: CCTCAA + variantCollapsed: C6CCTCAA + excludedAc: 1 an: 56433 - ac_hom: 0 - ac_het: 0 - af_hom: 0 - af_het: 0 filters: - - 2 - mitotip_score: ~ - mitotip_trna_prediction: ~ - pon_mt_trna_prediction: ~ - pon_ml_probability_of_pathogenicity: ~ + - NO_PASS_GENOTYPE vep: - allele: CTCAA consequence: intergenic_variant impact: MODIFIER - symbol: "" - gene: "" - feature_type: Intergenic - feature: "" - feature_biotype: "" - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: ~ - variant_class: insertion - minimised: ~ - symbol_source: ~ - hgnc_id: ~ - canonical: ~ - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - quality_info: - dp_mean: 2527.78 - mq_mean: 60 - tlod_mean: 0.537 - heteroplasmy_info: - heteroplasmy_below_min_het_threshold_hist: + featureType: Intergenic + dbsnpId: "1" + variantClass: insertion + qualityInfo: + dpMean: 2527.78 + mqMean: 60 + tlodMean: 0.537 + heteroplasmyInfo: + heteroplasmyBelowMinHetThresholdHist: - 1 - 0 - 0 @@ -913,7 +819,7 @@ expression: records - 0 - 0 - 0 - hl_hist: + hlHist: - 0 - 0 - 0 @@ -924,10 +830,8 @@ expression: records - 0 - 0 - 0 - common_low_heteroplasmy: false - max_hl: 0 - filter_histograms: - base_qual_hist: + filterHistograms: + baseQualHist: - 0 - 0 - 0 @@ -938,7 +842,7 @@ expression: records - 0 - 0 - 0 - position_hist: + positionHist: - 0 - 0 - 0 @@ -949,7 +853,7 @@ expression: records - 0 - 0 - 0 - strand_bias_hist: + strandBiasHist: - 0 - 0 - 0 @@ -960,7 +864,7 @@ expression: records - 0 - 0 - 0 - weak_evidence_hist: + weakEvidenceHist: - 0 - 0 - 0 @@ -971,7 +875,7 @@ expression: records - 0 - 0 - 0 - contamination_hist: + contaminationHist: - 0 - 0 - 0 @@ -982,8 +886,8 @@ expression: records - 0 - 0 - 0 - population_info: - pop_an: + populationInfo: + popAn: - 14347 - 392 - 5717 @@ -994,7 +898,7 @@ expression: records - 826 - 1493 - 20 - pop_ac_het: + popAcHet: - 0 - 0 - 0 @@ -1005,7 +909,7 @@ expression: records - 0 - 0 - 0 - pop_ac_hom: + popAcHom: - 0 - 0 - 0 @@ -1016,7 +920,7 @@ expression: records - 0 - 0 - 0 - pop_af_hom: + popAfHom: - 0 - 0 - 0 @@ -1027,7 +931,7 @@ expression: records - 0 - 0 - 0 - pop_af_het: + popAfHet: - 0 - 0 - 0 @@ -1038,7 +942,7 @@ expression: records - 0 - 0 - 0 - pop_hl_hist: + popHlHist: - 0 - 0 - 0 @@ -1139,9 +1043,8 @@ expression: records - 0 - 0 - 0 - haplogroup_info: - hap_defining_variant: false - hap_an: + haplogroupInfo: + hapAn: - 2679 - 1537 - 868 @@ -1171,7 +1074,7 @@ expression: records - 546 - 12 - 89 - hap_ac_het: + hapAcHet: - 0 - 0 - 0 @@ -1201,7 +1104,7 @@ expression: records - 0 - 0 - 0 - hap_ac_hom: + hapAcHom: - 0 - 0 - 0 @@ -1231,7 +1134,7 @@ expression: records - 0 - 0 - 0 - hap_af_het: + hapAfHet: - 0 - 0 - 0 @@ -1261,7 +1164,7 @@ expression: records - 0 - 0 - 0 - hap_af_hom: + hapAfHom: - 0 - 0 - 0 @@ -1291,7 +1194,7 @@ expression: records - 0 - 0 - 0 - hap_hl_hist: + hapHlHist: - 0 - 0 - 0 @@ -1582,7 +1485,7 @@ expression: records - 0 - 0 - 0 - hap_faf_hom: + hapFafHom: - 0 - 0 - 0 @@ -1612,11 +1515,9 @@ expression: records - 0 - 0 - 0 - hapmax_af_hom: ~ - hapmax_af_het: ~ - faf_hapmax_hom: 0 - age_info: - age_hist_hom_bin_freq: + fafHapmaxHom: 0 + ageInfo: + ageHistHomBinFreq: - 0 - 0 - 0 @@ -1627,9 +1528,9 @@ expression: records - 0 - 0 - 0 - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: + ageHistHomNSmaller: 0 + ageHistHomNLarger: 0 + ageHistHetBinFreq: - 0 - 