diff --git a/Cargo.lock b/Cargo.lock index 3f356491..ea817da3 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -5207,6 +5207,9 @@ dependencies = [ "noodles-csi", "noodles-tabix", "noodles-vcf", + "pbjson", + "pbjson-build", + "pbjson-types", "pretty_assertions", "procfs", "prost", diff --git a/Cargo.toml b/Cargo.toml index 7f09daff..49b75884 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -46,6 +46,8 @@ noodles-core = "0.14.0" noodles-csi = { version = "0.30.0", features = ["async"] } noodles-tabix = { version = "0.36.0", features = ["async"] } noodles-vcf = { version = "0.49", features = ["async"] } +pbjson = "0.6" +pbjson-types = "0.6" procfs = "0.16" prost = "0.12" rand = "0.8" @@ -69,7 +71,9 @@ tracing-subscriber = "0.3" uuid = { version = "1.4", features = ["v4", "fast-rng", "serde"] } [build-dependencies] +anyhow = "1.0" prost-build = "0.12" +pbjson-build = "0.6.2" [dev-dependencies] async-std = { version = "1.12", features = ["attributes"] } diff --git a/build.rs b/build.rs index 2b3415e4..cb078b03 100644 --- a/build.rs +++ b/build.rs @@ -1,21 +1,40 @@ -// The custom build script, needed as we use protocolbuffers. +// The custom 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 = [ + "varfish/v1/clinvar.proto", + "varfish/v1/sv.proto", + "varfish/v1/worker.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 = + PathBuf::from(env::var("OUT_DIR").unwrap()).join("proto_descriptor.bin"); -fn main() { - println!("cargo:rerun-if-changed=src/proto/varfish/v1/clinvar.proto"); - println!("cargo:rerun-if-changed=src/proto/varfish/v1/sv.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]") + // 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( - &[ - "src/proto/varfish/v1/clinvar.proto", - "src/proto/varfish/v1/sv.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(&[".varfish"])?; + + Ok(()) } diff --git a/src/proto/varfish/v1/clinvar.proto b/protos/varfish/v1/clinvar.proto similarity index 100% rename from src/proto/varfish/v1/clinvar.proto rename to protos/varfish/v1/clinvar.proto diff --git a/src/proto/varfish/v1/sv.proto b/protos/varfish/v1/sv.proto similarity index 100% rename from src/proto/varfish/v1/sv.proto rename to protos/varfish/v1/sv.proto diff --git a/protos/varfish/v1/worker.proto b/protos/varfish/v1/worker.proto new file mode 100644 index 00000000..b822ee68 --- /dev/null +++ b/protos/varfish/v1/worker.proto @@ -0,0 +1,27 @@ +// Protocol buffers related to the worker. + +syntax = "proto3"; + +package varfish.v1.worker; + +// Protocol buffer for storing a list of file identifier mappings. +message FileIdentifierMappings { + // Protocol buffer for storing file identifier mapping for one file. + message Mapping { + // Protocol buffer to store one mapping entry. + message Entry { + // Identifier as given in input file. + string src = 1; + // Identifier to use in output file. + string dst = 2; + } + + // Path to the file to obtain mapping for, as given on the command line. + string path = 1; + // List of identifier mappings. + repeated Entry entries = 2; + } + + // One file per mapping. + repeated Mapping mappings = 1; +} diff --git a/src/common/mod.rs b/src/common/mod.rs index 7c8e9533..88d5364d 100644 --- a/src/common/mod.rs +++ b/src/common/mod.rs @@ -525,6 +525,89 @@ macro_rules! flush_and_shutdown { }; } +// Per-file identifier mapping. +pub mod id_mapping { + // Actual implementation. + #[derive(serde::Serialize, serde::Deserialize, PartialEq, Eq, Clone, Debug, Default)] + pub struct FileIdentifierMappings { + // Per-file and per-identifier mapping. + pub mappings: indexmap::IndexMap>, + } + + impl FileIdentifierMappings { + // Load from JSON - deserialize via serde_json. + pub fn load_from_json(json: &str) -> Result { + let buf: crate::pbs::worker::FileIdentifierMappings = serde_json::from_str(json) + .map_err(|e| { + anyhow::anyhow!("could not deserialize FileIdentifierMappings: {}", e) + })?; + let mut mappings: indexmap::IndexMap<_, _> = Default::default(); + for mapping in &buf.mappings { + let mut map: indexmap::IndexMap<_, _> = Default::default(); + for entry in &mapping.entries { + map.insert(entry.src.to_string(), entry.dst.to_string()); + } + mappings.insert(mapping.path.to_string(), map); + } + Ok(FileIdentifierMappings { mappings }) + } + + // Load from path. + pub fn load_from_path + ToString>( + path: P, + ) -> Result { + Self::load_from_json( + std::fs::read_to_string(path.as_ref()) + .map_err(|e| anyhow::anyhow!("could not read {}: {}", path.to_string(), e))? + .as_str(), + ) + } + + // Obtain mapping. + pub fn mapping_for_file<'a>( + &'a self, + file_name: &str, + ) -> Result<&'a indexmap::IndexMap, anyhow::Error> { + self.mappings + .get(file_name) + .ok_or_else(|| anyhow::anyhow!("file name not in mapping: {}", &file_name)) + } + + // Map from file name and identifier. + pub fn map_identifier( + &self, + file_name: &str, + identifier: &str, + ) -> Result { + self.mapping_for_file(file_name)? + .get(identifier) + .map(|dst| dst.to_string()) + .ok_or_else(|| { + anyhow::anyhow!("identifier {} not in file {}", &identifier, &file_name) + }) + } + + // Get all file names in map. + pub fn file_names(&self) -> Vec { + self.mappings.keys().cloned().collect() + } + + // Get all source identifiers in file. + pub fn src_identifiers(&self, file_name: &str) -> Result, anyhow::Error> { + Ok(self.mapping_for_file(file_name)?.keys().cloned().collect()) + } + + // Get all destination identifiers in file. + pub fn dst_identifiers(&self, file_name: &str) -> Result, anyhow::Error> { + Ok(self + .mapping_for_file(file_name)? + .values() + .cloned() + .collect()) + } + } +} + #[cfg(test)] mod test { use noodles_vcf as vcf; @@ -641,4 +724,29 @@ mod test { insta::assert_debug_snapshot!(pedigree); insta::assert_debug_snapshot!(case_uuid); } + + #[test] + fn file_identifier_mappings() -> Result<(), anyhow::Error> { + let mapping = super::id_mapping::FileIdentifierMappings::load_from_json( + r#" + { + "mappings": [ + { + "path": "path/to/file", + "entries": [ + { + "src": "foo", + "dst": "bar" + } + ] + } + ] + } + "#, + )?; + + insta::assert_yaml_snapshot!(&mapping); + + Ok(()) + } } diff --git a/src/common/snapshots/varfish_server_worker__common__test__file_identifier_mappings.snap b/src/common/snapshots/varfish_server_worker__common__test__file_identifier_mappings.snap new file mode 100644 index 00000000..2415deef --- /dev/null +++ b/src/common/snapshots/varfish_server_worker__common__test__file_identifier_mappings.snap @@ -0,0 +1,7 @@ +--- +source: src/common/mod.rs +expression: "&mapping" +--- +mappings: + path/to/file: + foo: bar diff --git a/src/main.rs b/src/main.rs index cbf427df..7be439cc 100644 --- a/src/main.rs +++ b/src/main.rs @@ -1,6 +1,7 @@ //! VarFish Server Worker main executable pub mod common; +pub mod pbs; pub mod seqvars; pub mod strucvars; diff --git a/src/pbs.rs b/src/pbs.rs new file mode 100644 index 00000000..af343a85 --- /dev/null +++ b/src/pbs.rs @@ -0,0 +1,19 @@ +//! Data structures for (de-)serialization as generated by `prost-build`. + +/// Code generate for protobufs by `prost-build`. +pub mod clinvar { + include!(concat!(env!("OUT_DIR"), "/varfish.v1.clinvar.rs")); + include!(concat!(env!("OUT_DIR"), "/varfish.v1.clinvar.serde.rs")); +} + +/// Code generate for protobufs by `prost-build`. +pub mod svs { + include!(concat!(env!("OUT_DIR"), "/varfish.v1.svs.rs")); + include!(concat!(env!("OUT_DIR"), "/varfish.v1.svs.serde.rs")); +} + +/// Code generate for protobufs by `prost-build`. +pub mod worker { + include!(concat!(env!("OUT_DIR"), "/varfish.v1.worker.rs")); + include!(concat!(env!("OUT_DIR"), "/varfish.v1.worker.serde.rs")); +} diff --git a/src/seqvars/ingest/header.rs b/src/seqvars/ingest/header.rs index e7fb1ec6..90e96c42 100644 --- a/src/seqvars/ingest/header.rs +++ b/src/seqvars/ingest/header.rs @@ -212,6 +212,7 @@ fn add_contigs_38(builder: vcf::header::Builder) -> Result, + id_mapping: &Option>, genomebuild: GenomeRelease, file_date: &str, case_uuid: &uuid::Uuid, @@ -355,7 +356,24 @@ pub fn build_output_header( .iter() .cloned() .collect::>(); - if !ped_idv.eq(&input_idv) { + if let Some(id_mapping) = id_mapping { + let src_idv = id_mapping.keys().cloned().collect::>(); + if !src_idv.eq(&input_idv) { + anyhow::bail!( + "mapping source individuals = {:?} != input individuals: {:?}", + &src_idv, + &input_idv + ) + } + let dst_idv = id_mapping.values().cloned().collect::>(); + if !dst_idv.eq(&ped_idv) { + anyhow::bail!( + "mapping destination individuals = {:?} != pedigree individuals: {:?}", + &dst_idv, + &ped_idv + ) + } + } else if !ped_idv.eq(&input_idv) { anyhow::bail!( "pedigree individuals = {:?} != input individuals: {:?}", &ped_idv, @@ -364,13 +382,16 @@ pub fn build_output_header( } let mut sample_names = Vec::new(); - for name in input_header.sample_names() { - let i = pedigree - .individuals - .get(name) - .expect("checked equality above"); - if input_header.sample_names().contains(&i.name) { - sample_names.push(i.name.clone()); + for src_name in input_header.sample_names() { + let dst_name = if let Some(id_mapping) = id_mapping { + id_mapping.get(src_name).expect("checked above") + } else { + src_name + }; + + let i = pedigree.individuals.get(dst_name).expect("checked above"); + if input_header.sample_names().contains(src_name) { + sample_names.push(dst_name.clone()); } // Add SAMPLE entry. @@ -409,7 +430,15 @@ pub fn build_output_header( builder = builder.set_sample_names(sample_names.into_iter().collect()); } else { for name in input_header.sample_names() { - builder = builder.add_sample_name(name.clone()); + let name = if let Some(id_mapping) = id_mapping { + id_mapping + .get(name) + .ok_or_else(|| anyhow::anyhow!("mapping given but sample {} not found", name))? + .clone() + } else { + name.clone() + }; + builder = builder.add_sample_name(name); } } @@ -521,6 +550,7 @@ mod test { let output_vcf_header = super::build_output_header( &input_vcf_header, &Some(pedigree), + &None, crate::common::GenomeRelease::Grch37, "20230421", &uuid::Uuid::parse_str("00000000-0000-0000-0000-000000000000").unwrap(), @@ -563,6 +593,7 @@ mod test { let output_vcf_header = super::build_output_header( &input_vcf_header, &Some(pedigree), + &None, crate::common::GenomeRelease::Grch38, "20230421", &uuid::Uuid::parse_str("00000000-0000-0000-0000-000000000000").unwrap(), diff --git a/src/seqvars/ingest/mod.rs b/src/seqvars/ingest/mod.rs index 8f6c6dfc..4c139c91 100644 --- a/src/seqvars/ingest/mod.rs +++ b/src/seqvars/ingest/mod.rs @@ -48,6 +48,9 @@ pub struct Args { /// Maximal number of variants to write out; optional. #[clap(long)] pub max_var_count: Option, + /// Per-file identifier mapping, either a JSON or @-prefixed path to JSON. + #[clap(long)] + pub id_mapping: Option, } /// Return path component fo rth egiven assembly. @@ -284,6 +287,7 @@ async fn process_variants( input_reader: &mut AsyncVcfReader, output_header: &vcf::Header, input_header: &vcf::Header, + id_mapping: &Option>, args: &Args, ) -> Result<(), anyhow::Error> { // Open the frequency RocksDB database in read only mode. @@ -351,6 +355,11 @@ async fn process_variants( .collect::>(); let mut res = vec![usize::MAX; output_header.sample_names().len()]; for (input_idx, sample) in input_header.sample_names().iter().enumerate() { + let sample = if let Some(id_mapping) = id_mapping { + id_mapping.get(sample).expect("checked earlier") + } else { + sample + }; res[output_sample_to_idx[sample]] = input_idx; } res @@ -512,6 +521,51 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a .await .map_err(|e| anyhow::anyhow!("could not build VCF reader: {}", e))?; + tracing::info!("loading file identifier mappings..."); + let id_mapping = args + .id_mapping + .as_ref() + .map( + |id_mapping| -> Result>, anyhow::Error> { + let id_mappings = if id_mapping.starts_with('@') { + crate::common::id_mapping::FileIdentifierMappings::load_from_path( + id_mapping.trim_start_matches('@'), + ) + .map_err(|e| { + anyhow::anyhow!( + "could not load ID mapping from file {:?}: {}", + id_mapping.trim_start_matches('@'), + e + ) + }) + } else { + crate::common::id_mapping::FileIdentifierMappings::load_from_json(id_mapping) + .map_err(|e| { + anyhow::anyhow!( + "could not load ID mapping from JSON string {:?}: {}", + &id_mapping, + &e, + ) + }) + }?; + + if id_mappings.file_names().contains(&args.path_in) { + tracing::debug!("- we have an ID mapping for {}", &args.path_in); + Ok(Some( + id_mappings + .mapping_for_file(&args.path_in) + .cloned() + .expect("checked above"), + )) + } else { + tracing::debug!("- we have no ID mapping for {}", &args.path_in); + Ok(None) + } + }, + ) + .transpose()? + .flatten(); + tracing::info!("processing header..."); let mut input_header = input_reader .read_header() @@ -520,6 +574,7 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a let output_header = header::build_output_header( &input_header, &Some(pedigree), + &id_mapping, args.genomebuild, &args.file_date, &args.case_uuid, @@ -548,6 +603,7 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a &mut input_reader, &output_header, &input_header, + &id_mapping, args, ) .await?; @@ -603,6 +659,7 @@ mod test { .to_str() .expect("invalid path") .into(), + id_mapping: None, }; super::run(&args_common, &args).await?; @@ -632,6 +689,7 @@ mod test { genomebuild: GenomeRelease::Grch37, path_in, path_out, + id_mapping: None, }; super::run(&args_common, &args).await?; @@ -641,4 +699,75 @@ mod test { Ok(()) } + + #[rstest] + #[case::dragen_na12787("tests/seqvars/ingest/NA12878_dragen.vcf")] + #[case::gatk_hc_case_1("tests/seqvars/ingest/Case_1.vcf")] + #[tokio::test] + async fn result_snapshot_test_with_id_map(#[case] path: &str) -> Result<(), anyhow::Error> { + mehari::common::set_snapshot_suffix!( + "{}", + path.split('/').last().unwrap().replace('.', "_") + ); + + let tmpdir = temp_testdir::TempDir::default(); + + let path_ped = path.replace(".vcf", ".custom_id.ped"); + let path_out = tmpdir + .join("out.vcf") + .to_str() + .expect("invalid path") + .into(); + let args_common = Default::default(); + let args = super::Args { + file_date: String::from("20230421"), + case_uuid: uuid::Uuid::parse_str("00000000-0000-0000-0000-000000000000").unwrap(), + max_var_count: None, + path_mehari_db: "tests/seqvars/ingest/db".into(), + path_ped, + genomebuild: GenomeRelease::Grch37, + path_in: path.into(), + path_out, + id_mapping: Some( + r#" + { + "mappings": [ + { + "path": "tests/seqvars/ingest/NA12878_dragen.vcf", + "entries": [ + { + "src": "NA12878", + "dst": "my-custom-id" + } + ] + }, + { + "path": "tests/seqvars/ingest/Case_1.vcf", + "entries": [ + { + "src": "Case_1_index-N1-DNA1-WGS1", + "dst": "Case_1_index" + }, + { + "src": "Case_1_mother-N1-DNA1-WGS1", + "dst": "Case_1_mother" + }, + { + "src": "Case_1_father-N1-DNA1-WGS1", + "dst": "Case_1_father" + } + ] + } + ] + } + "# + .to_string(), + ), + }; + super::run(&args_common, &args).await?; + + insta::assert_snapshot!(std::fs::read_to_string(&args.path_out)?); + + Ok(()) + } } diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@Case_1_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@Case_1_vcf.snap new file mode 100644 index 00000000..e554671b --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@Case_1_vcf.snap @@ -0,0 +1,122 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##fileDate=20230421 +##SAMPLE= +##SAMPLE= +##SAMPLE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##x-varfish-case-uuid=00000000-0000-0000-0000-000000000000 +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father Case_1_index Case_1_mother +17 41249263 . G A . . gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_clinsig=benign;clinvar_rcv=RCV000112746;clinvar_vcv=VCV000055642;ANN=A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/23|c.591C>T|p.C197=|704/7088|591/5592|197/1864|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.C150=|644/7028|450/5451|150/1817|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/22|c.591C>T|p.C197=|610/3682|591/2280|197/760|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.C197=|698/3696|591/2100|197/700|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.C197=|704/7151|591/5655|197/1885|0| GT:AD:DP:GQ 0/0:52,0:52:99 0/0:46,0:46:99 0/1:21,21:42:99 +17 41252332 . T C . . ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-435A>G|p.?|555/7088|442/5592||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-435A>G|p.?|461/3682|442/2280||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||435| GT:AD:DP:GQ 0/0:25,0:25:75 0/1:14,14:28:99 0/1:19,21:40:99 +17 41252691 . ATATAAT A . . ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-795delATTATA|p.?|555/7088|442/5592||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795delATTATA|p.?|495/7028|301/5451||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-795delATTATA|p.?|461/3682|442/2280||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795delATTATA|p.?|549/3696|442/2100||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795delATTATA|p.?|555/7151|442/5655||795| GT:AD:DP:GQ 0/0:9,0:9:27 0/1:4,10:14:99 0/1:12,11:23:99 +17 41252693 . ATAAT A . . ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-797delATTA|p.?|555/7088|442/5592||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797delATTA|p.?|495/7028|301/5451||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-797delATTA|p.?|461/3682|442/2280||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797delATTA|p.?|549/3696|442/2100||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797delATTA|p.?|555/7151|442/5655||797| GT:AD:DP:GQ 0/0:9,0:9:27 0/0:14,0:14:42 0/1:11,11:22:99 +17 41252695 . AAT A . . ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-799delAT|p.?|555/7088|442/5592||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799delAT|p.?|495/7028|301/5451||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-799delAT|p.?|461/3682|442/2280||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799delAT|p.?|549/3696|442/2100||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799delAT|p.?|555/7151|442/5655||799| GT:AD:DP:GQ 0/1:3,6:9:79 0/0:14,0:14:42 0/0:22,0:22:66 +17 41252696 . A T . . ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-799T>A|p.?|555/7088|442/5592||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-799T>A|p.?|461/3682|442/2280||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||799| GT:AD:DP:GQ 0/1:6,3:9:78 0/1:10,4:14:98 0/0:22,0:22:67 +17 41252697 . A AT . . ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insA|p.?|461/3682|442/2280||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||801| GT:AD:DP:GQ 1/1:0,45:45:99 1/0:16,17:33:99 1/0:22,11:33:99 +17 41252697 . A ATT . . ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insAA|p.?|461/3682|442/2280||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||801| GT:AD:DP:GQ 0/0:45,0:45:99 0/1:17,16:33:99 0/1:12,21:33:99 +17 41254393 . G T . . ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1746C>A|p.?|554/7088|441/5592||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1746C>A|p.?|460/3682|441/2280||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||-1746| GT:AD:DP:GQ 0/1:29,8:37:66 ./.:.:.:. 0/0:32,3:35:47 +17 41273700 . C CA . . ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||-2334|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||-2334|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2333_80+2334insT|p.?|99/3682|80/2280||-2334|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||-2334|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||-2334| GT:AD:DP:GQ 0/0:14,0:14:42 0/0:6,1:7:10 0/1:5,5:10:65 +MT 73 . A G . . . GT:AD:DP:GQ 0/0:3975,0:3975:99 1/1:0,2871:2871:99 1/1:0,3320:3320:99 +MT 119 . T C . . . GT:AD:DP:GQ 0/0:5417,1:5418:99 1/1:0,4039:4039:99 1/1:1,4112:4113:99 +MT 189 . A G . . . GT:AD:DP:GQ 0/0:3069,0:3069:99 1/1:0,1721:1721:99 1/1:0,2204:2204:99 +MT 195 . T C . . . GT:AD:DP:GQ 0/0:2599,0:2599:99 1/1:0,1592:1592:99 1/1:0,1815:1815:99 +MT 204 . T C . . . GT:AD:DP:GQ 0/0:2180,0:2180:99 1/1:0,1424:1424:99 1/1:0,1304:1304:99 +MT 207 . G A . . . GT:AD:DP:GQ 0/0:2115,0:2115:99 1/1:0,1408:1408:99 1/1:0,1277:1277:99 +MT 263 . A G . . . GT:AD:DP:GQ 1/1:0,1288:1288:99 1/1:0,1204:1204:99 1/1:0,1031:1031:99 +MT 302 . A ACC . . . GT:AD:DP:GQ 0/1:157,687:844:99 0/0:1005,6:1011:99 0/0:800,3:803:99 +MT 310 . T TC . . . GT:AD:DP:GQ 1/1:0,1035:1035:99 1/1:0,1411:1411:99 1/1:1,1090:1091:99 +MT 477 . T C . . . GT:AD:DP:GQ 1/1:4,2129:2133:99 0/0:2266,1:2267:99 0/0:1725,0:1725:99 +MT 709 . G A . . . GT:AD:DP:GQ 0/0:2494,0:2494:99 1/1:0,2186:2186:99 1/1:1,1813:1814:99 +MT 750 . A G . . . GT:AD:DP:GQ 1/1:0,2757:2757:99 1/1:0,2392:2392:99 1/1:0,1621:1621:99 +MT 879 . T C . . . GT:AD:DP:GQ 0/0:2853,0:2853:99 0/0:2784,0:2784:99 0/1:1351,547:1898:99 +MT 1243 . T C . . . GT:AD:DP:GQ 0/0:2674,1:2675:99 1/1:0,2198:2198:99 1/1:0,1655:1655:99 +MT 1438 . A G . . . GT:AD:DP:GQ 1/1:0,3815:3815:99 1/1:0,3653:3653:99 1/1:0,2900:2900:99 +MT 1824 . T C . . . GT:AD:DP:GQ 1/1:0,2668:2668:99 0/0:2409,0:2409:99 0/0:1752,0:1752:99 +MT 2633 . A G . . . GT:AD:DP:GQ 0/0:2535,0:2535:99 0/1:1648,761:2409:99 0/0:2269,0:2269:99 +MT 2706 . A G . . . GT:AD:DP:GQ 0/0:3200,0:3200:99 1/1:0,2847:2847:99 1/1:0,2020:2020:99 +MT 3010 . G A . . . GT:AD:DP:GQ 1/1:0,2841:2841:99 0/0:2385,0:2385:99 0/0:1685,0:1685:99 +MT 3505 . A G . . . GT:AD:DP:GQ 0/0:2580,14:2594:99 1/1:0,2363:2363:99 1/1:0,1664:1664:99 +MT 3784 . T C . . . GT:AD:DP:GQ 0/1:480,2456:2936:99 0/0:2504,0:2504:99 0/0:1991,0:1991:99 +MT 4769 . A G . . . GT:AD:DP:GQ 1/1:0,2689:2689:99 1/1:0,2549:2549:99 1/1:0,2108:2108:99 +MT 5046 . G A . . . GT:AD:DP:GQ 0/0:2876,2:2878:99 1/1:0,2466:2466:99 1/1:0,1661:1661:99 +MT 5460 . G A . . . GT:AD:DP:GQ 0/0:2905,2:2907:99 1/1:0,2759:2759:99 1/1:2,1968:1970:99 +MT 7028 . C T . . . GT:AD:DP:GQ 0/0:2577,3:2580:99 1/1:2,2201:2203:99 1/1:1,1945:1946:99 +MT 7864 . C T . . . GT:AD:DP:GQ 0/0:3588,1:3589:99 1/1:0,3465:3465:99 1/1:0,2746:2746:99 +MT 8170 . A G . . . GT:AD:DP:GQ 0/0:2051,1:2052:99 1/1:0,2257:2257:99 1/1:0,1774:1774:99 +MT 8251 . G A . . . GT:AD:DP:GQ 0/0:2360,0:2360:99 1/1:0,2317:2317:99 1/1:1,1624:1625:99 +MT 8860 . A G . . . GT:AD:DP:GQ 1/1:0,3278:3278:99 1/1:0,3088:3088:99 1/1:0,2241:2241:99 +MT 8994 . G A . . . GT:AD:DP:GQ 0/0:2793,0:2793:99 1/1:0,2368:2368:99 1/1:1,1917:1918:99 +MT 9007 . A G . . . GT:AD:DP:GQ 1/1:0,2959:2959:99 0/0:2442,0:2442:99 0/0:1735,0:1735:99 +MT 9150 . A G . . . GT:AD:DP:GQ 1/1:0,3163:3163:99 0/0:3538,0:3538:99 0/0:2767,0:2767:99 +MT 9380 . G A . . . GT:AD:DP:GQ 1/1:1,3320:3321:99 0/0:3222,0:3222:99 0/0:2547,0:2547:99 +MT 10097 . A G . . . GT:AD:DP:GQ 0/0:2660,0:2660:99 0/1:1680,508:2188:99 0/0:1851,0:1851:99 +MT 11204 . T C . . . GT:AD:DP:GQ 0/0:3168,5:3173:99 1/1:0,2922:2922:99 1/1:0,2418:2418:99 +MT 11674 . C T . . . GT:AD:DP:GQ 0/0:2890,0:2890:99 1/1:0,2666:2666:99 1/1:1,2179:2180:99 +MT 11719 . G A . . . GT:AD:DP:GQ 0/0:3339,2:3341:99 1/1:0,3052:3052:99 1/1:0,2203:2203:99 +MT 11947 . A G . . . GT:AD:DP:GQ 0/0:2579,2:2581:99 1/1:0,2273:2273:99 1/1:0,1804:1804:99 +MT 12414 . T C . . . GT:AD:DP:GQ 0/0:2852,3:2855:99 1/1:1,2545:2546:99 1/1:0,1733:1733:99 +MT 12648 . A G . . . GT:AD:DP:GQ 0/0:1812,1:1813:99 1/1:2,1662:1664:99 1/1:4,1777:1781:99 +MT 12705 . C T . . . GT:AD:DP:GQ 0/0:2359,10:2369:99 1/1:1,2137:2138:99 1/1:1,1621:1622:99 +MT 13406 . G A . . . GT:AD:DP:GQ 0/0:2539,1:2540:99 0/0:2216,0:2216:99 0/1:1224,733:1957:99 +MT 13611 . A G . . . GT:AD:DP:GQ 0/0:3838,2:3840:99 1/1:0,3717:3717:99 1/1:1,2834:2835:99 +MT 13928 . G C . . . GT:AD:DP:GQ 0/0:2947,0:2947:99 1/1:0,2700:2700:99 1/1:0,1880:1880:99 +MT 14148 . A G . . . GT:AD:DP:GQ 0/0:3019,2:3021:99 1/1:0,2820:2820:99 1/1:0,1962:1962:99 +MT 14766 . C T . . . GT:AD:DP:GQ 0/0:3318,3:3321:99 1/1:2,3111:3113:99 1/1:3,2355:2358:99 +MT 15326 . A G . . . GT:AD:DP:GQ 1/1:0,3716:3716:99 1/1:0,3560:3560:99 1/1:0,2690:2690:99 +MT 15884 . G C . . . GT:AD:DP:GQ 0/0:3595,1:3596:99 1/1:0,3167:3167:99 1/1:1,2733:2734:99 +MT 16184 . C T . . . GT:AD:DP:GQ 0/0:1406,1:1407:99 1/1:0,1969:1969:99 1/1:0,1478:1478:99 +MT 16223 . C T . . . GT:AD:DP:GQ 0/0:1405,1:1406:99 1/1:0,2018:2018:99 1/1:0,1472:1472:99 +MT 16263 . T C . . . GT:AD:DP:GQ 1/1:2,1476:1478:99 0/0:1994,0:1994:99 0/0:1475,0:1475:99 +MT 16292 . C T . . . GT:AD:DP:GQ 0/0:1652,0:1652:99 1/1:1,1913:1914:99 1/1:0,1476:1476:99 +MT 16519 . T C . . . GT:AD:DP:GQ 1/1:0,1759:1759:99 1/1:0,4094:4094:99 1/1:0,1744:1744:99 diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@NA12878_dragen_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@NA12878_dragen_vcf.snap new file mode 100644 index 00000000..4a62dab9 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@NA12878_dragen_vcf.snap @@ -0,0 +1,184 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##fileDate=20230421 +##SAMPLE= +##PEDIGREE= +##x-varfish-case-uuid=00000000-0000-0000-0000-000000000000 +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT my-custom-id +17 41244000 . T C . . gnomad_exomes_an=31346;gnomad_exomes_hom=1591;gnomad_exomes_het=6707;gnomad_genomes_an=250954;gnomad_genomes_hom=16402;gnomad_genomes_het=55703;clinvar_clinsig=benign;clinvar_rcv=RCV000112115;clinvar_vcv=VCV000041818;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.3548A>G|p.K1183R|3661/7088|3548/5592|1183/1864|0|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.3407A>G|p.K1136R|3601/7028|3407/5451|1136/1817|0|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.788-951A>G|p.?