0 - 0 @@ -1640,12 +1541,12 @@ expression: records - 0 - 0 - 0 - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 35855 - dp_hist_alt_n_larger: 0 - dp_hist_all_bin_freq: + ageHistHetNSmaller: 0 + ageHistHetNLarger: 0 + depthInfo: + dpHistAllNLarger: 35855 + dpHistAltNLarger: 0 + dpHistAllBinFreq: - 0 - 0 - 216 @@ -1656,7 +1557,7 @@ expression: records - 3302 - 3802 - 4180 - dp_hist_alt_bin_freq: + dpHistAltBinFreq: - 0 - 0 - 0 @@ -1669,73 +1570,24 @@ expression: records - 0 - chrom: MT pos: 7 - ref_allele: A - alt_allele: G - variant_collapsed: A7G - excluded_ac: 1 + refAllele: A + altAllele: G + variantCollapsed: A7G + excludedAc: 1 an: 56433 - ac_hom: 0 - ac_het: 0 - af_hom: 0 - af_het: 0 filters: - - 2 - mitotip_score: ~ - mitotip_trna_prediction: ~ - pon_mt_trna_prediction: ~ - pon_ml_probability_of_pathogenicity: ~ + - NO_PASS_GENOTYPE vep: - allele: G consequence: intergenic_variant impact: MODIFIER - symbol: "" - gene: "" - feature_type: Intergenic - feature: "" - feature_biotype: "" - exon: ~ - intron: ~ - hgvsc: ~ - hgvsp: ~ - cdna_position: ~ - cds_position: ~ - protein_position: ~ - amino_acids: ~ - codons: ~ - dbsnp_id: "1" - distance: ~ - strand: ~ - variant_class: SNV - minimised: ~ - symbol_source: ~ - hgnc_id: ~ - canonical: ~ - tsl: ~ - appris: ~ - ccds: ~ - ensp: ~ - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: ~ - sift: ~ - polyphen: ~ - domains: [] - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - quality_info: - dp_mean: 2555.14 - mq_mean: ~ - tlod_mean: ~ - heteroplasmy_info: - heteroplasmy_below_min_het_threshold_hist: + featureType: Intergenic + dbsnpId: "1" + variantClass: SNV + qualityInfo: + dpMean: 2555.14 + heteroplasmyInfo: + heteroplasmyBelowMinHetThresholdHist: - 1 - 0 - 0 @@ -1746,7 +1598,7 @@ expression: records - 0 - 0 - 0 - hl_hist: + hlHist: - 0 - 0 - 0 @@ -1757,10 +1609,8 @@ expression: records - 0 - 0 - 0 - common_low_heteroplasmy: false - max_hl: 0 - filter_histograms: - base_qual_hist: + filterHistograms: + baseQualHist: - 0 - 0 - 0 @@ -1771,7 +1621,7 @@ expression: records - 0 - 0 - 0 - position_hist: + positionHist: - 0 - 0 - 0 @@ -1782,7 +1632,7 @@ expression: records - 0 - 0 - 0 - strand_bias_hist: + strandBiasHist: - 0 - 0 - 0 @@ -1793,7 +1643,7 @@ expression: records - 0 - 0 - 0 - weak_evidence_hist: + weakEvidenceHist: - 0 - 0 - 0 @@ -1804,7 +1654,7 @@ expression: records - 0 - 0 - 0 - contamination_hist: + contaminationHist: - 0 - 0 - 0 @@ -1815,8 +1665,8 @@ expression: records - 0 - 0 - 0 - population_info: - pop_an: + populationInfo: + popAn: - 14347 - 392 - 5717 @@ -1827,7 +1677,7 @@ expression: records - 826 - 1493 - 20 - pop_ac_het: + popAcHet: - 0 - 0 - 0 @@ -1838,7 +1688,7 @@ expression: records - 0 - 0 - 0 - pop_ac_hom: + popAcHom: - 0 - 0 - 0 @@ -1849,7 +1699,7 @@ expression: records - 0 - 0 - 0 - pop_af_hom: + popAfHom: - 0 - 0 - 0 @@ -1860,7 +1710,7 @@ expression: records - 0 - 0 - 0 - pop_af_het: + popAfHet: - 0 - 0 - 0 @@ -1871,7 +1721,7 @@ expression: records - 0 - 0 - 0 - pop_hl_hist: + popHlHist: - 0 - 0 - 0 @@ -1972,9 +1822,8 @@ expression: records - 0 - 0 - 0 - haplogroup_info: - hap_defining_variant: false - hap_an: + haplogroupInfo: + hapAn: - 2679 - 1537 - 868 @@ -2004,7 +1853,7 @@ expression: records - 546 - 12 - 89 - hap_ac_het: + hapAcHet: - 0 - 0 - 0 @@ -2034,7 +1883,7 @@ expression: records - 0 - 0 - 0 - hap_ac_hom: + hapAcHom: - 0 - 0 - 0 @@ -2064,7 +1913,7 @@ expression: records - 0 - 0 - 0 - hap_af_het: + hapAfHet: - 0 - 0 - 0 @@ -2094,7 +1943,7 @@ expression: records - 0 - 0 - 0 - hap_af_hom: + hapAfHom: - 0 - 0 - 0 @@ -2124,7 +1973,7 @@ expression: records - 0 - 0 - 0 - hap_hl_hist: + hapHlHist: - 0 - 0 - 0 @@ -2415,7 +2264,7 @@ expression: records - 0 - 0 - 0 - hap_faf_hom: + hapFafHom: - 0 - 0 - 0 @@ -2445,11 +2294,9 @@ expression: records - 0 - 0 - 0 - hapmax_af_hom: ~ - hapmax_af_het: ~ - faf_hapmax_hom: 0 - age_info: - age_hist_hom_bin_freq: + fafHapmaxHom: 0 + ageInfo: + ageHistHomBinFreq: - 0 - 0 - 0 @@ -2460,9 +2307,9 @@ expression: records - 0 - 0 - 0 - age_hist_hom_n_smaller: 0 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: + ageHistHomNSmaller: 0 + ageHistHomNLarger: 0 + ageHistHetBinFreq: - 0 - 0 - 0 @@ -2473,12 +2320,12 @@ expression: records - 0 - 0 - 0 - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 36388 - dp_hist_alt_n_larger: 0 - dp_hist_all_bin_freq: + ageHistHetNSmaller: 0 + ageHistHetNLarger: 0 + depthInfo: + dpHistAllNLarger: 36388 + dpHistAltNLarger: 0 + dpHistAllBinFreq: - 0 - 0 - 194 @@ -2489,7 +2336,7 @@ expression: records - 3254 - 3706 - 4067 - dp_hist_alt_bin_freq: + dpHistAltBinFreq: - 0 - 0 - 0 @@ -2502,54 +2349,40 @@ expression: records - 0 - chrom: MT pos: 12544 - ref_allele: A - alt_allele: G - variant_collapsed: A12544G - excluded_ac: 0 + refAllele: A + altAllele: G + variantCollapsed: A12544G an: 56434 - ac_hom: 19 - ac_het: 1 - af_hom: 0.000336676 - af_het: 0.0000177198 - filters: [] - mitotip_score: ~ - mitotip_trna_prediction: ~ - pon_mt_trna_prediction: ~ - pon_ml_probability_of_pathogenicity: ~ + acHom: 19 + acHet: 1 + afHom: 0.000336676 + afHet: 0.0000177198 vep: - allele: G consequence: missense_variant impact: MODERATE symbol: MT-ND5 gene: ENSG00000198786 - feature_type: Transcript + featureType: Transcript feature: ENST00000361567 - feature_biotype: protein_coding + featureBiotype: protein_coding exon: 1/1 - intron: ~ hgvsc: "ENST00000361567.2:c.208A>G" hgvsp: "ENSP00000354813.2:p.Thr70Ala" - cdna_position: "208" - cds_position: "208" - protein_position: "70" - amino_acids: T/A + cdnaPosition: "208" + cdsPosition: "208" + proteinPosition: "70" + aminoAcids: T/A codons: Aca/Gca - dbsnp_id: "1" - distance: ~ + dbsnpId: "1" strand: "1" - variant_class: SNV - minimised: ~ - symbol_source: HGNC - hgnc_id: "HGNC:7461" + variantClass: SNV + symbolSource: HGNC + hgncId: "HGNC:7461" canonical: true - tsl: ~ appris: P1 - ccds: ~ ensp: ENSP00000354813 - swissprot: ~ - trembl: ~ - uniparc: ~ - gene_pheno: "1" + genePheno: "1" sift: prediction: deleterious_low_confidence score: 0.02 @@ -2575,21 +2408,12 @@ expression: records source: PANTHER - id: TIGR01974 source: TIGRFAM - hgvs_offset: ~ - motif_name: ~ - motif_pos: ~ - high_inf_pos: ~ - motif_score_change: ~ - lof: ~ - lof_filter: ~ - lof_flags: ~ - lof_info: ~ - quality_info: - dp_mean: 3028.58 - mq_mean: 60 - tlod_mean: 10410.8 - heteroplasmy_info: - heteroplasmy_below_min_het_threshold_hist: + qualityInfo: + dpMean: 3028.58 + mqMean: 60 + tlodMean: 10410.8 + heteroplasmyInfo: + heteroplasmyBelowMinHetThresholdHist: - 0 - 0 - 0 @@ -2600,7 +2424,7 @@ expression: records - 0 - 0 - 0 - hl_hist: + hlHist: - 0 - 0 - 1 @@ -2611,10 +2435,9 @@ expression: records - 0 - 0 - 19 - common_low_heteroplasmy: false - max_hl: 1 - filter_histograms: - base_qual_hist: + maxHl: 1 + filterHistograms: + baseQualHist: - 0 - 0 - 0 @@ -2625,7 +2448,7 @@ expression: records - 0 - 0 - 0 - position_hist: + positionHist: - 0 - 0 - 0 @@ -2636,7 +2459,7 @@ expression: records - 0 - 0 - 0 - strand_bias_hist: + strandBiasHist: - 0 - 0 - 0 @@ -2647,7 +2470,7 @@ expression: records - 0 - 0 - 0 - weak_evidence_hist: + weakEvidenceHist: - 0 - 0 - 0 @@ -2658,7 +2481,7 @@ expression: records - 0 - 0 - 0 - contamination_hist: + contaminationHist: - 0 - 0 - 0 @@ -2669,8 +2492,8 @@ expression: records - 0 - 0 - 0 - population_info: - pop_an: + populationInfo: + popAn: - 14347 - 392 - 5718 @@ -2681,7 +2504,7 @@ expression: records - 826 - 1493 - 20 - pop_ac_het: + popAcHet: - 0 - 0 - 0 @@ -2692,7 +2515,7 @@ expression: records - 0 - 0 - 0 - pop_ac_hom: + popAcHom: - 5 - 0 - 1 @@ -2703,7 +2526,7 @@ expression: records - 0 - 0 - 0 - pop_af_hom: + popAfHom: - 0.000348505 - 0 - 0.000174886 @@ -2714,7 +2537,7 @@ expression: records - 0 - 0 - 0 - pop_af_het: + popAfHet: - 0 - 0 - 0 @@ -2725,7 +2548,7 @@ expression: records - 0 - 0 - 0 - pop_hl_hist: + popHlHist: - 0 - 0 - 0 @@ -2826,9 +2649,8 @@ expression: records - 0 - 0 - 0 - haplogroup_info: - hap_defining_variant: false - hap_an: + haplogroupInfo: + hapAn: - 2680 - 1537 - 868 @@ -2858,7 +2680,7 @@ expression: records - 546 - 12 - 89 - hap_ac_het: + hapAcHet: - 0 - 0 - 0 @@ -2888,7 +2710,7 @@ expression: records - 0 - 0 - 0 - hap_ac_hom: + hapAcHom: - 1 - 0 - 0 @@ -2918,7 +2740,7 @@ expression: records - 0 - 0 - 0 - hap_af_het: + hapAfHet: - 0 - 0 - 0 @@ -2948,7 +2770,7 @@ expression: records - 0 - 0 - 0 - hap_af_hom: + hapAfHom: - 0.000373134 - 0 - 0 @@ -2978,7 +2800,7 @@ expression: records - 0 - 0 - 0 - hap_hl_hist: + hapHlHist: - 0 - 0 - 0 @@ -3269,7 +3091,7 @@ expression: records - 0 - 0 - 0 - hap_faf_hom: + hapFafHom: - 0 - 0 - 0 @@ -3299,11 +3121,11 @@ expression: records - 0 - 0 - 0 - hapmax_af_hom: U - hapmax_af_het: U - faf_hapmax_hom: 0.00065881 - age_info: - age_hist_hom_bin_freq: + hapmaxAfHom: U + hapmaxAfHet: U + fafHapmaxHom: 0.00065881 + ageInfo: + ageHistHomBinFreq: - 0 - 0 - 0 @@ -3314,9 +3136,9 @@ expression: records - 3 - 0 - 0 - age_hist_hom_n_smaller: 1 - age_hist_hom_n_larger: 0 - age_hist_het_bin_freq: + ageHistHomNSmaller: 1 + ageHistHomNLarger: 0 + ageHistHetBinFreq: - 0 - 0 - 1 @@ -3327,12 +3149,12 @@ expression: records - 0 - 0 - 0 - age_hist_het_n_smaller: 0 - age_hist_het_n_larger: 0 - depth_info: - dp_hist_all_n_larger: 42619 - dp_hist_alt_n_larger: 19 - dp_hist_all_bin_freq: + ageHistHetNSmaller: 0 + ageHistHetNLarger: 0 + depthInfo: + dpHistAllNLarger: 42619 + dpHistAltNLarger: 19 + dpHistAllBinFreq: - 0 - 0 - 42 @@ -3343,7 +3165,7 @@ expression: records - 2274 - 2557 - 2968 - dp_hist_alt_bin_freq: + dpHistAltBinFreq: - 0 - 0 - 0 diff --git a/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__vep_gnomad2__test__vep_from_string_indel.snap b/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__vep_gnomad2__test__vep_from_string_indel.snap new file mode 100644 index 00000000..2444ed6b --- /dev/null +++ b/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__vep_gnomad2__test__vep_from_string_indel.snap @@ -0,0 +1,40 @@ +--- +source: src/pbs/gnomad/vep_gnomad2.rs +expression: vep +--- +allele: A +consequence: frameshift_variant +impact: HIGH +symbol: PCSK9 +gene: ENSG00000169174 +featureType: Transcript +feature: ENST00000452118 +featureBiotype: protein_coding +exon: 4/6 +hgvsc: "ENST00000452118.2:c.547_548insA" +hgvsp: "ENSP00000401598.2:p.Gly183GlufsTer23" +cdnaPosition: 627-628 +cdsPosition: 547-548 +proteinPosition: "183" +aminoAcids: G/EX +codons: ggc/gAgc +existingVariation: rs527413419 +dbsnpId: "1" +strand: "1" +variantClass: insertion +minimised: "1" +symbolSource: HGNC +hgncId: "20001" +ensp: ENSP00000401598 +trembl: B4DEZ9 +uniparc: UPI00017A6F55 +genePheno: "1" +gmaf: 0.0032 +amrMaf: 0.0113 +easMaf: 0.0014 +eurMaf: 0 +sasMaf: 0 +aaMaf: 0 +lof: HC +lofInfo: "GERP_DIST:364.1444&BP_DIST:304&PERCENTILE:0.885113268608414&DIST_FROM_LAST_EXON:210&50_BP_RULE:PASS&PHYLOCSF_TOO_SHORT" + diff --git a/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__vep_gnomad2__test__vep_from_string_snv.snap b/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__vep_gnomad2__test__vep_from_string_snv.snap new file mode 100644 index 00000000..2edb02ce --- /dev/null +++ b/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__vep_gnomad2__test__vep_from_string_snv.snap @@ -0,0 +1,47 @@ +--- +source: src/pbs/gnomad/vep_gnomad2.rs +expression: vep +--- +allele: G +consequence: missense_variant +impact: MODERATE +symbol: PCSK9 +gene: ENSG00000169174 +featureType: Transcript +feature: ENST00000302118 +featureBiotype: protein_coding +exon: 1/12 +hgvsc: "ENST00000302118.5:c.89C>G" +hgvsp: "ENSP00000303208.5:p.Ala30Gly" +cdnaPosition: "379" +cdsPosition: "89" +proteinPosition: "30" +aminoAcids: A/G +codons: gCg/gGg +dbsnpId: "1" +strand: "1" +variantClass: SNV +minimised: "1" +symbolSource: HGNC +hgncId: "20001" +canonical: true +ccds: CCDS603.1 +ensp: ENSP00000303208 +swissprot: Q8NBP7 +uniparc: UPI00001615E1 +genePheno: "1" +sift: + prediction: deleterious_low_confidence + score: 0.03 +polyphen: + prediction: possibly_damaging + score: 0.583 +domains: + - id: SignalP-noTM + source: Cleavage_site_(Signalp) + - id: PTHR10795 + source: hmmpanther + - id: PTHR10795 + source: hmmpanther +lofInfo: "DE_NOVO_DONOR_PROB:0.146539915246404&MUTANT_DONOR_MES:8.16693067332728&DE_NOVO_DONOR_POS:-119&INTRON_END:55509515&DE_NOVO_DONOR_MES_POS:-122&INTRON_START:55505718&EXON_END:55505717&EXON_START:55505221&DE_NOVO_DONOR_MES:-1.61109392005567" + diff --git a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__vep_gnomad3__test__vep_from_string.snap b/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__vep_gnomad3__test__vep_from_string.snap similarity index 61% rename from src/gnomad_pbs/snapshots/annonars__gnomad_pbs__vep_gnomad3__test__vep_from_string.snap rename to src/pbs/gnomad/snapshots/annonars__pbs__gnomad__vep_gnomad3__test__vep_from_string.snap index c12e1fc8..b5487008 100644 --- a/src/gnomad_pbs/snapshots/annonars__gnomad_pbs__vep_gnomad3__test__vep_from_string.snap +++ b/src/pbs/gnomad/snapshots/annonars__pbs__gnomad__vep_gnomad3__test__vep_from_string.snap @@ -1,5 +1,5 @@ --- -source: src/gnomad_pbs/vep_gnomad3.rs +source: src/pbs/gnomad/vep_gnomad3.rs expression: vep --- allele: G @@ -7,34 +7,26 @@ consequence: missense_variant impact: MODERATE symbol: MT-ND5 gene: ENSG00000198786 -feature_type: Transcript +featureType: Transcript feature: ENST00000361567 -feature_biotype: protein_coding +featureBiotype: protein_coding exon: 1/1 -intron: ~ hgvsc: "ENST00000361567.2:c.208A>G" hgvsp: "ENSP00000354813.2:p.Thr70Ala" -cdna_position: "208" -cds_position: "208" -protein_position: "70" -amino_acids: T/A +cdnaPosition: "208" +cdsPosition: "208" +proteinPosition: "70" +aminoAcids: T/A codons: Aca/Gca -dbsnp_id: "1" -distance: ~ +dbsnpId: "1" strand: "1" -variant_class: SNV -minimised: ~ -symbol_source: HGNC -hgnc_id: "HGNC:7461" +variantClass: SNV +symbolSource: HGNC +hgncId: "HGNC:7461" canonical: true -tsl: ~ appris: P1 -ccds: ~ ensp: ENSP00000354813 -swissprot: ~ -trembl: ~ -uniparc: ~ -gene_pheno: "1" +genePheno: "1" sift: prediction: deleterious_low_confidence score: 0.02 @@ -60,13 +52,4 @@ domains: source: PANTHER - id: TIGR01974 source: TIGRFAM -hgvs_offset: ~ -motif_name: ~ -motif_pos: ~ -high_inf_pos: ~ -motif_score_change: ~ -lof: ~ -lof_filter: ~ -lof_flags: ~ -lof_info: ~ diff --git a/src/gnomad_pbs/vep_common.rs b/src/pbs/gnomad/vep_common.rs similarity index 53% rename from src/gnomad_pbs/vep_common.rs rename to src/pbs/gnomad/vep_common.rs index fc59013f..05b6992f 100644 --- a/src/gnomad_pbs/vep_common.rs +++ b/src/pbs/gnomad/vep_common.rs @@ -1,8 +1,9 @@ -//! Protocolbuffers for common gnomAD VEP data structures. +//! Code generate for protobufs by `prost-build`. +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.vep_common.rs")); include!(concat!( env!("OUT_DIR"), - "/annonars.gnomad.v1.vep_common.rs" + "/annonars.gnomad.vep_common.serde.rs" )); impl From<(String, f32)> for Prediction { diff --git a/src/gnomad_pbs/vep_gnomad2.rs b/src/pbs/gnomad/vep_gnomad2.rs similarity index 98% rename from src/gnomad_pbs/vep_gnomad2.rs rename to src/pbs/gnomad/vep_gnomad2.rs index 5aa597b2..356b9ac8 100644 --- a/src/gnomad_pbs/vep_gnomad2.rs +++ b/src/pbs/gnomad/vep_gnomad2.rs @@ -1,10 +1,11 @@ -//! Protocolbuffers gnomAD v3 VEP data structures. +//! Code generate for protobufs by `prost-build`. use std::str::FromStr; +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.vep_gnomad2.rs")); include!(concat!( env!("OUT_DIR"), - "/annonars.gnomad.v1.vep_gnomad2.rs" + "/annonars.gnomad.vep_gnomad2.serde.rs" )); impl Vep { diff --git a/src/gnomad_pbs/vep_gnomad3.rs b/src/pbs/gnomad/vep_gnomad3.rs similarity index 97% rename from src/gnomad_pbs/vep_gnomad3.rs rename to src/pbs/gnomad/vep_gnomad3.rs index ad164a56..cc5bb2fc 100644 --- a/src/gnomad_pbs/vep_gnomad3.rs +++ b/src/pbs/gnomad/vep_gnomad3.rs @@ -1,10 +1,11 @@ -//! Protocolbuffers gnomAD v3 VEP data structures. +//! Code generate for protobufs by `prost-build`. use std::str::FromStr; +include!(concat!(env!("OUT_DIR"), "/annonars.gnomad.vep_gnomad3.rs")); include!(concat!( env!("OUT_DIR"), - "/annonars.gnomad.v1.vep_gnomad3.rs" + "/annonars.gnomad.vep_gnomad3.serde.rs" )); impl Vep { diff --git a/src/pbs/helixmtdb.rs b/src/pbs/helixmtdb.rs new file mode 100644 index 00000000..c654fe0a --- /dev/null +++ b/src/pbs/helixmtdb.rs @@ -0,0 +1,7 @@ +//! Code generate for protobufs by `prost-build`. + +include!(concat!(env!("OUT_DIR"), "/annonars.helixmtdb.base.rs")); +include!(concat!( + env!