|807/3682|788/2280||951|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-951A>G|p.?|895/3696|788/2100||951|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3548A>G|p.K1183R|3661/7151|3548/5655|1183/1885|0| GT:AD:DP:GQ 0/1:8,18:26:43 +17 41244435 . T C . . gnomad_exomes_an=31332;gnomad_exomes_hom=1505;gnomad_exomes_het=6415;gnomad_genomes_an=251032;gnomad_genomes_hom=16145;gnomad_genomes_het=55137;clinvar_clinsig=benign;clinvar_rcv=RCV000112006;clinvar_vcv=VCV000041815;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.3113A>G|p.E1038G|3226/7088|3113/5592|1038/1864|0|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2972A>G|p.E991G|3166/7028|2972/5451|991/1817|0|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.788-1386A>G|p.?|807/3682|788/2280||1386|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-1386A>G|p.?|895/3696|788/2100||1386|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3113A>G|p.E1038G|3226/7151|3113/5655|1038/1885|0| GT:AD:DP:GQ 0/1:12,14:26:47 +17 41244936 . G A . . gnomad_exomes_an=31324;gnomad_exomes_hom=4287;gnomad_exomes_het=6594;gnomad_genomes_an=251034;gnomad_genomes_hom=22738;gnomad_genomes_het=55898;clinvar_clinsig=benign;clinvar_rcv=RCV000111903;clinvar_vcv=VCV000041812;ANN=A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2612C>T|p.P871L|2725/7088|2612/5592|871/1864|0|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2471C>T|p.P824L|2665/7028|2471/5451|824/1817|0|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1825C>T|p.?|806/3682|787/2280||-1825|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1825C>T|p.?|894/3696|787/2100||-1825|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2612C>T|p.P871L|2725/7151|2612/5655|871/1885|0| GT:AD:DP:GQ 0/1:17,13:30:47 +17 41245237 . A G . . gnomad_exomes_an=31314;gnomad_exomes_hom=1492;gnomad_exomes_het=6416;gnomad_genomes_an=250946;gnomad_genomes_hom=16057;gnomad_genomes_het=55063;clinvar_clinsig=benign;clinvar_rcv=RCV000111822;clinvar_vcv=VCV000125554;ANN=G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2311T>C|p.L771=|2424/7088|2311/5592|771/1864|0|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2170T>C|p.L724=|2364/7028|2170/5451|724/1817|0|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1524T>C|p.?|806/3682|787/2280||-1524|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1524T>C|p.?|894/3696|787/2100||-1524|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2311T>C|p.L771=|2424/7151|2311/5655|771/1885|0| GT:AD:DP:GQ 0/1:18,11:29:46 +17 41245466 . G A . . gnomad_exomes_an=31338;gnomad_exomes_hom=1602;gnomad_exomes_het=6709;gnomad_genomes_an=251110;gnomad_genomes_hom=16420;gnomad_genomes_het=55707;clinvar_clinsig=benign;clinvar_rcv=RCV000111763;clinvar_vcv=VCV000125536;ANN=A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2082C>T|p.S694=|2195/7088|2082/5592|694/1864|0|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.1941C>T|p.S647=|2135/7028|1941/5451|647/1817|0|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1295C>T|p.?|806/3682|787/2280||-1295|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1295C>T|p.?|894/3696|787/2100||-1295|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2082C>T|p.S694=|2195/7151|2082/5655|694/1885|0| GT:AD:DP:GQ 0/1:11,8:19:48 +17 41247122 . A ACCT . . clinvar_clinsig=benign;clinvar_rcv=RCV000191391;clinvar_vcv=VCV000127125;ANN=ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|9/22|c.671-246_671-245insAGG|p.?|784/7088|671/5592||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.530-246_530-245insAGG|p.?|724/7028|530/5451||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|8/21|c.671-246_671-245insAGG|p.?|690/3682|671/2280||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.671-246_671-245insAGG|p.?|778/3696|671/2100||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.671-246_671-245insAGG|p.?|784/7151|671/5655||246| GT:AD:DP:GQ 0/1:18,11:29:45 +17 41247604 . A C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191392;clinvar_vcv=VCV000209447;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|9/22|c.670+259T>G|p.?|783/7088|670/5592||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.529+259T>G|p.?|723/7028|529/5451||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|8/21|c.670+259T>G|p.?|689/3682|670/2280||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.670+259T>G|p.?|777/3696|670/2100||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.670+259T>G|p.?|783/7151|670/5655||-259| GT:AD:DP:GQ 0/1:12,11:23:47 +17 41248164 . C T . . clinvar_clinsig=benign;clinvar_rcv=RCV000191394;clinvar_vcv=VCV000209449;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-225G>A|p.?|707/7088|594/5592||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-225G>A|p.?|647/7028|453/5451||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-225G>A|p.?|613/3682|594/2280||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-225G>A|p.?|701/3696|594/2100||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-225G>A|p.?|707/7151|594/5655||225| GT:AD:DP:GQ 0/1:14,7:21:44 +17 41248393 . C CAAAAAAAAAA . . ANN=CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-455_594-454insTTTTTTTTTT|p.?|707/7088|594/5592||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-455_453-454insTTTTTTTTTT|p.?|647/7028|453/5451||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-455_594-454insTTTTTTTTTT|p.?|613/3682|594/2280||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-455_594-454insTTTTTTTTTT|p.?|701/3696|594/2100||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-455_594-454insTTTTTTTTTT|p.?|707/7151|594/5655||455| GT:AD:DP:GQ 0/1:9,7:16:48 +17 41248484 . G C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191395;clinvar_vcv=VCV000209450;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-545C>G|p.?|707/7088|594/5592||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-545C>G|p.?|647/7028|453/5451||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-545C>G|p.?|613/3682|594/2280||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-545C>G|p.?|701/3696|594/2100||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-545C>G|p.?|707/7151|594/5655||545| GT:AD:DP:GQ 0/1:11,9:20:48 +17 41248588 . CA C . . ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-650delT|p.?|707/7088|594/5592||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-650delT|p.?|647/7028|453/5451||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-650delT|p.?|613/3682|594/2280||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-650delT|p.?|701/3696|594/2100||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-650delT|p.?|707/7151|594/5655||650| GT:AD:DP:GQ 0/1:9,10:19:42 +17 41249094 . A G . . gnomad_exomes_an=31332;gnomad_exomes_hom=1602;gnomad_exomes_het=6703;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191396;clinvar_vcv=VCV000209451;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.593+167T>C|p.?|706/7088|593/5592||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.452+167T>C|p.?|646/7028|452/5451||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.593+167T>C|p.?|612/3682|593/2280||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.593+167T>C|p.?|700/3696|593/2100||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.593+167T>C|p.?|706/7151|593/5655||-167| GT:AD:DP:GQ 0/1:9,7:16:48 +17 41249363 . TA T . . gnomad_exomes_an=31286;gnomad_exomes_hom=1497;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.548-58delT|p.?|661/7088|548/5592||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-58delT|p.?|601/7028|407/5451||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.548-58delT|p.?|567/3682|548/2280||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-58delT|p.?|655/3696|548/2100||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-58delT|p.?|661/7151|548/5655||58| GT:AD:DP:GQ 0/1:12,13:25:48 +17 41250047 . C CT . . ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.548-742_548-741insA|p.?|661/7088|548/5592||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-742_407-741insA|p.?|601/7028|407/5451||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.548-742_548-741insA|p.?|567/3682|548/2280||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-742_548-741insA|p.?|655/3696|548/2100||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-742_548-741insA|p.?|661/7151|548/5655||742| GT:AD:DP:GQ 0/1:13,7:20:18 +17 41250678 . C CT . . clinvar_clinsig=benign;clinvar_rcv=RCV000191403;clinvar_vcv=VCV000209458;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+1113_547+1114insA|p.?|660/7088|547/5592||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+1113_406+1114insA|p.?|600/7028|406/5451||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+1113_547+1114insA|p.?|566/3682|547/2280||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+1113_547+1114insA|p.?|654/3696|547/2100||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+1113_547+1114insA|p.?|660/7151|547/5655||-1114| GT:AD:DP:GQ 0/1:6,16:22:42 +17 41250923 . T C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191405;clinvar_vcv=VCV000209460;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+869A>G|p.?|660/7088|547/5592||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+869A>G|p.?|600/7028|406/5451||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+869A>G|p.?|566/3682|547/2280||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+869A>G|p.?|654/3696|547/2100||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+869A>G|p.?|660/7151|547/5655||-869| GT:AD:DP:GQ 0/1:13,9:22:47 +17 41251495 . C G . . clinvar_clinsig=benign;clinvar_rcv=RCV000191408;clinvar_vcv=VCV000209463;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+297G>C|p.?|660/7088|547/5592||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+297G>C|p.?|600/7028|406/5451||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+297G>C|p.?|566/3682|547/2280||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+297G>C|p.?|654/3696|547/2100||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+297G>C|p.?|660/7151|547/5655||-297| GT:AD:DP:GQ 0/1:11,15:26:48 +17 41251646 . T A . . gnomad_exomes_an=31294;gnomad_exomes_hom=1592;gnomad_exomes_het=6693;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000112727;clinvar_vcv=VCV000125879;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+146A>T|p.?|660/7088|547/5592||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+146A>T|p.?|600/7028|406/5451||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+146A>T|p.?|566/3682|547/2280||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+146A>T|p.?|654/3696|547/2100||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+146A>T|p.?|660/7151|547/5655||-146| GT:AD:DP:GQ 0/1:11,8:19:48 +17 41252575 . G A . . clinvar_clinsig=benign;clinvar_rcv=RCV000191411;clinvar_vcv=VCV000209466;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-678C>T|p.?|555/7088|442/5592||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-678C>T|p.?|495/7028|301/5451||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-678C>T|p.?|461/3682|442/2280||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-678C>T|p.?|549/3696|442/2100||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-678C>T|p.?|555/7151|442/5655||678| GT:AD:DP:GQ:PS 1|1:0,3:3:5:41252575 +17 41252591 . C CAT . . ANN=CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-695_442-694insAT|p.?|555/7088|442/5592||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-695_301-694insAT|p.?|495/7028|301/5451||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-695_442-694insAT|p.?|461/3682|442/2280||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-695_442-694insAT|p.?|549/3696|442/2100||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-695_442-694insAT|p.?|555/7151|442/5655||695| GT:AD:DP:GQ:PS 1|1:0,2:2:4:41252575 +17 41254174 . A G . . clinvar_clinsig=benign;clinvar_rcv=RCV000191423;clinvar_vcv=VCV000209478;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1965T>C|p.?|554/7088|441/5592||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1965T>C|p.?|494/7028|300/5451||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1965T>C|p.?|460/3682|441/2280||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1965T>C|p.?|548/3696|441/2100||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1965T>C|p.?|554/7151|441/5655||-1965| GT:AD:DP:GQ 0/1:14,13:27:48 +17 41254374 . C CTTTTTTTT . . ANN=CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1764_441+1765insAAAAAAAA|p.?|554/7088|441/5592||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1764_300+1765insAAAAAAAA|p.?|494/7028|300/5451||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1764_441+1765insAAAAAAAA|p.?|460/3682|441/2280||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1764_441+1765insAAAAAAAA|p.?|548/3696|441/2100||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1764_441+1765insAAAAAAAA|p.?|554/7151|441/5655||-1765| GT:AD:DP:GQ 0/1:6,7:13:48 +17 41254405 . C T . . clinvar_clinsig=benign;clinvar_rcv=RCV000256092;clinvar_vcv=VCV000264778;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1734G>A|p.?|554/7088|441/5592||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1734G>A|p.?|494/7028|300/5451||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1734G>A|p.?|460/3682|441/2280||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1734G>A|p.?|548/3696|441/2100||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1734G>A|p.?|554/7151|441/5655||-1734| GT:AD:DP:GQ 0/1:5,9:14:43 +17 41254486 . T G . . clinvar_clinsig=benign;clinvar_rcv=RCV000191424;clinvar_vcv=VCV000209479;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1653A>C|p.?|554/7088|441/5592||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1653A>C|p.?|494/7028|300/5451||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1653A>C|p.?|460/3682|441/2280||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1653A>C|p.?|548/3696|441/2100||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1653A>C|p.?|554/7151|441/5655||-1653| GT:AD:DP:GQ 0/1:8,15:23:46 +17 41254965 . C CT . . clinvar_clinsig=benign;clinvar_rcv=RCV000255713;clinvar_vcv=VCV000264845;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1173_441+1174insA|p.?|554/7088|441/5592||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1173_300+1174insA|p.?|494/7028|300/5451||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1173_441+1174insA|p.?|460/3682|441/2280||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1173_441+1174insA|p.?|548/3696|441/2100||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1173_441+1174insA|p.?|554/7151|441/5655||-1174| GT:AD:DP:GQ 0/1:14,8:22:22 +17 41255102 . A G . . clinvar_clinsig=benign;clinvar_rcv=RCV000191428;clinvar_vcv=VCV000209483;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1037T>C|p.?|554/7088|441/5592||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1037T>C|p.?|494/7028|300/5451||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1037T>C|p.?|460/3682|441/2280||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1037T>C|p.?|548/3696|441/2100||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1037T>C|p.?|554/7151|441/5655||-1037| GT:AD:DP:GQ:PS 0|1:19,12:31:46:41255102 +17 41255111 . A T . . clinvar_clinsig=benign;clinvar_rcv=RCV000191429;clinvar_vcv=VCV000209484;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1028T>A|p.?|554/7088|441/5592||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1028T>A|p.?|494/7028|300/5451||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1028T>A|p.?|460/3682|441/2280||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1028T>A|p.?|548/3696|441/2100||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1028T>A|p.?|554/7151|441/5655||-1028| GT:AD:DP:GQ:PS 0|1:19,12:31:46:41255102 +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64delT|p.?|554/7088|441/5592||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64delT|p.?|460/3682|441/2280||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||-64| GT:AD:DP:GQ:PS 0|1:11,6:17:43:41256074 +17 41256089 . AAAAAAAAAGAAAAG A . . gnomad_exomes_an=28388;gnomad_exomes_hom=1079;gnomad_exomes_het=5744;gnomad_genomes_an=167932;gnomad_genomes_hom=9911;gnomad_genomes_het=23697;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7088|441/5592||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+36_300+49delCTTTTCTTTTTTTT|p.?|494/7028|300/5451||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|460/3682|441/2280||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|548/3696|441/2100||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7151|441/5655||-36| GT:AD:DP:GQ:PS 0|1:13,6:19:43:41256074 +17 41257134 . T C . . gnomad_exomes_an=31346;gnomad_exomes_hom=4418;gnomad_exomes_het=6505;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000112024;clinvar_vcv=VCV000125614;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.213-161A>G|p.?|326/7088|213/5592||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-161A>G|p.?|266/7028|72/5451||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.213-161A>G|p.?|232/3682|213/2280||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-161A>G|p.?|320/3696|213/2100||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-161A>G|p.?|326/7151|213/5655||161| GT:AD:DP:GQ 0/1:14,15:29:48 +17 41257458 . A C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191434;clinvar_vcv=VCV000209489;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.213-485T>G|p.?|326/7088|213/5592||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-485T>G|p.?|266/7028|72/5451||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.213-485T>G|p.?|232/3682|213/2280||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-485T>G|p.?|320/3696|213/2100||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-485T>G|p.?|326/7151|213/5655||485| GT:AD:DP:GQ 0/1:11,15:26:48 +17 41258043 . C T . . clinvar_clinsig=benign;clinvar_rcv=RCV000191436;clinvar_vcv=VCV000209491;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.212+430G>A|p.?|325/7088|212/5592||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+430G>A|p.?|265/7028|71/5451||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.212+430G>A|p.?|231/3682|212/2280||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+430G>A|p.?|319/3696|212/2100||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+430G>A|p.?|325/7151|212/5655||-430| GT:AD:DP:GQ 0/1:14,13:27:48 +17 41258135 . T TA . . ANN=TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.212+337_212+338insT|p.?|325/7088|212/5592||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+337_71+338insT|p.?|265/7028|71/5451||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.212+337_212+338insT|p.?|231/3682|212/2280||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+337_212+338insT|p.?|319/3696|212/2100||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+337_212+338insT|p.?|325/7151|212/5655||-338| GT:AD:DP:GQ 1/1:3,11:14:4 +17 41259049 . C T . . clinvar_clinsig=benign;clinvar_rcv=RCV000191440;clinvar_vcv=VCV000209494;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-499G>A|p.?|248/7088|135/5592||499|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-499G>A|p.?|188/7028|-7/5451||499|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-499G>A|p.?|154/3682|135/2280||499|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-499G>A|p.?|242/3696|135/2100||499|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-499G>A|p.?|248/7151|135/5655||499| GT:AD:DP:GQ 0/1:8,8:16:48 +17 41259079 . A ATT . . ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-530_135-529insAA|p.?|248/7088|135/5592||530|,ATT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-530_-7-529insAA|p.?|188/7028|-7/5451||530|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-530_135-529insAA|p.?|154/3682|135/2280||530|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-530_135-529insAA|p.?|242/3696|135/2100||530|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-530_135-529insAA|p.?|248/7151|135/5655||530| GT:AD:DP:GQ 0/1:10,3:13:7 +17 41259113 . G A . . clinvar_clinsig=benign;clinvar_rcv=RCV000255936;clinvar_vcv=VCV000264811;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-563C>T|p.?|248/7088|135/5592||563|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-563C>T|p.?|188/7028|-7/5451||563|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-563C>T|p.?|154/3682|135/2280||563|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-563C>T|p.?|242/3696|135/2100||563|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-563C>T|p.?|248/7151|135/5655||563| GT:AD:DP:GQ 0/1:11,8:19:48 +17 41260352 . C CA . . clinvar_clinsig=benign;clinvar_rcv=RCV000255985;clinvar_vcv=VCV000264791;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-1803_135-1802insT|p.?|248/7088|135/5592||1803|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-1803_-7-1802insT|p.?|188/7028|-7/5451||1803|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-1803_135-1802insT|p.?|154/3682|135/2280||1803|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-1803_135-1802insT|p.?|242/3696|135/2100||1803|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-1803_135-1802insT|p.?|248/7151|135/5655||1803| GT:AD:DP:GQ 0/1:11,8:19:43 +17 41260723 . C CAAAAA . . ANN=CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2174_135-2173insTTTTT|p.?|248/7088|135/5592||2174|,CAAAAA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2174_-7-2173insTTTTT|p.?|188/7028|-7/5451||2174|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2174_135-2173insTTTTT|p.?|154/3682|135/2280||2174|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2174_135-2173insTTTTT|p.?|242/3696|135/2100||2174|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2174_135-2173insTTTTT|p.?|248/7151|135/5655||2174| GT:AD:DP:GQ 0/1:1,1:2:20 +17 41260808 . A G . . clinvar_clinsig=benign;clinvar_rcv=RCV000191445;clinvar_vcv=VCV000209499;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2258T>C|p.?|248/7088|135/5592||2258|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2258T>C|p.?|188/7028|-7/5451||2258|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2258T>C|p.?|154/3682|135/2280||2258|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2258T>C|p.?|242/3696|135/2100||2258|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2258T>C|p.?|248/7151|135/5655||2258| GT:AD:DP:GQ 0/1:12,3:15:32 +17 41261058 . T TCTATCTATCTACCTAC . . clinvar_clinsig=benign;clinvar_rcv=RCV000255302;clinvar_vcv=VCV000264813;ANN=TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7088|135/5592||2509|,TCTATCTATCTACCTAC|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2509_-7-2508insGTAGGTAGATAGATAG|p.?|188/7028|-7/5451||2509|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|154/3682|135/2280||2509|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|242/3696|135/2100||2509|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7151|135/5655||2509| GT:AD:DP:GQ 0/1:9,11:20:48 +17 41261233 . C T . . clinvar_clinsig=benign;clinvar_rcv=RCV000191449;clinvar_vcv=VCV000209503;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2683G>A|p.?|248/7088|135/5592||2683|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2683G>A|p.?|188/7028|-7/5451||2683|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2683G>A|p.?|154/3682|135/2280||2683|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2683G>A|p.?|242/3696|135/2100||2683|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2683G>A|p.?|248/7151|135/5655||2683| GT:AD:DP:GQ 0/1:12,15:27:48 +17 41263044 . A G . . clinvar_clinsig=benign;clinvar_rcv=RCV000191458;clinvar_vcv=VCV000209512;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-4494T>C|p.?|248/7088|135/5592||4494|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4494T>C|p.?|188/7028|-7/5451||4494|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-4494T>C|p.?|154/3682|135/2280||4494|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4494T>C|p.?|242/3696|135/2100||4494|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4494T>C|p.?|248/7151|135/5655||4494| GT:AD:DP:GQ 0/1:7,7:14:48 +17 41263117 . C CA . . ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-4568_135-4567insT|p.?|248/7088|135/5592||4568|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4568_-7-4567insT|p.?|188/7028|-7/5451||4568|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-4568_135-4567insT|p.?|154/3682|135/2280||4568|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4568_135-4567insT|p.?|242/3696|135/2100||4568|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4568_135-4567insT|p.?|248/7151|135/5655||4568| GT:AD:DP:GQ 0/1:13,10:23:34 +17 41263566 . T C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191462;clinvar_vcv=VCV000209516;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+4177A>G|p.?|247/7088|134/5592||-4177|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5016A>G|p.?|188/7028|-7/5451||5016|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+4177A>G|p.?|153/3682|134/2280||-4177|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+4177A>G|p.?|241/3696|134/2100||-4177|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+4177A>G|p.?|247/7151|134/5655||-4177| GT:AD:DP:GQ 0/1:11,8:19:48 +17 41264146 . G A . . clinvar_clinsig=benign;clinvar_rcv=RCV000191465;clinvar_vcv=VCV000209519;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3597C>T|p.?|247/7088|134/5592||-3597|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5596C>T|p.?|188/7028|-7/5451||5596|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3597C>T|p.?|153/3682|134/2280||-3597|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3597C>T|p.?|241/3696|134/2100||-3597|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3597C>T|p.?|247/7151|134/5655||-3597| GT:AD:DP:GQ 0/1:13,7:20:45 +17 41264364 . A G . . clinvar_clinsig=benign;clinvar_rcv=RCV000191467;clinvar_vcv=VCV000209521;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3379T>C|p.?|247/7088|134/5592||-3379|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5814T>C|p.?|188/7028|-7/5451||5814|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3379T>C|p.?|153/3682|134/2280||-3379|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3379T>C|p.?|241/3696|134/2100||-3379|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3379T>C|p.?|247/7151|134/5655||-3379| GT:AD:DP:GQ 0/1:8,16:24:45 +17 41264739 . C T . . clinvar_clinsig=benign;clinvar_rcv=RCV000255084;clinvar_vcv=VCV000264785;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3004G>A|p.?|247/7088|134/5592||-3004|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6189G>A|p.?|188/7028|-7/5451||6189|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3004G>A|p.?|153/3682|134/2280||-3004|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3004G>A|p.?|241/3696|134/2100||-3004|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3004G>A|p.?|247/7151|134/5655||-3004| GT:AD:DP:GQ:PS 0|1:14,15:29:48:41264739 +17 41264740 . TGA T . . ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3001_134+3002delTC|p.?|247/7088|134/5592||-3001|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6192_-7-6191delTC|p.?|188/7028|-7/5451||6191|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3001_134+3002delTC|p.?|153/3682|134/2280||-3001|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3001_134+3002delTC|p.?|241/3696|134/2100||-3001|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3001_134+3002delTC|p.?|247/7151|134/5655||-3001| GT:AD:DP:GQ 0/1:14,16:30:48 +17 41264743 . CT C . . ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2999delA|p.?|247/7088|134/5592||-2999|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6194delA|p.?|188/7028|-7/5451||6194|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2999delA|p.?|153/3682|134/2280||-2999|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2999delA|p.?|241/3696|134/2100||-2999|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2999delA|p.?|247/7151|134/5655||-2999| GT:AD:DP:GQ:PS 0|1:14,15:29:48:41264739 +17 41264749 . C G . . clinvar_clinsig=benign;clinvar_rcv=RCV000256095;clinvar_vcv=VCV000264823;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2994G>C|p.?|247/7088|134/5592||-2994|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6199G>C|p.?|188/7028|-7/5451||6199|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2994G>C|p.?|153/3682|134/2280||-2994|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2994G>C|p.?|241/3696|134/2100||-2994|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2994G>C|p.?|247/7151|134/5655||-2994| GT:AD:DP:GQ:PS 0|1:14,15:29:48:41264739 +17 41264750 . A T . . clinvar_clinsig=benign;clinvar_rcv=RCV000255162;clinvar_vcv=VCV000264824;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2993T>A|p.?|247/7088|134/5592||-2993|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6200T>A|p.?|188/7028|-7/5451||6200|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2993T>A|p.?|153/3682|134/2280||-2993|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2993T>A|p.?|241/3696|134/2100||-2993|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2993T>A|p.?|247/7151|134/5655||-2993| GT:AD:DP:GQ:PS 0|1:14,15:29:48:41264739 +17 41264751 . A AGGG . . ANN=AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2991_134+2992insCCC|p.?|247/7088|134/5592||-2992|,AGGG|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6202_-7-6201insCCC|p.?|188/7028|-7/5451||6202|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2991_134+2992insCCC|p.?|153/3682|134/2280||-2992|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2991_134+2992insCCC|p.?|241/3696|134/2100||-2992|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2991_134+2992insCCC|p.?|247/7151|134/5655||-2992| GT:AD:DP:GQ:PS 0|1:14,15:29:48:41264739 +17 41264753 . C T . . clinvar_clinsig=benign;clinvar_rcv=RCV000255582;clinvar_vcv=VCV000264819;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2990G>A|p.?|247/7088|134/5592||-2990|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6203G>A|p.?|188/7028|-7/5451||6203|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2990G>A|p.?|153/3682|134/2280||-2990|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2990G>A|p.?|241/3696|134/2100||-2990|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2990G>A|p.?|247/7151|134/5655||-2990| GT:AD:DP:GQ:PS 0|1:14,13:27:48:41264739 +17 41264755 . TGAAAC T . . ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2983_134+2987delGTTTC|p.?|247/7088|134/5592||-2983|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6210_-7-6206delGTTTC|p.?|188/7028|-7/5451||6206|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2983_134+2987delGTTTC|p.?|153/3682|134/2280||-2983|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2983_134+2987delGTTTC|p.?|241/3696|134/2100||-2983|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2983_134+2987delGTTTC|p.?|247/7151|134/5655||-2983| GT:AD:DP:GQ:PS 0|1:14,13:27:48:41264739 +17 41265776 . A G . . clinvar_clinsig=benign;clinvar_rcv=RCV000191470;clinvar_vcv=VCV000209524;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+1967T>C|p.?|247/7088|134/5592||-1967|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7226T>C|p.?|188/7028|-7/5451||7226|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+1967T>C|p.?|153/3682|134/2280||-1967|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1967T>C|p.?|241/3696|134/2100||-1967|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1967T>C|p.?|247/7151|134/5655||-1967| GT:AD:DP:GQ 0/1:23,14:37:44 +17 41266407 . C CT . . clinvar_clinsig=benign;clinvar_rcv=RCV000255595;clinvar_vcv=VCV000264777;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+1335_134+1336insA|p.?|247/7088|134/5592||-1336|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7858_-7-7857insA|p.?|188/7028|-7/5451||7858|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+1335_134+1336insA|p.?|153/3682|134/2280||-1336|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1335_134+1336insA|p.?|241/3696|134/2100||-1336|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1335_134+1336insA|p.?|247/7151|134/5655||-1336| GT:AD:DP:GQ 0/1:10,8:18:33 +17 41267050 . G A . . clinvar_clinsig=benign;clinvar_rcv=RCV000191477;clinvar_vcv=VCV000209531;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+693C>T|p.?|247/7088|134/5592||-693|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-8500C>T|p.?|188/7028|-7/5451||8500|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+693C>T|p.?|153/3682|134/2280||-693|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+693C>T|p.?|241/3696|134/2100||-693|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+693C>T|p.?|247/7151|134/5655||-693| GT:AD:DP:GQ 0/1:7,16:23:44 +17 41267518 . CA C . . ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+224delT|p.?|247/7088|134/5592||-224|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+8515delT|p.?|187/7028|-8/5451||-8515|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+224delT|p.?|153/3682|134/2280||-224|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+224delT|p.?|241/3696|134/2100||-224|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+224delT|p.?|247/7151|134/5655||-224| GT:AD:DP:GQ 0/1:11,8:19:35 +17 41268206 . A C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191483;clinvar_vcv=VCV000209537;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-410T>G|p.?|194/7088|81/5592||410|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7828T>G|p.?|187/7028|-8/5451||-7828|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-410T>G|p.?|100/3682|81/2280||410|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-410T>G|p.?|188/3696|81/2100||410|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-410T>G|p.?|194/7151|81/5655||410| GT:AD:DP:GQ:PS 0|1:13,9:22:46:41268206 +17 41268208 . C CT . . clinvar_clinsig=benign;clinvar_rcv=RCV000255730;clinvar_vcv=VCV000264808;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-413_81-412insA|p.?|194/7088|81/5592||413|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7825_-8+7826insA|p.?|187/7028|-8/5451||-7826|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-413_81-412insA|p.?|100/3682|81/2280||413|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-413_81-412insA|p.?|188/3696|81/2100||413|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-413_81-412insA|p.?|194/7151|81/5655||413| GT:AD:DP:GQ:PS 0|1:13,9:22:46:41268206 +17 41270229 . T G . . clinvar_clinsig=benign;clinvar_rcv=RCV000191491;clinvar_vcv=VCV000209545;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2433A>C|p.?|194/7088|81/5592||2433|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5805A>C|p.?|187/7028|-8/5451||-5805|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2433A>C|p.?|100/3682|81/2280||2433|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2433A>C|p.?|188/3696|81/2100||2433|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2433A>C|p.?|194/7151|81/5655||2433| GT:AD:DP:GQ 0/1:7,17:24:40 +17 41270277 . C T . . clinvar_clinsig=benign;clinvar_rcv=RCV000191493;clinvar_vcv=VCV000209547;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2481G>A|p.?|194/7088|81/5592||2481|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5757G>A|p.?|187/7028|-8/5451||-5757|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2481G>A|p.?|100/3682|81/2280||2481|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2481G>A|p.?|188/3696|81/2100||2481|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2481G>A|p.?|194/7151|81/5655||2481| GT:AD:DP:GQ 0/1:9,13:22:48 +17 41270463 . G A . . clinvar_clinsig=benign;clinvar_rcv=RCV000191497;clinvar_vcv=VCV000209551;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2667C>T|p.?|194/7088|81/5592||2667|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5571C>T|p.?|187/7028|-8/5451||-5571|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2667C>T|p.?|100/3682|81/2280||2667|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2667C>T|p.?|188/3696|81/2100||2667|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2667C>T|p.?|194/7151|81/5655||2667| GT:AD:DP:GQ 0/1:15,13:28:48 +17 41270666 . C A . . clinvar_clinsig=benign;clinvar_rcv=RCV000191498;clinvar_vcv=VCV000209552;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2870G>T|p.?|194/7088|81/5592||2870|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5368G>T|p.?|187/7028|-8/5451||-5368|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2870G>T|p.?|100/3682|81/2280||2870|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2870G>T|p.?|188/3696|81/2100||2870|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2870G>T|p.?|194/7151|81/5655||2870| GT:AD:DP:GQ 0/1:11,4:15:43 +17 41270778 . C CT . . clinvar_clinsig=benign;clinvar_rcv=RCV000256051;clinvar_vcv=VCV000264797;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2983_81-2982insA|p.?|194/7088|81/5592||2983|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5255_-8+5256insA|p.?|187/7028|-8/5451||-5256|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2983_81-2982insA|p.?|100/3682|81/2280||2983|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2983_81-2982insA|p.?|188/3696|81/2100||2983|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2983_81-2982insA|p.?|194/7151|81/5655||2983| GT:AD:DP:GQ 0/1:11,5:16:14 +17 41271293 . GA G . . ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-3498delT|p.?|194/7088|81/5592||3498|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+4740delT|p.?|187/7028|-8/5451||-4740|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-3498delT|p.?|100/3682|81/2280||3498|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-3498delT|p.?|188/3696|81/2100||3498|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-3498delT|p.?|194/7151|81/5655||3498| GT:AD:DP:GQ 0/1:10,10:20:48 +17 41273095 . G A . . clinvar_clinsig=benign;clinvar_rcv=RCV000191505;clinvar_vcv=VCV000209559;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2939C>T|p.?|193/7088|80/5592||-2939|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2939C>T|p.?|187/7028|-8/5451||-2939|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2939C>T|p.?|99/3682|80/2280||-2939|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2939C>T|p.?|187/3696|80/2100||-2939|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2939C>T|p.?|193/7151|80/5655||-2939| GT:AD:DP:GQ 0/1:12,8:20:47 +17 41273348 . T C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191507;clinvar_vcv=VCV000209561;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2686A>G|p.?|193/7088|80/5592||-2686|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2686A>G|p.?|187/7028|-8/5451||-2686|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2686A>G|p.?|99/3682|80/2280||-2686|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2686A>G|p.?|187/3696|80/2100||-2686|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2686A>G|p.?|193/7151|80/5655||-2686| GT:AD:DP:GQ 0/1:18,13:31:47 +17 41273379 . G C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191508;clinvar_vcv=VCV000209562;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2655C>G|p.?|193/7088|80/5592||-2655|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2655C>G|p.?|187/7028|-8/5451||-2655|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2655C>G|p.?|99/3682|80/2280||-2655|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2655C>G|p.?|187/3696|80/2100||-2655|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2655C>G|p.?|193/7151|80/5655||-2655| GT:AD:DP:GQ 0/1:19,14:33:47 +17 41273537 . A C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191510;clinvar_vcv=VCV000209564;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2497T>G|p.?|193/7088|80/5592||-2497|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2497T>G|p.?|187/7028|-8/5451||-2497|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2497T>G|p.?|99/3682|80/2280||-2497|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2497T>G|p.?|187/3696|80/2100||-2497|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2497T>G|p.?|193/7151|80/5655||-2497| GT:AD:DP:GQ 0/1:14,19:33:48 +17 41274778 . G A . . clinvar_clinsig=benign;clinvar_rcv=RCV000191511;clinvar_vcv=VCV000209565;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+1256C>T|p.?|193/7088|80/5592||-1256|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1256C>T|p.?|187/7028|-8/5451||-1256|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+1256C>T|p.?|99/3682|80/2280||-1256|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1256C>T|p.?|187/3696|80/2100||-1256|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1256C>T|p.?|193/7151|80/5655||-1256| GT:AD:DP:GQ 0/1:11,16:27:48 +17 41274906 . G A . . clinvar_clinsig=benign;clinvar_rcv=RCV000191514;clinvar_vcv=VCV000209568;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+1128C>T|p.?|193/7088|80/5592||-1128|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1128C>T|p.?|187/7028|-8/5451||-1128|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+1128C>T|p.?|99/3682|80/2280||-1128|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1128C>T|p.?|187/3696|80/2100||-1128|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1128C>T|p.?|193/7151|80/5655||-1128| GT:AD:DP:GQ 0/1:17,10:27:47 +17 41275081 . G GA . . clinvar_clinsig=benign;clinvar_rcv=RCV000191515;clinvar_vcv=VCV000209569;ANN=GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+952_80+953insT|p.?|193/7088|80/5592||-953|,GA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+952_-8+953insT|p.?|187/7028|-8/5451||-953|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+952_80+953insT|p.?|99/3682|80/2280||-953|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+952_80+953insT|p.?|187/3696|80/2100||-953|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+952_80+953insT|p.?|193/7151|80/5655||-953| GT:AD:DP:GQ 0/1:10,12:22:47 +17 41275151 . G C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191516;clinvar_vcv=VCV000209570;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+883C>G|p.?|193/7088|80/5592||-883|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+883C>G|p.?|187/7028|-8/5451||-883|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+883C>G|p.?|99/3682|80/2280||-883|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+883C>G|p.?|187/3696|80/2100||-883|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+883C>G|p.?|193/7151|80/5655||-883| GT:AD:DP:GQ 0/1:15,13:28:48 +17 41275366 . GTTTTTTT G . . ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+661_80+667delAAAAAAA|p.?|193/7088|80/5592||-661|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+661_-8+667delAAAAAAA|p.?|187/7028|-8/5451||-661|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+661_80+667delAAAAAAA|p.?|99/3682|80/2280||-661|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+661_80+667delAAAAAAA|p.?|187/3696|80/2100||-661|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+661_80+667delAAAAAAA|p.?|193/7151|80/5655||-661| GT:AD:DP:GQ 0/1:10,11:21:48 +17 41275645 . A G . . clinvar_clinsig=benign;clinvar_rcv=RCV000191517;clinvar_vcv=VCV000209571;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+389T>C|p.?|193/7088|80/5592||-389|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+389T>C|p.?|187/7028|-8/5451||-389|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+389T>C|p.?|99/3682|80/2280||-389|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+389T>C|p.?|187/3696|80/2100||-389|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+389T>C|p.?|193/7151|80/5655||-389| GT:AD:DP:GQ 0/1:15,17:32:48 +17 41276247 . A G . . gnomad_exomes_an=31318;gnomad_exomes_hom=1611;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000111495;clinvar_vcv=VCV000125468;ANN=G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-19-115T>C|p.?|95/7088|-19/5592||115|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-115T>C|p.?|89/7028|-106/5451||115|,G|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||115|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-115T>C|p.?|89/3696|-19/2100||115|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-115T>C|p.?|95/7151|-19/5655||115| GT:AD:DP:GQ 0/1:18,10:28:44 +17 41276348 . T C . . clinvar_clinsig=benign;clinvar_rcv=RCV000191520;clinvar_vcv=VCV000209574;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-19-216A>G|p.?|95/7088|-19/5592||216|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-216A>G|p.?|89/7028|-106/5451||216|,C|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||216|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-216A>G|p.?|89/3696|-19/2100||216|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-216A>G|p.?|95/7151|-19/5655||216| GT:AD:DP:GQ 0/1:17,13:30:47 +17 41277187 . G C . . gnomad_exomes_an=29432;gnomad_exomes_hom=4088;gnomad_exomes_het=6345;gnomad_genomes_an=128296;gnomad_genomes_hom=11705;gnomad_genomes_het=29182;clinvar_clinsig=benign;clinvar_rcv=RCV000169537;clinvar_vcv=VCV000189123;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-20+101C>G|p.?|94/7088|-20/5592||-101|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-107+107C>G|p.?|88/7028|-107/5451||-107|,C|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||1055|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-20+107C>G|p.?|88/3696|-20/2100||-107|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-20+101C>G|p.?|94/7151|-20/5655||-101| GT:AD:DP:GQ 0/1:14,14:28:48 +MT 152 . T C . . . GT:GQ:AD:DP 1/1:98:2,10582:10584 +MT 263 . A G . . . GT:GQ:AD:DP 1/1:98:0,7628:7628 +MT 302 . A AC . . . GT:GQ:AD:DP 1/1:97:40,3496:3536 +MT 310 . T TC . . . GT:GQ:AD:DP 1/1:97:100,3642:3742 +MT 310 . T C . . . GT:GQ:AD:DP 0/1:22:3649,93:3742 +MT 539 . T A . . . GT:GQ:AD:DP 0/1:22:6115,290:6405 +MT 596 . T A . . . GT:GQ:AD:DP 0/1:18:7690,160:7850 +MT 605 . T A . . . GT:GQ:AD:DP 0/1:22:5916,142:6058 +MT 610 . T A . . . GT:GQ:AD:DP 0/1:3:5986,143:6129 +MT 616 . T A . . . GT:GQ:AD:DP 0/1:0:6178,83:6261 +MT 750 . A G . . . GT:GQ:AD:DP 1/1:98:1,7818:7819 +MT 1438 . A G . . . GT:GQ:AD:DP 1/1:98:2,9168:9170 +MT 2141 . T TAG . . . GT:GQ:AD:DP 0/1:20:6260,26:6286 +MT 2259 . C T . . . GT:GQ:AD:DP 1/1:98:3,7525:7528 +MT 2645 . G A . . . GT:GQ:AD:DP 0/1:22:9159,34:9193 +MT 3572 . T G . . . GT:GQ:AD:DP 0/1:22:7257,638:7895 +MT 3572 . T A . . . GT:GQ:AD:DP 0/1:21:7575,320:7895 +MT 3577 . A C . . . GT:GQ:AD:DP 0/1:22:7519,460:7979 +MT 3578 . T A . . . GT:GQ:AD:DP 0/1:22:7352,569:7921 +MT 3578 . T G . . . GT:GQ:AD:DP 0/1:22:7610,311:7921 +MT 3583 . A C . . . GT:GQ:AD:DP 0/1:22:7746,303:8049 +MT 3590 . T A . . . GT:GQ:AD:DP 0/1:22:6859,779:7638 +MT 3593 . T G . . . GT:GQ:AD:DP 0/1:1:7844,234:8078 +MT 3595 . A C . . . GT:GQ:AD:DP 0/1:21:7958,153:8111 +MT 3599 . T A . . . GT:GQ:AD:DP 0/1:22:7408,505:7913 +MT 3605 . T A . . . GT:GQ:AD:DP 0/1:22:5371,274:5645 +MT 3614 . T A . . . GT:GQ:AD:DP 0/1:20:5553,136:5689 +MT 3631 . T A . . . GT:GQ:AD:DP 0/1:20:5740,153:5893 +MT 3633 . T A . . . GT:GQ:AD:DP 0/1:11:5829,114:5943 +MT 4434 . T G . . . GT:GQ:AD:DP 0/1:1:7711,167:7878 +MT 4491 . G A . . . GT:GQ:AD:DP 0/1:14:6096,12:6108 +MT 4745 . A G . . . GT:GQ:AD:DP:PS 1|1:94:0,4255:4255:4745 +MT 4769 . A G . . . GT:GQ:AD:DP:PS 1|1:96:0,4115:4115:4745 +MT 6518 . C T . . . GT:GQ:AD:DP 0/1:21:9464,40:9504 +MT 7337 . G A . . . GT:GQ:AD:DP 1/1:93:2,8853:8855 +MT 8129 . A C . . . GT:GQ:AD:DP 0/1:20:7971,202:8173 +MT 8860 . A G . . . GT:GQ:AD:DP 1/1:92:0,4988:4988 +MT 13326 . T C . . . GT:GQ:AD:DP 1/1:98:2,9161:9163 +MT 13680 . C T . . . GT:GQ:AD:DP 1/1:98:25,5556:5581 +MT 13680 . C G . . . GT:GQ:AD:DP 0/1:26:5557,24:5581 +MT 13752 . T G . . . GT:GQ:AD:DP 0/1:22:4714,65:4779 +MT 13762 . T G . . . GT:GQ:AD:DP 0/1:22:4509,180:4689 +MT 13768 . T G . . . GT:GQ:AD:DP 0/1:22:4623,155:4778 +MT 13769 . T G . . . GT:GQ:AD:DP 0/1:22:4684,115:4799 +MT 14831 . G A . . . GT:GQ:AD:DP 1/1:98:17,8829:8846 +MT 14831 . G C . . . GT:GQ:AD:DP 0/1:50:8832,14:8846 +MT 14872 . C T . . . GT:GQ:AD:DP 1/1:98:5,6662:6667 +MT 14918 . G A . . . GT:GQ:AD:DP 0/1:21:6570,237:6807 +MT 15326 . A G . . . GT:GQ:AD:DP 1/1:98:1,7647:7648 +MT 16023 . G A . . . GT:GQ:AD:DP 0/1:52:2572,6705:9277 diff --git a/src/seqvars/prefilter/mod.rs b/src/seqvars/prefilter/mod.rs index e9745f7d..538bdd44 100644 --- a/src/seqvars/prefilter/mod.rs +++ b/src/seqvars/prefilter/mod.rs @@ -235,7 +235,7 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a ¶ms.prefilter_path, )?); let mut writer = - open_vcf_writer(&out_path_helpers.last().expect("just pushed").path_out()).await?; + open_vcf_writer(out_path_helpers.last().expect("just pushed").path_out()).await?; writer.write_header(&header).await.map_err(|e| { anyhow::anyhow!( "could not write header to {}: {}", diff --git a/src/seqvars/query/interpreter/genotype.rs b/src/seqvars/query/interpreter/genotype.rs index 24298769..78d06cf6 100644 --- a/src/seqvars/query/interpreter/genotype.rs +++ b/src/seqvars/query/interpreter/genotype.rs @@ -338,15 +338,13 @@ mod test { .into_iter() .collect(); let seq_var = SequenceVariant { - call_info: vec![ - (( - INDEX_NAME.into(), - CallInfo { - genotype: Some(sample_gt.into()), - ..Default::default() - }, - )), - ] + call_info: vec![( + INDEX_NAME.into(), + CallInfo { + genotype: Some(sample_gt.into()), + ..Default::default() + }, + )] .into_iter() .collect(), ..Default::default() diff --git a/src/strucvars/ingest/header.rs b/src/strucvars/ingest/header.rs index 0dad5291..4655daa0 100644 --- a/src/strucvars/ingest/header.rs +++ b/src/strucvars/ingest/header.rs @@ -39,6 +39,7 @@ fn caller_version(sv_caller: &mehari::annotate::strucvars::SvCaller) -> String { pub fn build_output_header( input_sample_names: &SampleNames, input_sv_callers: &[&mehari::annotate::strucvars::SvCaller], + id_mapping: Option<&indexmap::IndexMap>, pedigree: Option<&mehari::ped::PedigreeByName>, genomebuild: GenomeRelease, file_date: &str, @@ -192,23 +193,37 @@ pub fn build_output_header( .iter() .map(|(name, _)| name.clone()) .collect::>(); - let input_idv = input_sample_names.iter().cloned().collect::>(); + let input_idv = input_sample_names + .iter() + .map(|name| { + if let Some(id_mapping) = id_mapping { + id_mapping.get(name).expect("checked earlier") + } else { + name + } + }) + .cloned() + .collect::>(); if !ped_idv.eq(&input_idv) { anyhow::bail!( - "pedigree individuals = {:?} != input individuals: {:?