("OUT_DIR"), + "/annonars.helixmtdb.base.serde.rs" +)); diff --git a/src/pbs/mod.rs b/src/pbs/mod.rs index 8ca7d998..f52ec7ab 100644 --- a/src/pbs/mod.rs +++ b/src/pbs/mod.rs @@ -1,3 +1,9 @@ //! Code generate for protobufs by `prost-build`. -pub mod annonars; +pub mod clinvar; +pub mod cons; +pub mod dbsnp; +pub mod functional; +pub mod genes; +pub mod gnomad; +pub mod helixmtdb; diff --git a/src/server/actix_server/annos_range.rs b/src/server/actix_server/annos_range.rs index 38e1562e..e59b4276 100644 --- a/src/server/actix_server/annos_range.rs +++ b/src/server/actix_server/annos_range.rs @@ -97,7 +97,7 @@ async fn handle( data.annos[genome_release][anno_db] .as_ref() .map(|db| { - fetch_pos_protobuf::( + fetch_pos_protobuf::( db, anno_db.cf_name(), query.start_pos(), @@ -153,7 +153,7 @@ async fn handle( data.annos[genome_release][anno_db] .as_ref() .map(|db| { - fetch_pos_protobuf::( + fetch_pos_protobuf::( db, anno_db.cf_name(), query.start_pos(), @@ -167,7 +167,7 @@ async fn handle( data.annos[genome_release][anno_db] .as_ref() .map(|db| { - fetch_pos_protobuf::( + fetch_pos_protobuf::( db, anno_db.cf_name(), query.start_pos(), @@ -188,14 +188,14 @@ async fn handle( .as_ref() .expect("gnomAD must have db version"); if db_version.starts_with("2.") { - fetch_pos_protobuf::( + fetch_pos_protobuf::( db, anno_db.cf_name(), query.start_pos(), query.stop_pos(), ) } else if db_version.starts_with("3.") { - fetch_pos_protobuf::( + fetch_pos_protobuf::( db, anno_db.cf_name(), query.start_pos(), @@ -215,7 +215,7 @@ async fn handle( data.annos[genome_release][anno_db] .as_ref() .map(|db| { - fetch_pos_protobuf::( + fetch_pos_protobuf::( db, anno_db.cf_name(), query.start_pos(), diff --git a/src/server/actix_server/annos_variant.rs b/src/server/actix_server/annos_variant.rs index 1952d397..7a5f6299 100644 --- a/src/server/actix_server/annos_variant.rs +++ b/src/server/actix_server/annos_variant.rs @@ -93,7 +93,7 @@ async fn handle( data.annos[genome_release][anno_db] .as_ref() .map(|db| { - fetch_var_protobuf::( + fetch_var_protobuf::( db, anno_db.cf_name(), query.clone().into_inner().into(), @@ -141,7 +141,7 @@ async fn handle( data.annos[genome_release][anno_db] .as_ref() .map(|db| { - fetch_var_protobuf::( + fetch_var_protobuf::( db, anno_db.cf_name(), query.clone().into_inner().into(), @@ -154,7 +154,7 @@ async fn handle( data.annos[genome_release][anno_db] .as_ref() .map(|db| { - fetch_var_protobuf::( + fetch_var_protobuf::( db, anno_db.cf_name(), query.clone().into_inner().into(), @@ -174,13 +174,13 @@ async fn handle( .as_ref() .expect("gnomAD must have db version"); if db_version.starts_with("2.") { - fetch_var_protobuf::( + fetch_var_protobuf::( db, anno_db.cf_name(), query.clone().into_inner().into(), ) } else if db_version.starts_with("3.") { - fetch_var_protobuf::( + fetch_var_protobuf::( db, anno_db.cf_name(), query.clone().into_inner().into(), @@ -205,7 +205,7 @@ async fn handle( pos: start.pos - 2, }; let stop = query.clone().into_inner().into(); - fetch_pos_protobuf::( + fetch_pos_protobuf::( db, anno_db.cf_name(), start, diff --git a/src/server/actix_server/genes_clinvar.rs b/src/server/actix_server/genes_clinvar.rs index 201f9bbe..a6de034f 100644 --- a/src/server/actix_server/genes_clinvar.rs +++ b/src/server/actix_server/genes_clinvar.rs @@ -7,7 +7,7 @@ use actix_web::{ }; use prost::Message; -use crate::pbs::annonars::clinvar::v1::per_gene::ClinvarPerGeneRecord; +use crate::pbs::clinvar::per_gene::ClinvarPerGeneRecord; use super::error::CustomError; use serde_with::{formats::CommaSeparator, StringWithSeparator}; @@ -59,7 +59,7 @@ async fn handle( .get_cf(&cf_genes, hgnc_id) .map_err(|e| CustomError::new(anyhow::anyhow!