}", + "pedigree individuals = {:?} != (mapped) input individuals: {:?}", &ped_idv, &input_idv ) } for name in input_sample_names { + let name = if let Some(id_mapping) = id_mapping { + id_mapping.get(name).expect("checked earlier") + } else { + name + }; + let i = pedigree .individuals .get(name) .expect("checked equality above"); - if input_sample_names.contains(&i.name) { - builder = builder.add_sample_name(i.name.clone()); - } + builder = builder.add_sample_name(i.name.clone()); // Add SAMPLE entry. builder = builder.insert( @@ -243,6 +258,11 @@ pub fn build_output_header( } } else { for name in input_sample_names { + let name = if let Some(id_mapping) = id_mapping { + id_mapping.get(name).expect("checked earlier") + } else { + name + }; builder = builder.add_sample_name(name.clone()); } } @@ -312,6 +332,7 @@ mod test { let output_vcf_header = super::build_output_header( input_vcf_header.sample_names(), &sv_caller_refs, + None, Some(&pedigree), crate::common::GenomeRelease::Grch37, "20230421", @@ -358,6 +379,7 @@ mod test { let output_vcf_header = super::build_output_header( input_vcf_header.sample_names(), &sv_caller_refs, + None, Some(&pedigree), crate::common::GenomeRelease::Grch38, "20230421", diff --git a/src/strucvars/ingest/mod.rs b/src/strucvars/ingest/mod.rs index b70d29ba..2e79968c 100644 --- a/src/strucvars/ingest/mod.rs +++ b/src/strucvars/ingest/mod.rs @@ -5,7 +5,6 @@ use crate::common::{self, worker_version, GenomeRelease}; use crate::flush_and_shutdown; use futures::future::join_all; use mehari::annotate::strucvars::guess_sv_caller; -use mehari::common::io::std::is_gz; use mehari::common::noodles::{open_vcf_writer, AsyncVcfReader, AsyncVcfWriter}; use noodles_vcf as vcf; use rand_core::SeedableRng; @@ -56,6 +55,9 @@ pub struct Args { /// Maximal number of variants to write out; optional. #[clap(long)] pub max_var_count: Option, + /// Per-file identifier mapping, either a JSON or @-prefixed path to JSON. + #[clap(long)] + pub id_mapping: Option, } async fn write_ingest_record( @@ -358,6 +360,50 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a tracing::info!("opening input file..."); let mut input_readers = open_vcf_readers(&args.path_in).await?; + tracing::info!("loading file identifier mappings..."); + let id_mappings = args + .id_mapping + .as_ref() + .map( + |id_mapping| -> Result { + let id_mappings = if id_mapping.starts_with('@') { + crate::common::id_mapping::FileIdentifierMappings::load_from_path( + id_mapping.trim_start_matches('@'), + ) + .map_err(|e| { + anyhow::anyhow!( + "could not load ID mapping from file {:?}: {}", + id_mapping.trim_start_matches('@'), + e + ) + }) + } else { + crate::common::id_mapping::FileIdentifierMappings::load_from_json(id_mapping) + .map_err(|e| { + anyhow::anyhow!( + "could not load ID mapping from JSON string {:?}: {}", + &id_mapping, + &e, + ) + }) + }?; + + let paths_in = args.path_in.iter().cloned().collect::>(); + let paths_mapped = id_mappings.file_names().iter().cloned().collect::>(); + + if paths_in != paths_mapped { + return Err(anyhow::anyhow!( + "input files and ID mappings do not match: {:?} != {:?}", + paths_in, + paths_mapped + )); + } + + Ok(id_mappings) + }, + ) + .transpose()?; + tracing::info!("guessing SV callers..."); let input_sv_callers = { let mut sv_callers = Vec::new(); @@ -377,12 +423,52 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a .into_iter() .collect::, _>>() .map_err(|e| anyhow::anyhow!("problem reading header: {}", e))?; - let sample_names = input_headers + let orig_sample_names = input_headers .first() .expect("must have at least one input file") .sample_names(); + let sample_names = orig_sample_names + .iter() + .map(|name| { + if let Some(id_mappings) = &id_mappings { + let mapping = id_mappings + .mapping_for_file(args.path_in.first().expect("count checked above")) + .expect("checked above"); + mapping + .get(name) + .cloned() + .ok_or_else(|| anyhow::anyhow!("no mapping for sample name: {}", name)) + } else { + Ok(name.clone()) + } + }) + .collect::, _>>()?; for (indexno, other_input_header) in input_headers.iter().enumerate().skip(1) { - if other_input_header.sample_names() != sample_names { + let other_sample_names = if let Some(id_mappings) = &id_mappings { + let mapping = id_mappings + .mapping_for_file(&args.path_in[indexno]) + .expect("checked above"); + other_input_header + .sample_names() + .iter() + .map(|s| { + mapping.get(s).cloned().ok_or_else(|| { + anyhow::anyhow!( + "no mapping for sample name: {} in file: {}", + s, + &args.path_in[indexno] + ) + }) + }) + .collect::, _>>()? + } else { + other_input_header + .sample_names() + .iter() + .cloned() + .collect::>() + }; + if other_sample_names != sample_names { return Err(anyhow::anyhow!( "input file #{} has different sample names than first one: {}", indexno, @@ -391,8 +477,13 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a } } let output_header = header::build_output_header( - sample_names, + &orig_sample_names, &input_sv_callers.iter().collect::>(), + id_mappings.as_ref().map(|id_mappings| { + id_mappings + .mapping_for_file(args.path_in.first().expect("count checked above")) + .expect("checked above") + }), Some(&pedigree), args.genomebuild, &args.file_date, @@ -401,8 +492,36 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a ) .map_err(|e| anyhow::anyhow!("problem building output header: {}", e))?; + // Use output file helper. + let out_path_helper = crate::common::s3::OutputPathHelper::new(&args.path_out)?; + { - let mut output_writer = open_vcf_writer(&args.path_out).await?; + // Map sample names in input headers. + let mapped_input_headers = if let Some(id_mappings) = &id_mappings { + let mut mapped_input_headers = Vec::new(); + for i in 0..input_headers.len() { + let mapping = id_mappings + .mapping_for_file(&args.path_in[i]) + .expect("checked above"); + let mut input_header = input_headers[i].clone(); + let orig_sample_names = input_header.sample_names().clone(); + input_header.sample_names_mut().clear(); + for sample_name in orig_sample_names { + let mapped_sample_name = + mapping.get(&sample_name).cloned().ok_or_else(|| { + anyhow::anyhow!("no mapping for sample name: {}", sample_name) + })?; + input_header.sample_names_mut().insert(mapped_sample_name); + } + mapped_input_headers.push(input_header); + } + mapped_input_headers + } else { + input_headers.clone() + }; + + // Perform actual writing + let mut output_writer = open_vcf_writer(out_path_helper.path_out()).await?; output_writer .write_header(&output_header) .await @@ -412,7 +531,7 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a &pedigree, &mut output_writer, &mut input_readers, - &input_headers, + &mapped_input_headers, &input_sv_callers, args, ) @@ -421,15 +540,8 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a flush_and_shutdown!(output_writer); } - if is_gz(&args.path_out) { - tracing::info!("Creating TBI index for BGZF VCF file..."); - crate::common::noodles::build_tbi(&args.path_out, &format!("{}.tbi", &args.path_out)) - .await - .map_err(|e| anyhow::anyhow!("problem building TBI: {}", e))?; - tracing::info!("... done writing TBI index"); - } else { - tracing::info!("(not building TBI index for plain text VCF file"); - } + out_path_helper.create_tbi_for_bgzf().await?; + out_path_helper.upload_for_s3().await?; tracing::info!( "All of `strucvars ingest` completed in {:?}", @@ -468,6 +580,7 @@ mod test { rng_seed: Some(42), file_date: String::from("20230421"), case_uuid: String::from("d2bad2ec-a75d-44b9-bd0a-83a3f1331b7c"), + id_mapping: None, }; super::run(&args_common, &args).await?; @@ -505,6 +618,7 @@ mod test { rng_seed: Some(42), file_date: String::from("20230421"), case_uuid: String::from("d2bad2ec-a75d-44b9-bd0a-83a3f1331b7c"), + id_mapping: None, }; super::run(&args_common, &args).await?; @@ -539,6 +653,7 @@ mod test { rng_seed: Some(42), file_date: String::from("20230421"), case_uuid: String::from("d2bad2ec-a75d-44b9-bd0a-83a3f1331b7c"), + id_mapping: None, }; super::run(&args_common, &args).await?; @@ -578,6 +693,7 @@ mod test { rng_seed: Some(42), file_date: String::from("20230421"), case_uuid: String::from("d2bad2ec-a75d-44b9-bd0a-83a3f1331b7c"), + id_mapping: None, }; super::run(&args_common, &args).await?; @@ -586,4 +702,105 @@ mod test { Ok(()) } + + #[tracing_test::traced_test] + #[tokio::test] + async fn smoke_test_singleton_with_id_mapping() -> Result<(), anyhow::Error> { + let tmpdir = temp_testdir::TempDir::default(); + + let args_common = Default::default(); + let args = super::Args { + max_var_count: None, + path_in: vec![ + String::from("tests/strucvars/ingest/dragen-cnv-min.vcf.gz"), + String::from("tests/strucvars/ingest/dragen-sv-min.vcf.gz"), + String::from("tests/strucvars/ingest/gcnv-min.vcf.gz"), + String::from("tests/strucvars/ingest/manta-min.vcf.gz"), + String::from("tests/strucvars/ingest/melt-min.vcf.gz"), + String::from("tests/strucvars/ingest/sniffles2-min.vcf.gz"), + ], + path_cov_vcf: vec![], + path_ped: "tests/strucvars/ingest/dragen-cnv-min.custom_id.ped".into(), + genomebuild: GenomeRelease::Grch37, + path_out: tmpdir + .join("out.vcf") + .to_str() + .expect("invalid path") + .into(), + min_overlap: 0.8, + slack_bnd: 50, + slack_ins: 50, + rng_seed: Some(42), + file_date: String::from("20230421"), + case_uuid: String::from("d2bad2ec-a75d-44b9-bd0a-83a3f1331b7c"), + id_mapping: Some( + r#" + { + "mappings": [ + { + "path": "tests/strucvars/ingest/dragen-cnv-min.vcf.gz", + "entries": [ + { + "src": "SAMPLE", + "dst": "my-custom-id" + } + ] + }, + { + "path": "tests/strucvars/ingest/dragen-sv-min.vcf.gz", + "entries": [ + { + "src": "SAMPLE", + "dst": "my-custom-id" + } + ] + }, + { + "path": "tests/strucvars/ingest/gcnv-min.vcf.gz", + "entries": [ + { + "src": "SAMPLE", + "dst": "my-custom-id" + } + ] + }, + { + "path": "tests/strucvars/ingest/manta-min.vcf.gz", + "entries": [ + { + "src": "SAMPLE", + "dst": "my-custom-id" + } + ] + }, + { + "path": "tests/strucvars/ingest/melt-min.vcf.gz", + "entries": [ + { + "src": "SAMPLE", + "dst": "my-custom-id" + } + ] + }, + { + "path": "tests/strucvars/ingest/sniffles2-min.vcf.gz", + "entries": [ + { + "src": "SAMPLE", + "dst": "my-custom-id" + } + ] + } + ] + } + "# + .into(), + ), + }; + super::run(&args_common, &args).await?; + + insta::assert_snapshot!(std::fs::read_to_string(&args.path_out)?); + + Ok(()) + } } diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__test__smoke_test_singleton_with_id_mapping.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__test__smoke_test_singleton_with_id_mapping.snap new file mode 100644 index 00000000..48dc8c26 --- /dev/null +++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__test__smoke_test_singleton_with_id_mapping.snap @@ -0,0 +1,77 @@ +--- +source: src/strucvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##fileDate=20230421 +##x-varfish-genome-build=GRCh37 +##SAMPLE= +##PEDIGREE= +##x-varfish-case-uuid=d2bad2ec-a75d-44b9-bd0a-83a3f1331b7c +##x-varfish-version= +##x-varfish-version= +##x-varfish-version= +##x-varfish-version= +##x-varfish-version= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT my-custom-id +1 1000 . N . . SVCLAIM=J;SVTYPE=INS;END=1000;SVLEN=1;callers=Melt GT:GQ:pec:pev:src:srv:amq:cn:anc:pc 1/1:2:1:1:2:2:.:.:.:. +1 1000 . N . . SVCLAIM=DJ;SVTYPE=DEL;END=1049;SVLEN=50;callers=Sniffles GT:GQ:pec:pev:src:srv:amq:cn:anc:pc 1/1:60:.:.:33:33:.:.:.:. +1 2000 . N . . SVCLAIM=J;SVTYPE=INS;END=2000;SVLEN=1;callers=Melt GT:GQ:pec:pev:src:srv:amq:cn:anc:pc 0/0:60:4:0:24:24:.:.:.:. +1 3000 . N . . SVCLAIM=J;SVTYPE=INS;END=3000;SVLEN=1;callers=Melt GT:GQ:pec:pev:src:srv:amq:cn:anc:pc 0/0:28:23:0:24:1:.:.:.:. +1 3000 . N . . SVCLAIM=J;SVTYPE=INV;END=3589;SVLEN=590;callers=Sniffles GT:GQ:pec:pev:src:srv:amq:cn:anc:pc 0/1:24:.:.:37:10:.:.:.:. +1 4000 . N . . SVCLAIM=DJ;SVTYPE=DUP;END=17584;SVLEN=13585;callers=Sniffles GT:GQ:pec:pev:src:srv:amq:cn:anc:pc 0/1:60:.:.:61:18:.:.:.:. +1 5000 . N N]chrUn_JTFH01000344v1_decoy:679] . . SVCLAIM=J;SVTYPE=BND;END=679;chr2=chrUn_JTFH01000344v1_decoy;callers=Sniffles GT:GQ:pec:pev:src:srv:amq:cn:anc:pc 0/1:15:.:.:31:8:.:.:.:. +1 1283844 . N . . SVCLAIM=D;SVTYPE=CNV;END=1284844;SVLEN=1001;callers=DragenCnv GT:GQ:pec:pev:src:srv:amq:cn:anc:pc 0/1:.:.:.:.:.:.:1:.:1 +1 1598413 . N . . SVCLAIM=DJ;SVTYPE=DEL;END=1598580;SVLEN=168;callers=DragenSv GT:GQ:pec:pev:src:srv:amq:cn:anc:pc 1/1:53:2:2:20:20:.:.:.:. +1 4124001 . N . . SVCLAIM=D;SVTYPE=DEL;END=4125000;SVLEN=1000;callers=Gcnv GT:GQ:pec:pev:src:srv:amq:cn:anc:pc 1:.:.:.:.:.:.:1:.:1 diff --git a/src/strucvars/mod.rs b/src/strucvars/mod.rs index da33e784..2197c9f7 100644 --- a/src/strucvars/mod.rs +++ b/src/strucvars/mod.rs @@ -1,5 +1,4 @@ pub mod aggregate; pub mod ingest; -pub mod pbs; pub mod query; pub mod txt_to_bin; diff --git a/src/strucvars/pbs.rs b/src/strucvars/pbs.rs deleted file mode 100644 index 07668675..00000000 --- a/src/strucvars/pbs.rs +++ /dev/null @@ -1,3 +0,0 @@ -//! Data structures for (de-)serialization as generated by `prost-build`. - -include!(concat!(env!("OUT_DIR"), "/varfish.v1.svs.rs")); diff --git a/src/strucvars/query/bgdbs.rs b/src/strucvars/query/bgdbs.rs index 4ce5e2de..e5585d85 100644 --- a/src/strucvars/query/bgdbs.rs +++ b/src/strucvars/query/bgdbs.rs @@ -9,10 +9,7 @@ use serde::{Deserialize, Serialize}; use strum_macros::{Display, EnumString}; use tracing::info; -use crate::{ - common::{trace_rss_now, GenomeRelease, CHROMS}, - strucvars::pbs, -}; +use crate::common::{trace_rss_now, GenomeRelease, CHROMS}; use super::{ schema::ChromRange, @@ -147,18 +144,20 @@ pub fn load_bg_db_records(path: &Path) -> Result { let fcontents = std::fs::read(path).map_err(|e| anyhow::anyhow!("error reading {:?}: {}", &path, e))?; - let bg_db = pbs::BackgroundDatabase::decode(std::io::Cursor::new(fcontents)) + let bg_db = crate::pbs::svs::BackgroundDatabase::decode(std::io::Cursor::new(fcontents)) .map_err(|e| anyhow::anyhow!("error decoding {:?}: {}", &path, e))?; let record_count = bg_db.records.len(); for record in bg_db.records.into_iter() { let chrom_no = record.chrom_no as usize; - let begin = match pbs::SvType::try_from(record.sv_type).expect("invalid sv_type") { - pbs::SvType::Bnd | pbs::SvType::Ins => record.start - 2, - _ => record.start - 1, - }; - let end = match pbs::SvType::try_from(record.sv_type).expect("invalid sv_type") { - pbs::SvType::Bnd | pbs::SvType::Ins => record.start - 1, + let begin = + match crate::pbs::svs::SvType::try_from(record.sv_type).expect("invalid sv_type") { + crate::pbs::svs::SvType::Bnd | crate::pbs::svs::SvType::Ins => record.start - 2, + _ => record.start - 1, + }; + let end = match crate::pbs::svs::SvType::try_from(record.sv_type).expect("invalid sv_type") + { + crate::pbs::svs::SvType::Bnd | crate::pbs::svs::SvType::Ins => record.start - 1, _ => record.stop, }; let key = begin..end; @@ -167,13 +166,15 @@ pub fn load_bg_db_records(path: &Path) -> Result { result.records[chrom_no].push(BgDbRecord { begin: record.start - 1, end: record.stop, - sv_type: match pbs::SvType::try_from(record.sv_type).expect("invalid sv_type") { - pbs::SvType::Del => SvType::Del, - pbs::SvType::Dup => SvType::Dup, - pbs::SvType::Inv => SvType::Inv, - pbs::SvType::Ins => SvType::Ins, - pbs::SvType::Bnd => SvType::Bnd, - pbs::SvType::Cnv => SvType::Cnv, + sv_type: match crate::pbs::svs::SvType::try_from(record.sv_type) + .expect("invalid sv_type") + { + crate::pbs::svs::SvType::Del => SvType::Del, + crate::pbs::svs::SvType::Dup => SvType::Dup, + crate::pbs::svs::SvType::Inv => SvType::Inv, + crate::pbs::svs::SvType::Ins => SvType::Ins, + crate::pbs::svs::SvType::Bnd => SvType::Bnd, + crate::pbs::svs::SvType::Cnv => SvType::Cnv, }, count: record.count, }); diff --git a/src/strucvars/query/clinvar.rs b/src/strucvars/query/clinvar.rs index a64e3737..a6b48945 100644 --- a/src/strucvars/query/clinvar.rs +++ b/src/strucvars/query/clinvar.rs @@ -13,11 +13,6 @@ use super::{ schema::{Pathogenicity, StructuralVariant, SvType}, }; -/// Data structures for (de-)serialization as generated by `prost-build`. -pub mod pbs { - include!(concat!(env!("OUT_DIR"), "/varfish.v1.clinvar.rs")); -} - /// Alias for the interval tree that we use. type IntervalTree = ArrayBackedIntervalTree; @@ -27,7 +22,7 @@ type IntervalTree = ArrayBackedIntervalTree; #[derive(Default, Debug)] pub struct ClinvarSv { /// Records, stored by chromosome. - pub records: Vec>, + pub records: Vec>, /// Interval trees, stored by chromosome. pub trees: Vec, } @@ -39,7 +34,7 @@ impl ClinvarSv { chrom_range: &ChromRange, chrom_map: &IndexMap, min_patho: Option, - ) -> Vec { + ) -> Vec { let chrom_idx = *chrom_map .get(&chrom_range.chromosome) .expect("invalid chromosome"); @@ -107,7 +102,7 @@ pub fn load_clinvar_sv( std::path::Path::new(path_db).join(format!("{}/strucvars/clinvar.bin", genome_release)); let fcontents = std::fs::read(&path).map_err(|e| anyhow::anyhow!("error reading {:?}: {}", &path, e))?; - let bg_db = pbs::SvDatabase::decode(std::io::Cursor::new(fcontents)) + let bg_db = crate::pbs::clinvar::SvDatabase::decode(std::io::Cursor::new(fcontents)) .map_err(|e| anyhow::anyhow!("error decoding {:?}: {}", &path, e))?; let mut total_count = 0; diff --git a/src/strucvars/query/genes.rs b/src/strucvars/query/genes.rs index 348131e4..ae5fa38b 100644 --- a/src/strucvars/query/genes.rs +++ b/src/strucvars/query/genes.rs @@ -7,7 +7,7 @@ use prost::Message; use serde::Deserialize; use tracing::info; -use crate::{common::GenomeRelease, strucvars::pbs}; +use crate::{common::GenomeRelease, pbs}; /// Information to store for the interlink table. #[derive(Default, Debug)] @@ -40,7 +40,7 @@ fn load_xlink_db(path: &Path) -> Result { let fcontents = std::fs::read(path).map_err(|e| anyhow::anyhow!("error reading {:?}: {}", &path, e))?; - let xlink_db = pbs::XlinkDatabase::decode(std::io::Cursor::new(fcontents)) + let xlink_db = pbs::svs::XlinkDatabase::decode(std::io::Cursor::new(fcontents)) .map_err(|e| anyhow::anyhow!("error decoding {:?}: {}", &path, e))?; let mut total_count = 0; diff --git a/src/strucvars/query/masked.rs b/src/strucvars/query/masked.rs index 67c10d98..22e60c26 100644 --- a/src/strucvars/query/masked.rs +++ b/src/strucvars/query/masked.rs @@ -9,7 +9,7 @@ use tracing::info; use crate::{ common::{trace_rss_now, GenomeRelease, CHROMS}, - strucvars::pbs, + pbs, }; use super::{ @@ -141,7 +141,7 @@ pub fn load_masked_db_records(path: &Path) -> Result { let fcontents = std::fs::read(path).map_err(|e| anyhow::anyhow!("error reading {:?}: {}", &path, e))?; - let masked_db = pbs::MaskedDatabase::decode(std::io::Cursor::new(fcontents)) + let masked_db = pbs::svs::MaskedDatabase::decode(std::io::Cursor::new(fcontents)) .map_err(|e| anyhow::anyhow!("error decoding {:?}: {}", &path, e))?; for record in masked_db.records.into_iter() { @@ -316,8 +316,8 @@ mod test { let tmpdir = temp_testdir::TempDir::default(); let path_bin = tmpdir.join("masked_db.bin"); - let data = super::pbs::MaskedDatabase { - records: vec![super::pbs::MaskedDbRecord { + let data = super::pbs::svs::MaskedDatabase { + records: vec![super::pbs::svs::MaskedDbRecord { chrom_no: 0, start: 1, stop: 2, diff --git a/src/strucvars/query/schema.rs b/src/strucvars/query/schema.rs index f9f4196e..6554ed51 100644 --- a/src/strucvars/query/schema.rs +++ b/src/strucvars/query/schema.rs @@ -10,7 +10,7 @@ use regex::Regex; use serde::{Deserialize, Deserializer, Serialize}; use strum_macros::{Display, EnumIter, EnumString}; -use super::{clinvar, masked::MaskedBreakpointCount}; +use super::masked::MaskedBreakpointCount; /// Range with 1-based positions #[derive(Serialize, Deserialize, PartialEq, Debug, Clone)] @@ -1545,34 +1545,34 @@ impl StructuralVariant { } } -impl From for clinvar::pbs::VariationType { +impl From for crate::pbs::clinvar::VariationType { fn from(val: VariationType) -> Self { match val { - VariationType::Complex => clinvar::pbs::VariationType::Complex, - VariationType::Microsatellite => clinvar::pbs::VariationType::Microsatellite, - VariationType::Dup => clinvar::pbs::VariationType::Dup, - VariationType::Del => clinvar::pbs::VariationType::Del, - VariationType::Bnd => clinvar::pbs::VariationType::Bnd, - VariationType::Cnv => clinvar::pbs::VariationType::Cnv, - VariationType::Inv => clinvar::pbs::VariationType::Inv, - VariationType::Ins => clinvar::pbs::VariationType::Ins, + VariationType::Complex => crate::pbs::clinvar::VariationType::Complex, + VariationType::Microsatellite => crate::pbs::clinvar::VariationType::Microsatellite, + VariationType::Dup => crate::pbs::clinvar::VariationType::Dup, + VariationType::Del => crate::pbs::clinvar::VariationType::Del, + VariationType::Bnd => crate::pbs::clinvar::VariationType::Bnd, + VariationType::Cnv => crate::pbs::clinvar::VariationType::Cnv, + VariationType::Inv => crate::pbs::clinvar::VariationType::Inv, + VariationType::Ins => crate::pbs::clinvar::VariationType::Ins, } } } -impl TryInto for clinvar::pbs::VariationType { +impl TryInto for crate::pbs::clinvar::VariationType { type Error = anyhow::Error; fn try_into(self) -> Result { Ok(match self { - clinvar::pbs::VariationType::Complex => VariationType::Complex, - clinvar::pbs::VariationType::Microsatellite => VariationType::Microsatellite, - clinvar::pbs::VariationType::Dup => VariationType::Dup, - clinvar::pbs::VariationType::Del => VariationType::Del, - clinvar::pbs::VariationType::Bnd => VariationType::Bnd, - clinvar::pbs::VariationType::Cnv => VariationType::Cnv, - clinvar::pbs::VariationType::Inv => VariationType::Inv, - clinvar::pbs::VariationType::Ins => VariationType::Ins, + crate::pbs::clinvar::VariationType::Complex => VariationType::Complex, + crate::pbs::clinvar::VariationType::Microsatellite => VariationType::Microsatellite, + crate::pbs::clinvar::VariationType::Dup => VariationType::Dup, + crate::pbs::clinvar::VariationType::Del => VariationType::Del, + crate::pbs::clinvar::VariationType::Bnd => VariationType::Bnd, + crate::pbs::clinvar::VariationType::Cnv => VariationType::Cnv, + crate::pbs::clinvar::VariationType::Inv => VariationType::Inv, + crate::pbs::clinvar::VariationType::Ins => VariationType::Ins, }) } } @@ -1621,28 +1621,28 @@ pub enum Pathogenicity { Pathogenic, } -impl From for clinvar::pbs::Pathogenicity { +impl From for crate::pbs::clinvar::Pathogenicity { fn from(val: Pathogenicity) -> Self { match val { - Pathogenicity::Benign => clinvar::pbs::Pathogenicity::Benign, - Pathogenicity::LikelyBenign => clinvar::pbs::Pathogenicity::LikelyBenign, - Pathogenicity::Uncertain => clinvar::pbs::Pathogenicity::Uncertain, - Pathogenicity::LikelyPathogenic => clinvar::pbs::Pathogenicity::LikelyPathogenic, - Pathogenicity::Pathogenic => clinvar::pbs::Pathogenicity::Pathogenic, + Pathogenicity::Benign => crate::pbs::clinvar::Pathogenicity::Benign, + Pathogenicity::LikelyBenign => crate::pbs::clinvar::Pathogenicity::LikelyBenign, + Pathogenicity::Uncertain => crate::pbs::clinvar::Pathogenicity::Uncertain, + Pathogenicity::LikelyPathogenic => crate::pbs::clinvar::Pathogenicity::LikelyPathogenic, + Pathogenicity::Pathogenic => crate::pbs::clinvar::Pathogenicity::Pathogenic, } } } -impl TryInto for clinvar::pbs::Pathogenicity { +impl TryInto for crate::pbs::clinvar::Pathogenicity { type Error = anyhow::Error; fn try_into(self) -> Result { Ok(match self { - clinvar::pbs::Pathogenicity::Benign => Pathogenicity::Benign, - clinvar::pbs::Pathogenicity::LikelyBenign => Pathogenicity::LikelyBenign, - clinvar::pbs::Pathogenicity::Uncertain => Pathogenicity::Uncertain, - clinvar::pbs::Pathogenicity::LikelyPathogenic => Pathogenicity::LikelyPathogenic, - clinvar::pbs::Pathogenicity::Pathogenic => Pathogenicity::Pathogenic, + crate::pbs::clinvar::Pathogenicity::Benign => Pathogenicity::Benign, + crate::pbs::clinvar::Pathogenicity::LikelyBenign => Pathogenicity::LikelyBenign, + crate::pbs::clinvar::Pathogenicity::Uncertain => Pathogenicity::Uncertain, + crate::pbs::clinvar::Pathogenicity::LikelyPathogenic => Pathogenicity::LikelyPathogenic, + crate::pbs::clinvar::Pathogenicity::Pathogenic => Pathogenicity::Pathogenic, }) } } diff --git a/src/strucvars/txt_to_bin/clinvar/input.rs b/src/strucvars/txt_to_bin/clinvar/input.rs index 0ed3c9d2..401fc311 100644 --- a/src/strucvars/txt_to_bin/clinvar/input.rs +++ b/src/strucvars/txt_to_bin/clinvar/input.rs @@ -3,7 +3,7 @@ //! Note that not the full model is implemented, only the parts that are needed for the //! conversion of the ClinVar structural variants. -use crate::strucvars::query::clinvar::pbs::{Pathogenicity, VariationType}; +use crate::pbs::clinvar::{Pathogenicity, VariationType}; /// Accession of a ClinVar record. #[derive(Debug, serde::Deserialize, serde::Serialize)] diff --git a/src/strucvars/txt_to_bin/clinvar/mod.rs b/src/strucvars/txt_to_bin/clinvar/mod.rs index f0960341..c25f644e 100644 --- a/src/strucvars/txt_to_bin/clinvar/mod.rs +++ b/src/strucvars/txt_to_bin/clinvar/mod.rs @@ -8,7 +8,7 @@ use thousands::Separable; use crate::{ common::{build_chrom_map, trace_rss_now}, - strucvars::query::clinvar::pbs::{Pathogenicity, SvDatabase, SvRecord}, + pbs::clinvar::{Pathogenicity, SvDatabase, SvRecord}, }; pub mod input; @@ -71,10 +71,8 @@ fn convert_jsonl_to_protobuf( // there can be multiple measures, we consider them all for measure in &record.reference_clinvar_assertion.measures.measures { // convert from JSONL to protocolbuffers: variation type - let variation_type: Result< - crate::strucvars::query::clinvar::pbs::VariationType, - anyhow::Error, - > = measure.r#type.try_into(); + let variation_type: Result = + measure.r#type.try_into(); let variation_type = if let Ok(variation_type) = variation_type { variation_type as i32 } else { diff --git a/src/strucvars/txt_to_bin/clinvar/snapshots/varfish_server_worker__strucvars__txt_to_bin__clinvar__test__run_convert_jsonl_to_protobuf@Grch37.snap b/src/strucvars/txt_to_bin/clinvar/snapshots/varfish_server_worker__strucvars__txt_to_bin__clinvar__test__run_convert_jsonl_to_protobuf@Grch37.snap index 0293635e..1de492b9 100644 --- a/src/strucvars/txt_to_bin/clinvar/snapshots/varfish_server_worker__strucvars__txt_to_bin__clinvar__test__run_convert_jsonl_to_protobuf@Grch37.snap +++ b/src/strucvars/txt_to_bin/clinvar/snapshots/varfish_server_worker__strucvars__txt_to_bin__clinvar__test__run_convert_jsonl_to_protobuf@Grch37.snap @@ -1,293 +1,271 @@ --- -source: src/db/to_bin/clinvar/mod.rs +source: src/strucvars/txt_to_bin/clinvar/mod.rs expression: records --- -- chrom_no: 6 +- chromNo: 6 start: 101528 stop: 227833 - variation_type: 2 - pathogenicity: 0 + variationType: Dup rcv: 50292 -- chrom_no: 0 - start: 147228867 +- start: 147228867 stop: 147248577 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 50299 -- chrom_no: 6 +- chromNo: 6 start: 70356011 stop: 70537428 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 50317 -- chrom_no: 6 +- chromNo: 6 start: 10649696 stop: 11329787 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 50319 -- chrom_no: 20 +- chromNo: 20 start: 35734654 stop: 35879759 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 50337 -- chrom_no: 0 - start: 149041013 +- start: 149041013 stop: 149699420 - variation_type: 2 - pathogenicity: 0 + variationType: Dup rcv: 50339 -- chrom_no: 1 +- chromNo: 1 start: 242930600 stop: 243007359 - variation_type: 2 - pathogenicity: 0 + variationType: Dup rcv: 50458 -- chrom_no: 5 +- chromNo: 5 start: 259528 stop: 307998 - variation_type: 2 - pathogenicity: 0 + variationType: Dup rcv: 50474 -- chrom_no: 5 +- chromNo: 5 start: 259528 stop: 293493 - variation_type: 2 - pathogenicity: 0 + variationType: Dup rcv: 50518 -- chrom_no: 2 +- chromNo: 2 start: 2342852 stop: 2796629 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 50588 -- chrom_no: 10 +- chromNo: 10 start: 196966 stop: 244236 - variation_type: 3 - pathogenicity: 2 + variationType: Del + pathogenicity: Uncertain rcv: 50265 -- chrom_no: 0 - start: 148867551 +- start: 148867551 stop: 149699420 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50266 -- chrom_no: 1 +- chromNo: 1 start: 242930600 stop: 243059659 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50281 -- chrom_no: 22 +- chromNo: 22 start: 155231256 stop: 155251871 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50305 -- chrom_no: 22 +- chromNo: 22 start: 155231256 stop: 155251871 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50306 -- chrom_no: 0 - start: 149041013 +- start: 149041013 stop: 149699420 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50340 -- chrom_no: 4 +- chromNo: 4 start: 629455 stop: 820475 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50363 -- chrom_no: 11 +- chromNo: 11 start: 61091958 stop: 61921447 - variation_type: 3 - pathogenicity: 2 + variationType: Del + pathogenicity: Uncertain rcv: 50369 -- chrom_no: 1 +- chromNo: 1 start: 242930600 stop: 243007359 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50463 -- chrom_no: 5 +- chromNo: 5 start: 259528 stop: 307998 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50482 -- chrom_no: 15 +- chromNo: 15 start: 89817659 stop: 89861760 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 3614 -- chrom_no: 7 +- chromNo: 7 start: 53536328 stop: 53598019 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 4182 -- chrom_no: 7 +- chromNo: 7 start: 53537321 stop: 53574220 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 4183 -- chrom_no: 16 +- chromNo: 16 start: 3543558 stop: 3543559 - variation_type: 1 - pathogenicity: 4 + variationType: Microsatellite + pathogenicity: Pathogenic rcv: 4692 -- chrom_no: 4 +- chromNo: 4 start: 77436046 stop: 77444215 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 6747 -- chrom_no: 8 +- chromNo: 8 start: 139570503 stop: 139571539 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 7011 -- chrom_no: 21 +- chromNo: 21 start: 40742514 stop: 40762546 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 536272 -- chrom_no: 22 +- chromNo: 22 start: 69080668 stop: 69177002 - variation_type: 2 - pathogenicity: 4 + variationType: Dup + pathogenicity: Pathogenic rcv: 539041 -- chrom_no: 16 +- chromNo: 16 start: 56769999 stop: 56774226 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 554988 -- chrom_no: 22 +- chromNo: 22 start: 68890034 stop: 69177002 - variation_type: 2 - pathogenicity: 4 + variationType: Dup + pathogenicity: Pathogenic rcv: 633513 -- chrom_no: 3 +- chromNo: 3 start: 77116840 stop: 77134716 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 638336 -- chrom_no: 1 +- chromNo: 1 start: 233194517 stop: 233198703 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 638545 -- chrom_no: 22 +- chromNo: 22 start: 103031893 stop: 103045546 - variation_type: 2 - pathogenicity: 4 + variationType: Dup + pathogenicity: Pathogenic rcv: 640484 -- chrom_no: 1 +- chromNo: 1 start: 32358735 stop: 32358736 - variation_type: 2 - pathogenicity: 4 + variationType: Dup + pathogenicity: Pathogenic rcv: 6031 -- chrom_no: 11 +- chromNo: 11 start: 115120779 stop: 115120779 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 8451 -- chrom_no: 11 +- chromNo: 11 start: 114836472 stop: 114836472 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 8460 -- chrom_no: 0 - start: 228345537 +- start: 228345537 stop: 228345537 - variation_type: 3 - pathogenicity: 3 + variationType: Del + pathogenicity: LikelyPathogenic rcv: 256421 -- chrom_no: 13 +- chromNo: 13 start: 21775989 stop: 21776009 - variation_type: 3 - pathogenicity: 3 + variationType: Del + pathogenicity: LikelyPathogenic rcv: 256440 -- chrom_no: 20 +- chromNo: 20 start: 47545768 stop: 47545769 - variation_type: 2 - pathogenicity: 3 + variationType: Dup + pathogenicity: LikelyPathogenic rcv: 256480 -- chrom_no: 17 +- chromNo: 17 start: 43479513 stop: 43479513 - variation_type: 3 - pathogenicity: 3 + variationType: Del + pathogenicity: LikelyPathogenic rcv: 416351 -- chrom_no: 1 +- chromNo: 1 start: 179454322 stop: 179454323 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 256437 -- chrom_no: 16 +- chromNo: 16 start: 12899881 stop: 12899882 - variation_type: 2 - pathogenicity: 4 + variationType: Dup + pathogenicity: Pathogenic rcv: 5360 -- chrom_no: 2 +- chromNo: 2 start: 33100045 stop: 33100046 - variation_type: 0 - pathogenicity: 3 + pathogenicity: LikelyPathogenic rcv: 1849900 -- chrom_no: 13 +- chromNo: 13 start: 99641905 stop: 99641906 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 2265366 -- chrom_no: 22 +- chromNo: 22 start: 154156796 stop: 154227925 - variation_type: 0 - pathogenicity: 3 + pathogenicity: LikelyPathogenic rcv: 852264 -- chrom_no: 14 +- chromNo: 14 start: 38632006 stop: 38632007 - variation_type: 2 - pathogenicity: 4 + variationType: Dup + pathogenicity: Pathogenic rcv: 622432 -- chrom_no: 7 +- chromNo: 7 start: 144900557 stop: 144900557 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 622481 -- chrom_no: 0 - start: 1718780 +- start: 1718780 stop: 1718782 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 623933 - diff --git a/src/strucvars/txt_to_bin/clinvar/snapshots/varfish_server_worker__strucvars__txt_to_bin__clinvar__test__run_convert_jsonl_to_protobuf@Grch38.snap b/src/strucvars/txt_to_bin/clinvar/snapshots/varfish_server_worker__strucvars__txt_to_bin__clinvar__test__run_convert_jsonl_to_protobuf@Grch38.snap index 607b9160..cf58b30a 100644 --- a/src/strucvars/txt_to_bin/clinvar/snapshots/varfish_server_worker__strucvars__txt_to_bin__clinvar__test__run_convert_jsonl_to_protobuf@Grch38.snap +++ b/src/strucvars/txt_to_bin/clinvar/snapshots/varfish_server_worker__strucvars__txt_to_bin__clinvar__test__run_convert_jsonl_to_protobuf@Grch38.snap @@ -1,269 +1,254 @@ --- -source: src/db/to_bin/clinvar/mod.rs +source: src/strucvars/txt_to_bin/clinvar/mod.rs expression: records --- -- chrom_no: 6 +- chromNo: 6 start: 101528 stop: 227833 - variation_type: 2 - pathogenicity: 0 + variationType: Dup rcv: 50292 -- chrom_no: 0 - start: 147756734 +- start: 147756734 stop: 147776466 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 50299 -- chrom_no: 6 +- chromNo: 6 start: 70891025 stop: 71072442 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 50317 -- chrom_no: 6 +- chromNo: 6 start: 10610069 stop: 11290160 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 50319 -- chrom_no: 20 +- chromNo: 20 start: 7743711 stop: 7865746 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 50337 -- chrom_no: 1 +- chromNo: 1 start: 241988449 stop: 242065208 - variation_type: 2 - pathogenicity: 0 + variationType: Dup rcv: 50458 -- chrom_no: 5 +- chromNo: 5 start: 259528 stop: 307998 - variation_type: 2 - pathogenicity: 0 + variationType: Dup rcv: 50474 -- chrom_no: 5 +- chromNo: 5 start: 259528 stop: 293493 - variation_type: 2 - pathogenicity: 0 + variationType: Dup rcv: 50518 -- chrom_no: 2 +- chromNo: 2 start: 2301168 stop: 2754945 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 50588 -- chrom_no: 10 +- chromNo: 10 start: 196966 stop: 244236 - variation_type: 3 - pathogenicity: 2 + variationType: Del + pathogenicity: Uncertain rcv: 50265 -- chrom_no: 6 +- chromNo: 6 start: 61006478 stop: 62410831 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50266 -- chrom_no: 1 +- chromNo: 1 start: 241988449 stop: 242126245 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50281 -- chrom_no: 22 +- chromNo: 22 start: 156001591 stop: 156022206 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50305 -- chrom_no: 22 +- chromNo: 22 start: 156001591 stop: 156022206 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50306 -- chrom_no: 4 +- chromNo: 4 start: 629340 stop: 820360 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50363 -- chrom_no: 11 +- chromNo: 11 start: 60698177 stop: 61527666 - variation_type: 3 - pathogenicity: 2 + variationType: Del + pathogenicity: Uncertain rcv: 50369 -- chrom_no: 1 +- chromNo: 1 start: 241988449 stop: 242065208 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50463 -- chrom_no: 5 +- chromNo: 5 start: 259528 stop: 307998 - variation_type: 3 - pathogenicity: 0 + variationType: Del rcv: 50482 -- chrom_no: 15 +- chromNo: 15 start: 89751251 stop: 89795352 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 3614 -- chrom_no: 7 +- chromNo: 7 start: 52623768 stop: 52685459 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 4182 -- chrom_no: 7 +- chromNo: 7 start: 52624761 stop: 52661660 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 4183 -- chrom_no: 8 +- chromNo: 8 start: 32973498 stop: 33001604 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 4682 -- chrom_no: 16 +- chromNo: 16 start: 3640264 stop: 3640265 - variation_type: 1 - pathogenicity: 4 + variationType: Microsatellite + pathogenicity: Pathogenic rcv: 4692 -- chrom_no: 4 +- chromNo: 4 start: 78140222 stop: 78148391 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 6747 -- chrom_no: 8 +- chromNo: 8 start: 136676051 stop: 136677087 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 7011 -- chrom_no: 16 +- chromNo: 16 start: 58692638 stop: 58696865 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 554988 -- chrom_no: 3 +- chromNo: 3 start: 76195687 stop: 76213563 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 638336 -- chrom_no: 1 +- chromNo: 1 start: 232329807 stop: 232333993 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 638545 -- chrom_no: 1 +- chromNo: 1 start: 32133666 stop: 32133667 - variation_type: 2 - pathogenicity: 4 + variationType: Dup + pathogenicity: Pathogenic rcv: 6031 -- chrom_no: 11 +- chromNo: 11 start: 114682974 stop: 114682974 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 8451 -- chrom_no: 11 +- chromNo: 11 start: 114398667 stop: 114398667 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 8460 -- chrom_no: 0 - start: 228157836 +- start: 228157836 stop: 228157836 - variation_type: 3 - pathogenicity: 3 + variationType: Del + pathogenicity: LikelyPathogenic rcv: 256421 -- chrom_no: 13 +- chromNo: 13 start: 21307830 stop: 21307850 - variation_type: 3 - pathogenicity: 3 + variationType: Del + pathogenicity: LikelyPathogenic rcv: 256440 -- chrom_no: 20 +- chromNo: 20 start: 46125854 stop: 46125855 - variation_type: 2 - pathogenicity: 3 + variationType: Dup + pathogenicity: LikelyPathogenic rcv: 256480 -- chrom_no: 17 +- chromNo: 17 start: 45899548 stop: 45899548 - variation_type: 3 - pathogenicity: 3 + variationType: Del + pathogenicity: LikelyPathogenic rcv: 416351 -- chrom_no: 1 +- chromNo: 1 start: 178589595 stop: 178589596 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 256437 -- chrom_no: 16 +- chromNo: 16 start: 12996564 stop: 12996565 - variation_type: 2 - pathogenicity: 4 + variationType: Dup + pathogenicity: Pathogenic rcv: 5360 -- chrom_no: 13 +- chromNo: 13 start: 99175568 stop: 99175569 - variation_type: 2 - pathogenicity: 2 + variationType: Dup + pathogenicity: Uncertain rcv: 2265366 -- chrom_no: 14 +- chromNo: 14 start: 38339805 stop: 38339806 - variation_type: 2 - pathogenicity: 4 + variationType: Dup + pathogenicity: Pathogenic rcv: 622432 -- chrom_no: 7 +- chromNo: 7 start: 143818387 stop: 143818387 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 622481 -- chrom_no: 0 - start: 1787341 +- start: 1787341 stop: 1787343 - variation_type: 3 - pathogenicity: 4 + variationType: Del + pathogenicity: Pathogenic rcv: 623933 -- chrom_no: 7 +- chromNo: 7 start: 86652314 stop: 86662912 - variation_type: 2 - pathogenicity: 4 + variationType: Dup + pathogenicity: Pathogenic rcv: 498744 -- chrom_no: 9 +- chromNo: 9 start: 129162520 stop: 129249183 - variation_type: 4 - pathogenicity: 4 + variationType: Bnd + pathogenicity: Pathogenic rcv: 2468904 -- chrom_no: 6 +- chromNo: 6 start: 102178523 stop: 102225311 - variation_type: 4 - pathogenicity: 4 + variationType: Bnd + pathogenicity: Pathogenic rcv: 2468904 - diff --git a/src/strucvars/txt_to_bin/masked.rs b/src/strucvars/txt_to_bin/masked.rs index 561a17e5..907aff88 100644 --- a/src/strucvars/txt_to_bin/masked.rs +++ b/src/strucvars/txt_to_bin/masked.rs @@ -8,7 +8,7 @@ use thousands::Separable; use crate::{ common::{build_chrom_map, trace_rss_now}, - strucvars::pbs::{MaskedDatabase, MaskedDbRecord}, + pbs::svs::{MaskedDatabase, MaskedDbRecord}, }; /// Module with code supporting the parsing. diff --git a/src/strucvars/txt_to_bin/vardbs/mod.rs b/src/strucvars/txt_to_bin/vardbs/mod.rs index 6de75dbd..4e7ea6f0 100644 --- a/src/strucvars/txt_to_bin/vardbs/mod.rs +++ b/src/strucvars/txt_to_bin/vardbs/mod.rs @@ -10,9 +10,8 @@ use prost::Message; use thousands::Separable; use crate::common::{build_chrom_map, trace_rss_now}; -use crate::strucvars; +use crate::pbs::svs::{BackgroundDatabase, BgDbRecord}; use crate::strucvars::aggregate::output::Record as InhouseDbRecord; -use crate::strucvars::pbs::{BackgroundDatabase, BgDbRecord}; use crate::strucvars::query::schema::SvType; use self::input::InputRecord; @@ -61,12 +60,12 @@ where .unwrap_or_else(|| panic!("unknown chrom2: {:?}", &record.chromosome2)) as i32, sv_type: match record.sv_type { - SvType::Del => strucvars::pbs::SvType::Del, - SvType::Dup => strucvars::pbs::SvType::Dup, - SvType::Inv => strucvars::pbs::SvType::Inv, - SvType::Ins => strucvars::pbs::SvType::Ins, - SvType::Bnd => strucvars::pbs::SvType::Bnd, - SvType::Cnv => strucvars::pbs::SvType::Cnv, + SvType::Del => crate::pbs::svs::SvType::Del, + SvType::Dup => crate::pbs::svs::SvType::Dup, + SvType::Inv => crate::pbs::svs::SvType::Inv, + SvType::Ins => crate::pbs::svs::SvType::Ins, + SvType::Bnd => crate::pbs::svs::SvType::Bnd, + SvType::Cnv => crate::pbs::svs::SvType::Cnv, } as i32, start: record.begin + 1, stop: record.end, diff --git a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Dbvar-dbvar.snap b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Dbvar-dbvar.snap index 12b02b48..002f3b59 100644 --- a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Dbvar-dbvar.snap +++ b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Dbvar-dbvar.snap @@ -2,597 +2,399 @@ source: src/strucvars/txt_to_bin/vardbs/mod.rs expression: records --- -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1 stop: 2300000 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1 stop: 16200000 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 19818 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 22118 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 52000 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 82189 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 87466 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 88143 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 127330 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 356281 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 717485 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 10059 stop: 10059 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10351 stop: 13950 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10351 stop: 18900 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10377 stop: 177417 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10377 stop: 471368 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10377 stop: 812484 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10377 stop: 998287 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 10380 stop: 10380 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10469 stop: 23975 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 79204 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 79589 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 79864 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 80652 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 81231 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 81298 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 81448 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 81829 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 86730 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 87005 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 87096 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 87610 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 87845 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 89163 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 90440 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 91558 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 91591 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 92013 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 92392 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 177368 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 235938 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10501 stop: 78200 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10529 stop: 177368 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 10627 stop: 10627 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 10657 stop: 10657 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 10726 stop: 10726 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 10752 stop: 10752 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10801 stop: 14400 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10801 stop: 114750 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11099 stop: 47000 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11100 stop: 29200 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11189 stop: 36287 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11189 stop: 36787 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 11481 stop: 35484 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11599 stop: 72400 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11600 stop: 26700 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 11601 stop: 15700 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 11601 stop: 20700 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 12048 stop: 89237 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 12048 stop: 177033 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 12601 stop: 27100 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 12701 stop: 13400 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 12701 stop: 17551 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 12751 stop: 17501 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 12751 stop: 17551 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 12751 stop: 17751 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 12801 stop: 17501 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 12801 stop: 17551 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 13516 stop: 91073 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 14701 stop: 17501 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 14801 stop: 17501 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 14874 stop: 368661 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 15801 stop: 16100 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 16201 stop: 20700 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 18888 stop: 35451 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 19225 stop: 4401691 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 19742 stop: 28927 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 19851 stop: 20551 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 20141 stop: 242707 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 20141 stop: 356281 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 20141 stop: 606093 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 20141 stop: 887162 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 20701 stop: 95200 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 20848 stop: 20848 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 20853 stop: 20853 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 21064 stop: 28577 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 21064 stop: 35983 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 21411 stop: 82189 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 21829 stop: 88143 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 22118 stop: 22723 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 22118 stop: 35020 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 22723 stop: 23661 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 22801 stop: 26900 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 23661 stop: 24819 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 23946 stop: 88271 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 24301 stop: 25700 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 24301 stop: 26900 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 24301 stop: 128700 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 24310 stop: 35804991 count: 1 diff --git a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Dgv-dgv.snap b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Dgv-dgv.snap index dd8acf87..78ef9000 100644 --- a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Dgv-dgv.snap +++ b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Dgv-dgv.snap @@ -2,597 +2,377 @@ source: src/strucvars/txt_to_bin/vardbs/mod.rs expression: records --- -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1 +- start: 1 stop: 2300000 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 22118 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 10001 stop: 127330 count: 26 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 10191 +- start: 10191 stop: 10281 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10377 stop: 177417 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 10377 stop: 1018704 count: 186 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 10499 stop: 177368 count: 38 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10501 stop: 78200 count: 4 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 10726 stop: 10726 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11099 stop: 47000 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11100 stop: 29200 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11189 stop: 36787 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11599 stop: 72400 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 12601 stop: 27100 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 22118 stop: 22723 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 22118 stop: 35020 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 23661 stop: 24819 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 27980 stop: 177346 count: 14 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 27981 +- start: 27981 stop: 177346 count: 4 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 28989 stop: 35387 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 30626 stop: 35020 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 32400 stop: 35100 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 33700 stop: 36300 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 35020 stop: 41109 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 37489 stop: 43587 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 38889 stop: 40687 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 40901 stop: 51900 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 44989 stop: 51487 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 45531 +- start: 45531 stop: 121042 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 45789 stop: 46987 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 45889 stop: 53987 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 46501 stop: 71800 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 47689 stop: 51487 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 49298 stop: 82154 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 51800 +- start: 51800 stop: 52300 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 52089 stop: 54387 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 53700 +- start: 53700 stop: 63800 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 53900 +- start: 53900 stop: 54800 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 54665 stop: 54666 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 55100 +- start: 55100 stop: 56000 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 55394 +- start: 55394 stop: 86303 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 56400 +- start: 56400 stop: 57400 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 57600 +- start: 57600 stop: 58500 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 59599 stop: 59599 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 60901 stop: 71500 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 61200 +- start: 61200 stop: 64200 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 61723 stop: 792480 count: 47 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 61723 +- start: 61723 stop: 824124 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 61723 stop: 837073 count: 59 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 62399 +- start: 62399 stop: 62489 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 63489 stop: 66287 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 65800 +- start: 65800 stop: 66900 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 66008 +- start: 66008 stop: 79078 count: 8 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 66350 +- start: 66350 stop: 66427 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 66531 stop: 66532 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 66576 stop: 66577 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 66789 stop: 68887 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 68497 stop: 70627 count: 488 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 73202 +- start: 73202 stop: 137452 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 74600 +- start: 74600 stop: 75100 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 75800 +- start: 75800 stop: 90300 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 77882 stop: 88084 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 79210 stop: 79211 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 83999 stop: 86600 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 88084 stop: 91317 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 90069 stop: 90069 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 90179 stop: 90179 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 90259 stop: 90259 count: 6 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 91000 +- start: 91000 stop: 92100 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 91317 stop: 93605 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 91317 stop: 125400 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 91589 stop: 98387 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 93001 stop: 116200 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 93605 stop: 95437 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 93889 stop: 96487 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 95078 stop: 95078 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 95437 stop: 96652 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 96652 stop: 98749 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 98749 stop: 105358 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 99689 stop: 100887 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 101801 stop: 126400 count: 13 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 103089 stop: 105787 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 105358 stop: 120257 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 106699 stop: 119600 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 106789 stop: 109187 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 106789 stop: 111287 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 106800 stop: 112800 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 109889 stop: 111187 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 116700 stop: 118900 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 120257 stop: 124525 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 121042 +- start: 121042 stop: 137674 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 121042 stop: 170730 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 122200 stop: 125000 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 125400 stop: 129243 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 125400 stop: 176984 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 126200 stop: 128500 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 129243 stop: 133502 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 130299 stop: 144500 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 135100 stop: 148500 count: 1 diff --git a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@DgvGs-dgv_gs.snap b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@DgvGs-dgv_gs.snap index 8e20618e..58290e4d 100644 --- a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@DgvGs-dgv_gs.snap +++ b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@DgvGs-dgv_gs.snap @@ -2,597 +2,347 @@ source: src/strucvars/txt_to_bin/vardbs/mod.rs expression: records --- -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 82189 count: 13 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10001 stop: 127330 count: 30 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10499 stop: 235938 count: 13 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 21064 stop: 35983 count: 12 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 46501 stop: 71800 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 49298 stop: 98602 count: 16 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 49298 +- start: 49298 stop: 98602 count: 16 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 61723 +- start: 61723 stop: 356542 count: 37 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 70007 stop: 88084 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 86778 stop: 91967 count: 13 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 87433 +- start: 87433 stop: 89163 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 91317 stop: 125400 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 121042 stop: 176984 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 136181 +- start: 136181 stop: 137811 count: 5 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 227601 stop: 267719 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 317720 stop: 351915 count: 12 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 317770 stop: 471337 count: 9 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 348092 +- start: 348092 stop: 461014 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 350531 stop: 435382 count: 16 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 404112 +- start: 404112 stop: 471337 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 437342 stop: 468644 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 459944 stop: 464929 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 460229 stop: 471368 count: 14 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 521413 +- start: 521413 stop: 575095 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 521413 stop: 706368 count: 4 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 521413 stop: 850675 count: 6 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 521553 stop: 546384 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 522577 +- start: 522577 stop: 641599 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 544966 stop: 569604 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 546384 stop: 549347 count: 13 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 563896 stop: 570775 count: 24 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 564452 +- start: 564452 stop: 574333 count: 4 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 564582 +- start: 564582 stop: 570178 count: 4 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 637238 stop: 730328 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 668630 stop: 851378 count: 63 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 712111 stop: 764840 count: 202 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 713044 +- start: 713044 stop: 755966 count: 4 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 723901 stop: 727245 count: 25 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 724314 +- start: 724314 stop: 727245 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 738914 stop: 809773 count: 20 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 751887 stop: 762622 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 754201 +- start: 754201 stop: 759100 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 766101 +- start: 766101 stop: 809773 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 766408 +- start: 766408 stop: 769112 count: 195 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 769117 stop: 852664 count: 60 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 775292 +- start: 775292 stop: 792588 count: 16 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 812998 stop: 1708649 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 834801 +- start: 834801 stop: 1029900 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 850017 stop: 1097335 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 869249 +- start: 869249 stop: 870860 count: 71 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 869310 stop: 870645 count: 130 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 869497 +- start: 869497 stop: 870645 count: 277 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 873391 +- start: 873391 stop: 874049 count: 8 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 947113 +- start: 947113 stop: 948003 count: 5 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 963659 +- start: 963659 stop: 964567 count: 242 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 964980 +- start: 964980 stop: 965488 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1010973 stop: 1014683 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1011188 +- start: 1011188 stop: 1014828 count: 15 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1034317 stop: 1035340 count: 30 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1058898 +- start: 1058898 stop: 1058993 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1074379 stop: 1076572 count: 19 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1137003 stop: 1138283 count: 9 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1142700 +- start: 1142700 stop: 1143161 count: 939 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1183198 +- start: 1183198 stop: 1183861 count: 92 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1223189 +- start: 1223189 stop: 1226049 count: 49 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1223580 stop: 1225633 count: 5 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1226063 +- start: 1226063 stop: 1314437 count: 26 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1285180 +- start: 1285180 stop: 1287127 count: 9 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1285340 stop: 1286900 count: 24 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1302378 +- start: 1302378 stop: 1302882 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1352531 +- start: 1352531 stop: 1453590 count: 19 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1385069 stop: 1405538 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1387455 +- start: 1387455 stop: 1443716 count: 59 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1393861 stop: 1431581 count: 22 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1400225 +- start: 1400225 stop: 1409107 count: 34 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1414245 +- start: 1414245 stop: 1416792 count: 30 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1415099 +- start: 1415099 stop: 1462190 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1432368 stop: 1470064 count: 12 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1443538 +- start: 1443538 stop: 1445764 count: 112 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1465911 +- start: 1465911 stop: 1466268 count: 346 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1500941 +- start: 1500941 stop: 1672603 count: 7 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1522874 +- start: 1522874 stop: 1524674 count: 30 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1540850 stop: 1541970 count: 8 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1540930 +- start: 1540930 stop: 1541970 count: 56 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1559466 stop: 1683706 count: 5 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1582548 +- start: 1582548 stop: 1647400 count: 5 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1584529 +- start: 1584529 stop: 1685076 count: 36 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1598413 +- start: 1598413 stop: 1598601 count: 450 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1616990 +- start: 1616990 stop: 1653672 count: 6 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1620684 +- start: 1620684 stop: 1692321 count: 322 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1627805 stop: 1692321 count: 80 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1634170 stop: 1655791 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1635205 +- start: 1635205 stop: 1680442 count: 20 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1642103 stop: 1672603 count: 7 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1649047 +- start: 1649047 stop: 1650677 count: 69 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1658945 +- start: 1658945 stop: 1691900 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1662938 +- start: 1662938 stop: 1672603 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1866297 +- start: 1866297 stop: 1867172 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1910347 +- start: 1910347 stop: 1911917 count: 16 diff --git a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Exac-exac.snap b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Exac-exac.snap index 203c650e..bbfe0c5c 100644 --- a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Exac-exac.snap +++ b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@Exac-exac.snap @@ -2,597 +2,371 @@ source: src/strucvars/txt_to_bin/vardbs/mod.rs expression: records --- -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 69089 stop: 899565 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 69089 stop: 949863 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 861409 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 861409 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 866474 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 871281 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 883988 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 892658 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 892658 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 900576 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 901999 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 901999 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 901999 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 909749 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 861263 +- start: 861263 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 861263 +- start: 861263 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 957847 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 970709 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 861263 +- start: 861263 stop: 981650 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 985976 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 985976 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 985976 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 987200 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 861263 +- start: 861263 stop: 1025811 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 861263 stop: 1159353 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 871150 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 878631 stop: 970709 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 879076 stop: 907535 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 880896 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 883868 +- start: 883868 stop: 889554 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 896671 +- start: 896671 stop: 899565 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 898715 +- start: 898715 stop: 900576 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 905655 +- start: 905655 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 905655 +- start: 905655 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 905655 +- start: 905655 stop: 912007 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 905655 +- start: 905655 stop: 912007 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 905655 stop: 985976 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 908878 +- start: 908878 stop: 909960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 948952 stop: 957847 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 976856 +- start: 976856 stop: 985976 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 977334 stop: 985976 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1018272 stop: 1025811 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1102484 stop: 1120527 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1111010 stop: 1111779 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1117119 stop: 1226079 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1117119 stop: 1237431 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1117739 stop: 1119476 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1117739 stop: 1120527 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1117739 stop: 1223221 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1117739 stop: 1256479 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1117739 stop: 1267323 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1117739 +- start: 1117739 stop: 1451473 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1139412 stop: 1342602 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1152890 stop: 1164178 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1152890 stop: 1164178 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1179569 +- start: 1179569 stop: 1444692 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1190581 stop: 1203377 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1190581 stop: 1203377 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1198724 +- start: 1198724 stop: 1203377 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1222146 +- start: 1222146 stop: 1236077 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1222146 stop: 1237431 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1225649 +- start: 1225649 stop: 1226079 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1225855 +- start: 1225855 stop: 1226525 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1225855 stop: 1451473 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1233200 stop: 1233498 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1233391 stop: 1249750 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1237366 stop: 1238664 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1245967 +- start: 1245967 stop: 1260027 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1245967 stop: 1278143 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1245967 stop: 1278143 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1245967 stop: 1463247 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1250202 stop: 1251003 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1262289 +- start: 1262289 stop: 1263148 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1262289 +- start: 1262289 stop: 1289491 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1262289 +- start: 1262289 stop: 1289491 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1262289 +- start: 1262289 stop: 1342404 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1267016 stop: 1334056 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1293834 stop: 1461916 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1309179 stop: 1460676 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1322609 +- start: 1322609 stop: 1342404 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1323155 +- start: 1323155 stop: 1389883 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1328160 +- start: 1328160 stop: 1337641 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1328774 stop: 1334691 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1328774 +- start: 1328774 stop: 1337641 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1333611 stop: 1337641 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1337461 stop: 1342404 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1337461 stop: 1342404 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1337461 stop: 1342602 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1337461 stop: 1342602 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1337461 stop: 1342602 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1342287 stop: 1342404 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1342287 stop: 1342404 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1342287 stop: 1342404 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1342287 stop: 1342404 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1342287 stop: 1342404 count: 1 diff --git a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@G1k-g1k.snap b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@G1k-g1k.snap index b5aaaec0..3fd6da22 100644 --- a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@G1k-g1k.snap +++ b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@G1k-g1k.snap @@ -2,597 +2,336 @@ source: src/strucvars/txt_to_bin/vardbs/mod.rs expression: records --- -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 645710 stop: 645710 count: 35 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 668630 stop: 850204 count: 60 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 713044 stop: 755966 count: 205 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 738570 +- start: 738570 stop: 742020 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 766600 +- start: 766600 stop: 769112 count: 181 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 773090 stop: 852664 count: 61 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 775292 +- start: 775292 stop: 791968 count: 15 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 794496 +- start: 794496 stop: 799549 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 812283 stop: 812283 count: 58 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 813866 stop: 813866 count: 9 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 873391 +- start: 873391 stop: 874042 count: 7 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 939918 +- start: 939918 stop: 939968 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 947113 +- start: 947113 stop: 948003 count: 4 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 963826 stop: 974172 count: 42 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 988572 +- start: 988572 stop: 988623 count: 235 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1019492 +- start: 1019492 stop: 1019819 