("problem querying database: {}", e)))? .ok_or_else(|| CustomError::new(anyhow::anyhow!("no such gene: {}", hgnc_id)))?; - let record = crate::pbs::annonars::clinvar::v1::per_gene::ClinvarPerGeneRecord::decode( + let record = crate::pbs::clinvar::per_gene::ClinvarPerGeneRecord::decode( std::io::Cursor::new(raw_buf), ) .map_err(|e| CustomError::new(anyhow::anyhow!("problem decoding value: {}", e)))?; diff --git a/src/server/actix_server/genes_info.rs b/src/server/actix_server/genes_info.rs index b8997977..bd57c9ea 100644 --- a/src/server/actix_server/genes_info.rs +++ b/src/server/actix_server/genes_info.rs @@ -7,7 +7,7 @@ use actix_web::{ }; use prost::Message; -use crate::genes::pbs; +use crate::pbs::genes; use super::error::CustomError; use serde_with::{formats::CommaSeparator, StringWithSeparator}; @@ -29,7 +29,7 @@ struct Request { struct Container { // TODO: add data version /// The resulting gene information. - pub genes: indexmap::IndexMap, + pub genes: indexmap::IndexMap, } /// Query for annotations for one variant. @@ -55,7 +55,7 @@ async fn handle( .get_cf(&cf_genes, hgnc_id) .map_err(|e| CustomError::new(anyhow::anyhow!("problem querying database: {}", e)))? .ok_or_else(|| CustomError::new(anyhow::anyhow!("no such gene: {}", hgnc_id)))?; - let record = pbs::Record::decode(std::io::Cursor::new(raw_buf)) + let record = genes::Record::decode(std::io::Cursor::new(raw_buf)) .map_err(|e| CustomError::new(anyhow::anyhow!("problem decoding value: {}", e)))?; genes.insert(hgnc_id.to_string(), record); } diff --git a/src/server/mod.rs b/src/server/mod.rs index ea418dca..7a8d2746 100644 --- a/src/server/mod.rs +++ b/src/server/mod.rs @@ -11,7 +11,7 @@ use rayon::prelude::*; use crate::{ common::{self, cli::GenomeRelease}, - genes::pbs, + pbs::genes, }; /// Encode annotation database. @@ -271,10 +271,10 @@ fn extract_gene_names( iter.seek(b""); while iter.valid() { if let Some(iter_value) = iter.value() { - let record = pbs::Record::decode(std::io::Cursor::new(iter_value))?; - let pbs::Record { hgnc, .. } = record; + let record = genes::Record::decode(std::io::Cursor::new(iter_value))?; + let genes::Record { hgnc, .. } = record; if let Some(hgnc) = hgnc { - let pbs::HgncRecord { + let genes::HgncRecord { hgnc_id, symbol, name, diff --git a/utils/docker/Dockerfile b/utils/docker/Dockerfile index 9aadca76..e5d7e1c8 100644 --- a/utils/docker/Dockerfile +++ b/utils/docker/Dockerfile @@ -14,7 +14,7 @@ # Pinning Rust version for now because of this issue: # # - https://github.com/rust-lang/rust/issues/95926 -FROM rust:1-buster AS builder +FROM rust:1-bookworm AS builder # Build dependencies first. # @@ -44,6 +44,7 @@ RUN cargo build --release # Now copy in the rest of the sources. COPY build.rs /usr/src/annonars/ COPY src /usr/src/annonars/src/ +COPY protos /usr/src/annonars/protos/ COPY utils/alpine-linker-script.sh /usr/src/annonars/utils/ RUN chmod a+rx /usr/src/annonars/utils/alpine-linker-script.sh COPY .cargo /usr/src/annonars/.cargo/ @@ -56,7 +57,7 @@ RUN cargo build --release # Runtime # --------------------------------------------------------------------------- -FROM debian:buster-slim AS runtime +FROM debian:bookworm-slim AS runtime # Copy application binary from builder image COPY --from=builder \