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1058898 +- start: 1058898 stop: 1058978 count: 299 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1086817 +- start: 1086817 stop: 1087023 count: 333 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1142714 +- start: 1142714 stop: 1143140 count: 919 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1161693 +- start: 1161693 stop: 1161756 count: 338 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1171539 stop: 1179729 count: 65 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1240709 +- start: 1240709 stop: 1240791 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1249799 stop: 1265722 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1294138 +- start: 1294138 stop: 1294195 count: 16 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1304952 stop: 1323528 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1388953 +- start: 1388953 stop: 1410796 count: 41 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1392382 +- start: 1392382 stop: 1423433 count: 40 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 1393861 stop: 1427383 count: 63 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1400225 +- start: 1400225 stop: 1409107 count: 34 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1417868 +- start: 1417868 stop: 1417928 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1424924 +- start: 1424924 stop: 1462190 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1438168 +- start: 1438168 stop: 1449503 count: 7 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1441334 +- start: 1441334 stop: 1443842 count: 7 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1443538 +- start: 1443538 stop: 1445747 count: 108 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 1517860 stop: 1517860 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1519512 +- start: 1519512 stop: 1520127 count: 13 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1522876 +- start: 1522876 stop: 1524674 count: 29 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1582548 +- start: 1582548 stop: 1645946 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 1595368 stop: 1612441 count: 34 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1601719 +- start: 1601719 stop: 1682577 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 1609210 stop: 1615827 count: 43 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1626665 +- start: 1626665 stop: 1681048 count: 118 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 1627805 stop: 1673809 count: 252 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1649047 +- start: 1649047 stop: 1650523 count: 67 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1649620 +- start: 1649620 stop: 1650651 count: 66 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1772216 +- start: 1772216 stop: 1773658 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1922946 +- start: 1922946 stop: 1924578 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2024547 +- start: 2024547 stop: 2027383 count: 20 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 2028833 stop: 2052740 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2162106 +- start: 2162106 stop: 2163200 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2303828 +- start: 2303828 stop: 2320328 count: 5 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2372200 +- start: 2372200 stop: 2374164 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 2374226 stop: 2379823 count: 26 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 2397655 stop: 2401469 count: 96 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2407712 +- start: 2407712 stop: 2407853 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2524546 +- start: 2524546 stop: 2527727 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2623324 +- start: 2623324 stop: 2623405 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2630903 +- start: 2630903 stop: 2630960 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 2684305 stop: 2719507 count: 10 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2693016 +- start: 2693016 stop: 2697186 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2701516 +- start: 2701516 stop: 2701566 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2704855 +- start: 2704855 stop: 2704917 count: 11 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2813287 +- start: 2813287 stop: 2813338 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2813548 +- start: 2813548 stop: 2813618 count: 22 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 2847963 stop: 2898365 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2848661 +- start: 2848661 stop: 2850131 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2911536 +- start: 2911536 stop: 2911850 count: 1175 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 2918659 +- start: 2918659 stop: 2919946 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 2920631 stop: 3005757 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 2937832 stop: 2979482 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 3009447 stop: 3137148 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 3011887 stop: 3011887 count: 63 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 3063073 +- start: 3063073 stop: 3063279 count: 7 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 3098371 +- start: 3098371 stop: 3098489 count: 596 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 3144724 stop: 3209782 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 3186949 +- start: 3186949 stop: 3187104 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 3209922 +- start: 3209922 stop: 3212186 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 3481851 +- start: 3481851 stop: 3481916 count: 17 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 3488273 +- start: 3488273 stop: 3488330 count: 314 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 3508964 +- start: 3508964 stop: 3515259 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 3527608 stop: 3553912 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 3527725 stop: 3603484 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 3581723 +- start: 3581723 stop: 3582247 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 3670490 +- start: 3670490 stop: 3671676 count: 8 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 3672777 stop: 3685462 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 3698222 stop: 3711516 count: 4 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 3703963 stop: 3703963 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 3734485 stop: 3844788 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 3995268 stop: 3995268 count: 2459 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 3995323 stop: 4001974 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 4000527 stop: 4147217 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 4005849 stop: 4114592 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 4075955 +- start: 4075955 stop: 4077963 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 4155146 +- start: 4155146 stop: 4155460 count: 1479 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 4174656 +- start: 4174656 stop: 4174707 count: 4 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 4194291 +- start: 4194291 stop: 4196163 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 4197459 stop: 4220364 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 4204667 +- start: 4204667 stop: 4204717 count: 2405 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 4232074 +- start: 4232074 stop: 4233113 count: 2 diff --git a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadCnv4-gnomad-cnv.snap b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadCnv4-gnomad-cnv.snap index 6f117ad2..ceca06a0 100644 --- a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadCnv4-gnomad-cnv.snap +++ b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadCnv4-gnomad-cnv.snap @@ -2,189 +2,107 @@ source: src/strucvars/txt_to_bin/vardbs/mod.rs expression: records --- -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 925634 +- start: 925634 stop: 931187 count: 464277 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 925634 +- start: 925634 stop: 935994 count: 464296 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 925634 stop: 935994 count: 464292 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 925634 stop: 966359 count: 464272 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 925634 +- start: 925634 stop: 968686 count: 464297 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 925634 +- start: 925634 stop: 1062827 count: 464291 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 925634 stop: 1084604 count: 464287 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 935675 +- start: 935675 stop: 948701 count: 464297 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 940979 stop: 943475 count: 464294 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 940979 stop: 944898 count: 464262 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 940979 +- start: 940979 stop: 948330 count: 464296 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 942006 stop: 944898 count: 464294 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 943158 +- start: 943158 stop: 945751 count: 464297 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 948034 +- start: 948034 stop: 952237 count: 464297 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 948034 +- start: 948034 stop: 954621 count: 464297 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 960487 stop: 965817 count: 464295 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 960487 +- start: 960487 stop: 976739 count: 464295 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 961196 +- start: 961196 stop: 964057 count: 464296 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 970180 +- start: 970180 stop: 971621 count: 464297 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 970180 +- start: 970180 stop: 975355 count: 464297 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 970180 +- start: 970180 stop: 981271 count: 464294 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 970180 stop: 981271 count: 464297 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 972764 +- start: 972764 stop: 974402 count: 464297 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 974405 +- start: 974405 stop: 976739 count: 434899 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 998865 +- start: 998865 stop: 1008377 count: 453104 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 998865 +- start: 998865 stop: 1014638 count: 464297 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 998865 stop: 1022560 count: 464296 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1007979 +- start: 1007979 stop: 1035422 count: 464296 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1034787 stop: 1056216 count: 464284 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 1034787 stop: 1072673 count: 464293 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 1040822 +- start: 1040822 stop: 1048759 count: 464280 diff --git a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadSv2-gnomad_sv.snap b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadSv2-gnomad_sv.snap index dd84d10c..1bae0586 100644 --- a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadSv2-gnomad_sv.snap +++ b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadSv2-gnomad_sv.snap @@ -2,597 +2,364 @@ source: src/strucvars/txt_to_bin/vardbs/mod.rs expression: records --- -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 10641 stop: 10643 count: 140 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 20999 +- start: 20999 stop: 26000 count: 138 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 39999 stop: 47200 count: 852 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 50940 +- start: 50940 stop: 51053 count: 81 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 54664 stop: 54666 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 54719 stop: 54721 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 62398 +- start: 62398 stop: 62489 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 66349 +- start: 66349 stop: 66427 count: 12 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 66530 stop: 66532 count: 5 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 66575 stop: 66577 count: 5 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 79209 stop: 79211 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 86748 stop: 86750 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 121034 stop: 121130 count: 129 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 136999 stop: 155500 count: 2156 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 141474 stop: 155000 count: 127 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 149999 +- start: 149999 stop: 155000 count: 1075 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 151999 stop: 177400 count: 72 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 156999 stop: 166000 count: 380 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 167899 stop: 174000 count: 76 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 243915 +- start: 243915 stop: 244232 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 251747 stop: 251749 count: 7 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 317718 stop: 367000 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 319999 +- start: 319999 stop: 327650 count: 3283 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 353799 stop: 363550 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 353999 +- start: 353999 stop: 359000 count: 5225 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 360999 stop: 366100 count: 22 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 363999 +- start: 363999 stop: 401750 count: 4087 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 364299 +- start: 364299 stop: 370000 count: 659 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 366999 +- start: 366999 stop: 384100 count: 1978 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 368999 +- start: 368999 stop: 374000 count: 101 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 371199 +- start: 371199 stop: 376900 count: 332 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 375999 +- start: 375999 stop: 382450 count: 484 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 380499 +- start: 380499 stop: 386800 count: 48 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 383999 +- start: 383999 stop: 390000 count: 283 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 395499 stop: 471184 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 406349 +- start: 406349 stop: 415250 count: 1536 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 412999 stop: 461500 count: 40 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 433999 +- start: 433999 stop: 441000 count: 1560 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 439999 stop: 471050 count: 13 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 445999 +- start: 445999 stop: 461000 count: 695 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 455999 +- start: 455999 stop: 468000 count: 472 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 459499 stop: 467000 count: 26 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 460999 +- start: 460999 stop: 466000 count: 349 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 461999 stop: 470342 count: 1251 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 462999 +- start: 462999 stop: 468000 count: 167 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 521999 stop: 638000 count: 618 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 530885 stop: 530887 count: 13 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 530885 stop: 530887 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 531072 stop: 531074 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 531099 +- start: 531099 stop: 613750 count: 6666 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 531999 stop: 537000 count: 1330 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 535816 +- start: 535816 stop: 536117 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 535999 +- start: 535999 stop: 541000 count: 1055 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 536037 stop: 536215 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 544839 stop: 544841 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 547598 stop: 547802 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 548449 stop: 564400 count: 872 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 569999 stop: 580000 count: 698 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 569999 stop: 593000 count: 502 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 571749 +- start: 571749 stop: 585025 count: 3523 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 574749 +- start: 574749 stop: 581950 count: 534 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 582699 stop: 593000 count: 600 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 591099 +- start: 591099 stop: 596200 count: 366 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 598599 stop: 605000 count: 1028 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 603329 +- start: 603329 stop: 603403 count: 629 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 604999 stop: 613000 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 656999 +- start: 656999 stop: 665000 count: 54 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 667724 stop: 724000 count: 125 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 668629 stop: 668631 count: 189 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 668629 stop: 850205 count: 220 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 685999 stop: 700425 count: 3 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 711672 stop: 711674 count: 21 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 713366 stop: 713368 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 718807 stop: 718809 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 720319 stop: 720321 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 721937 stop: 721939 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 721937 stop: 773013 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 727999 stop: 733650 count: 680 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 728091 stop: 728093 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 728091 +- start: 728091 stop: 776880 count: 5 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 737016 stop: 737018 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 738609 +- start: 738609 stop: 742016 count: 12 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 744699 stop: 751000 count: 274 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 746763 +- start: 746763 stop: 747331 count: 35 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 750054 stop: 750056 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 754259 stop: 857641 count: 97 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 755402 stop: 755404 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 755451 stop: 756062 count: 35 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 755459 stop: 755461 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 755633 stop: 755635 count: 709 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 755706 +- start: 755706 stop: 755892 count: 816 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 755890 stop: 755892 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 755891 stop: 758321 count: 671 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 756038 stop: 756040 count: 467 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 756258 stop: 758459 count: 4180 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 756376 stop: 756378 count: 49 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 756571 stop: 758603 count: 38 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 757420 +- start: 757420 stop: 834328 count: 7 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 757478 stop: 758945 count: 3 diff --git a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadSv4-gnomad-sv.snap b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadSv4-gnomad-sv.snap index 4047007d..343aa5b6 100644 --- a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadSv4-gnomad-sv.snap +++ b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@GnomadSv4-gnomad-sv.snap @@ -2,14403 +2,13191 @@ source: src/strucvars/txt_to_bin/vardbs/mod.rs expression: records --- -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 10000 stop: 295666 count: 139 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 10434 stop: 10434 count: 8450 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 10440 stop: 10440 count: 466 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 10450 stop: 10450 count: 21691 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 10464 stop: 10464 count: 3117 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 10533 stop: 10533 count: 8036 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 10590 stop: 10590 count: 1655 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 11000 stop: 51000 count: 5857 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 12000 stop: 32000 count: 66 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 22000 +- start: 22000 stop: 30000 count: 1262 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 40000 +- start: 40000 stop: 47000 count: 12569 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 5 +- svType: Cnv start: 46000 stop: 99350 count: 55 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 48000 stop: 128000 count: 18823 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 51946 stop: 51946 count: 18 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 54390 stop: 54390 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 54771 stop: 54789 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 59101 +- start: 59101 stop: 59202 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 61303 stop: 61350 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 62399 +- start: 62399 stop: 62489 count: 2 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 1 +- svType: Dup start: 64000 stop: 74000 count: 6538 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 66086 stop: 66086 count: 1 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 66115 stop: 66115 count: 1408 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 66129 +- start: 66129 stop: 66613 count: 61 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 66156 stop: 66156 count: 2396 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 66205 stop: 66205 count: 14 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 66218 stop: 66218 count: 18988 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 66282 +- start: 66282 stop: 66570 count: 8 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 66311 +- start: 66311 stop: 66427 count: 9 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 66340 stop: 66394 count: 298 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 66350 +- start: 66350 stop: 66427 count: 165 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 3 +- svType: Ins start: 66452 stop: 66459 count: 1071 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 66574 stop: 66574 count: 13 -- chrom_no: 0 - chrom_no2: 0 - sv_type: 4 +- svType: Bnd start: 66606 stop: 66606 count: 21661 -- chrom_no: 0 - 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chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 159594 stop: 160265 count: 3 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 4 +- chromNo: 5 + chromNo2: 5 + svType: Bnd start: 159916 stop: 159916 count: 3 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 160000 stop: 170000 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 160059 stop: 164031 count: 1 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 161127 stop: 161784 count: 3 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 162920 stop: 163754 count: 21 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 165759 stop: 191162 count: 1 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 166068 stop: 166732 count: 75 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 166721 stop: 182311 count: 1 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 4 +- chromNo: 5 + chromNo2: 5 + svType: Bnd start: 166776 stop: 166776 count: 38 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 4 +- chromNo: 5 + chromNo2: 5 + svType: Bnd start: 166791 stop: 166791 count: 1 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 3 +- chromNo: 5 + chromNo2: 5 + svType: Ins start: 170955 stop: 170984 count: 4 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 171207 stop: 171267 count: 6 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 171265 stop: 182162 count: 8 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 171270 stop: 173524 count: 1256 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 171635 stop: 173581 count: 7 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 171735 stop: 173752 count: 8044 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 172971 stop: 173914 count: 3 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 3 +- chromNo: 5 + chromNo2: 5 + svType: Ins start: 173504 stop: 173507 count: 1 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 173692 stop: 174225 count: 1 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 174290 stop: 174567 count: 11 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 175833 stop: 175884 count: 3 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 176000 stop: 182000 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 176209 stop: 177244 count: 10 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 176712 stop: 177349 count: 76 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 177000 stop: 250000 count: 33 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 177131 stop: 290985 count: 5 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 179000 stop: 187000 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 180702 stop: 181349 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 3 +- chromNo: 5 + chromNo2: 5 + svType: Ins start: 185635 stop: 185686 count: 4818 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 186520 stop: 186640 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 187555 stop: 219694 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 4 +- chromNo: 5 + chromNo2: 5 + svType: Bnd start: 187749 stop: 187749 count: 96 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 4 +- chromNo: 5 + chromNo2: 5 + svType: Bnd start: 188466 stop: 188466 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 4 +- chromNo: 5 + chromNo2: 5 + svType: Bnd start: 188495 stop: 188495 count: 1 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 4 +- chromNo: 5 + chromNo2: 5 + svType: Bnd start: 188822 stop: 188822 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 190000 stop: 198000 count: 1 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 190310 stop: 190766 count: 6 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 192003 stop: 192249 count: 6 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 192853 stop: 196024 count: 3 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 193312 stop: 193406 count: 632 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 4 +- chromNo: 5 + chromNo2: 5 + svType: Bnd start: 193418 stop: 193418 count: 338 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 196403 stop: 199352 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 4 +- chromNo: 5 + chromNo2: 5 + svType: Bnd start: 196713 stop: 448092 count: 132 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 4 +- chromNo: 5 + chromNo2: 5 + svType: Bnd start: 196714 stop: 196714 count: 129 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 1 +- chromNo: 5 + chromNo2: 5 + svType: Dup start: 197539 stop: 303217 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 198109 stop: 198202 count: 9 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 198205 stop: 198288 count: 2 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 198996 stop: 199556 count: 100 -- chrom_no: 5 - chrom_no2: 5 - sv_type: 0 +- chromNo: 5 + chromNo2: 5 start: 199370 stop: 208011 count: 123 -- chrom_no: 6 - chrom_no2: 6 - sv_type: 0 +- chromNo: 6 + chromNo2: 6 start: 10000 stop: 16000 count: 4289 -- chrom_no: 6 - chrom_no2: 6 - sv_type: 1 +- chromNo: 6 + chromNo2: 6 + svType: Dup start: 10000 stop: 38000 count: 14 -- chrom_no: 6 - chrom_no2: 6 - sv_type: 1 +- chromNo: 6 + chromNo2: 6 + svType: Dup start: 10000 stop: 22000 count: 4 -- chrom_no: 6 - chrom_no2: 6 - sv_type: 4 +- chromNo: 6 + chromNo2: 6 + svType: Bnd start: 10082 stop: 10082 count: 55 -- chrom_no: 6 - 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chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 60000 stop: 1036000 count: 2 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 60000 stop: 268000 count: 30 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 61742 stop: 61824 count: 3 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 61817 stop: 61935 count: 18 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 61843 stop: 61965 count: 22 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 61843 stop: 61935 count: 150 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 64900 stop: 107200 count: 2823 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 65000 stop: 77000 count: 4827 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 65500 stop: 111250 count: 50053 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 73000 stop: 120000 count: 140 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 75639 stop: 75725 count: 1 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 76450 stop: 82000 count: 48221 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 81066 stop: 81365 count: 7 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 81235 stop: 81365 count: 1 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 3 +- chromNo: 7 + chromNo2: 7 + svType: Ins start: 81623 stop: 81638 count: 2 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 82508 stop: 83506 count: 46 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 83694 stop: 84117 count: 1 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 87223 stop: 87331 count: 7 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 87251 stop: 87412 count: 408 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 87265 stop: 87331 count: 1 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 3 +- chromNo: 7 + chromNo2: 7 + svType: Ins start: 87451 stop: 87452 count: 2 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 3 +- chromNo: 7 + chromNo2: 7 + svType: Ins start: 87493 stop: 87495 count: 35 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 90350 stop: 99150 count: 5319 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 93962 stop: 94480 count: 1 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 93962 stop: 94508 count: 9 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 94551 stop: 94793 count: 2 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 101700 stop: 107000 count: 35 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 103998 stop: 104728 count: 30 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 110387 stop: 120250 count: 2 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 124000 stop: 134550 count: 7 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 128000 stop: 135000 count: 10 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 4 +- chromNo: 7 + chromNo2: 7 + svType: Bnd start: 131743 stop: 131743 count: 313 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 136900 stop: 142750 count: 1 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 0 +- chromNo: 7 + chromNo2: 7 start: 138000 stop: 144000 count: 21403 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 144950 stop: 151500 count: 74 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 145000 stop: 151100 count: 8765 -- chrom_no: 7 - chrom_no2: 7 - sv_type: 1 +- chromNo: 7 + chromNo2: 7 + svType: Dup start: 148000 stop: 154000 count: 118 -- chrom_no: 7 - 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chrom_no2: 11 - sv_type: 4 +- chromNo: 11 + chromNo2: 11 + svType: Bnd start: 49107 stop: 49107 count: 2 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 49597 stop: 50118 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 4 +- chromNo: 11 + chromNo2: 11 + svType: Bnd start: 50810 stop: 50810 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 51945 stop: 52520 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 52215 stop: 154681 count: 5 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 52553 stop: 52699 count: 3 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 3 +- chromNo: 11 + chromNo2: 11 + svType: Ins start: 53327 stop: 53370 count: 32 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 53707 stop: 54348 count: 19 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 53812 stop: 54596 count: 2 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 53870 stop: 54477 count: 12 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 54151 stop: 54741 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 54484 stop: 55101 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 4 +- chromNo: 11 + chromNo2: 11 + svType: Bnd start: 55217 stop: 55217 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 4 +- chromNo: 11 + chromNo2: 11 + svType: Bnd start: 55702 stop: 55702 count: 7 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 55812 stop: 55873 count: 8 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 55956 stop: 56656 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 56008 stop: 56064 count: 9 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 56251 stop: 111293 count: 3 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 56293 stop: 56391 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 56588 stop: 57196 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 4 +- chromNo: 11 + chromNo2: 11 + svType: Bnd start: 56762 stop: 56762 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 56893 stop: 57563 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 57182 stop: 57533 count: 82 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 57201 stop: 63327 count: 2 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 57260 stop: 57856 count: 2 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 57281 stop: 57378 count: 1 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 57501 stop: 57562 count: 6 -- chrom_no: 11 - chrom_no2: 11 - sv_type: 0 +- chromNo: 11 + chromNo2: 11 start: 57941 stop: 58595 count: 1 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16000000 stop: 16024150 count: 120 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16003500 stop: 16249600 count: 1894 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16023000 stop: 16035000 count: 61522 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16023050 stop: 16030000 count: 4 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16023250 stop: 16111900 count: 1 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16024000 stop: 16030000 count: 12 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16036975 stop: 16042000 count: 92 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16042000 stop: 16052000 count: 3 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16042150 stop: 16051500 count: 1 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16043600 stop: 16110400 count: 7 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16043800 stop: 16052250 count: 90 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16044700 stop: 16053700 count: 32 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16045975 stop: 16052000 count: 4002 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16046500 stop: 16053200 count: 165 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16047475 stop: 16065000 count: 1 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16049050 stop: 16055500 count: 5382 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16049500 stop: 16057500 count: 5 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16049500 stop: 16056400 count: 27 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16049800 stop: 16066300 count: 55456 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16049800 stop: 16055000 count: 138 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16052600 stop: 16065000 count: 1 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16057900 stop: 16081500 count: 52901 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16058000 stop: 16064000 count: 41 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16059000 stop: 16064625 count: 1270 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16060000 stop: 16066475 count: 2642 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16060000 stop: 16110400 count: 41 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16060300 stop: 16067000 count: 1578 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16060600 stop: 16082000 count: 6 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16062775 stop: 16082000 count: 1 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16067800 stop: 16073000 count: 5 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16068550 stop: 16074000 count: 10 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16069000 stop: 16090000 count: 28 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16069150 stop: 16110400 count: 435 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16070800 stop: 16078000 count: 44120 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16070850 stop: 16110400 count: 51800 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16071000 stop: 16077100 count: 868 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16072750 stop: 16082000 count: 114 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16074000 stop: 16082200 count: 186 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16075000 stop: 16081275 count: 667 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16081975 stop: 16110400 count: 4442 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16093500 stop: 16100000 count: 91 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16106400 stop: 16112000 count: 55 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16110100 stop: 16232650 count: 406 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16227400 stop: 16259200 count: 780 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16258400 stop: 16290500 count: 178 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16259800 stop: 16280000 count: 14718 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16262000 stop: 16267000 count: 55 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16266400 stop: 16278000 count: 934 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16279000 stop: 16285800 count: 157 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16282600 stop: 16296400 count: 48121 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16282900 stop: 16296100 count: 570 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16283450 stop: 16315200 count: 2837 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16289150 stop: 16429050 count: 4774 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16291600 stop: 16296700 count: 36690 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16294600 stop: 16305700 count: 28 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16297600 stop: 16306000 count: 9619 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16298000 stop: 16304000 count: 10016 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16299000 stop: 16307200 count: 3025 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16301800 stop: 16307200 count: 152 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16302000 stop: 16307100 count: 49514 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16305000 stop: 16310000 count: 55 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16306000 stop: 16312300 count: 1194 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16306000 stop: 16313800 count: 739 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16306450 stop: 16312600 count: 41776 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16312000 stop: 16318000 count: 496 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16317050 stop: 16323300 count: 66 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16318000 stop: 16331500 count: 7717 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16327000 stop: 16332800 count: 23244 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16327000 stop: 16334500 count: 6890 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16332100 stop: 16344100 count: 36 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16338250 stop: 16348150 count: 13521 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16342000 stop: 16348000 count: 1611 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16345000 stop: 16351050 count: 91 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16352000 stop: 16362000 count: 3616 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16360000 stop: 16393000 count: 44257 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16362500 stop: 16372000 count: 3529 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16363000 stop: 16428100 count: 36 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16370000 stop: 16378900 count: 5241 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16371000 stop: 16376200 count: 15719 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16373350 stop: 16379100 count: 1893 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16380350 stop: 16387150 count: 10271 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16390900 stop: 16396000 count: 8703 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16414600 stop: 16456000 count: 28 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 16422000 stop: 16428050 count: 51848 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16422000 stop: 16440150 count: 18395 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16422000 stop: 16430000 count: 239 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16422000 stop: 16431050 count: 1783 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16422400 stop: 16428000 count: 91 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16422400 stop: 16429000 count: 81 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16432000 stop: 16437100 count: 2184 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16453900 stop: 16460800 count: 66 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16457450 stop: 16473100 count: 153 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 5 +- chromNo: 12 + chromNo2: 12 + svType: Cnv start: 16472450 stop: 16493950 count: 45 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16479000 stop: 16485000 count: 13289 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 1 +- chromNo: 12 + chromNo2: 12 + svType: Dup start: 16486300 stop: 16494100 count: 15824 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 18900048 stop: 18900434 count: 17 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 18900061 stop: 18900405 count: 21 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 18901224 stop: 18901819 count: 5 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 18901742 stop: 18902369 count: 185 -- chrom_no: 12 - chrom_no2: 12 - sv_type: 0 +- chromNo: 12 + chromNo2: 12 start: 18901968 stop: 18902959 count: 53 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 16022637 stop: 16096437 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 16022637 stop: 16037637 count: 2087 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 16038087 stop: 16045637 count: 11 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 16038537 stop: 16043637 count: 17470 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 16052637 stop: 16058637 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 16065637 stop: 16095987 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 16068037 stop: 16080637 count: 30 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 16070187 stop: 16075637 count: 36614 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 16079637 stop: 16086625 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 5 +- chromNo: 13 + chromNo2: 13 + svType: Cnv start: 16091637 stop: 16097937 count: 105 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18223523 stop: 18237230 count: 572 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18223848 stop: 18224220 count: 46 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18223869 stop: 18224246 count: 6 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18224224 stop: 18224256 count: 3 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18224237 stop: 18226123 count: 10 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18224329 stop: 18224895 count: 2 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18224637 stop: 18231837 count: 1027 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 5 +- chromNo: 13 + chromNo2: 13 + svType: Cnv start: 18224637 stop: 18273287 count: 28 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18224819 stop: 18224951 count: 2 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18224858 stop: 18225555 count: 61 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18225523 stop: 18249523 count: 6387 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18225523 stop: 18231637 count: 639 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18226114 stop: 18226404 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18226634 stop: 18226752 count: 14 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18227941 stop: 18228004 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18233260 stop: 18236498 count: 2 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18233523 stop: 18286523 count: 14935 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18233570 stop: 18234268 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18233952 stop: 18234003 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18234658 stop: 18234947 count: 5 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18235655 stop: 18235759 count: 2 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18235800 stop: 18235910 count: 9 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18235834 stop: 18235940 count: 133 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18236364 stop: 18239039 count: 41 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18237000 stop: 18237451 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18237828 stop: 18238155 count: 149 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18238068 stop: 18238111 count: 3 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18239416 stop: 18239751 count: 19 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18241057 stop: 18241200 count: 6 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18241958 stop: 18242116 count: 11 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18242089 stop: 18242384 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18242667 stop: 18243137 count: 87 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18242750 stop: 18242807 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18242789 stop: 18243545 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18244999 stop: 18245150 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18246024 stop: 18247566 count: 2 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18247629 stop: 18247777 count: 16 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 4 +- chromNo: 13 + chromNo2: 13 + svType: Bnd start: 18247733 stop: 18247733 count: 57 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18250441 stop: 18250492 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18252283 stop: 18252849 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18252537 stop: 18257637 count: 26348 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18253010 stop: 18253482 count: 3 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 4 +- chromNo: 13 + chromNo2: 13 + svType: Bnd start: 18253404 stop: 18253404 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18256433 stop: 18256618 count: 3 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18256474 stop: 18259029 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18257445 stop: 18257494 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18257813 stop: 18257940 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18258919 stop: 18259079 count: 2 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18259292 stop: 18259603 count: 7 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18259629 stop: 18260283 count: 2 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18259637 stop: 18268137 count: 23819 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18261155 stop: 18261294 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18261698 stop: 18261765 count: 73 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18263549 stop: 18263648 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18264346 stop: 18264514 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18267453 stop: 18267781 count: 89 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18269235 stop: 18269957 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18270523 stop: 18538637 count: 57 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18270933 stop: 18271228 count: 74 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18270935 stop: 18271350 count: 8 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18274772 stop: 18275214 count: 7 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18276080 stop: 18284630 count: 23356 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18277185 stop: 18277365 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18277673 stop: 18277698 count: 2 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18277790 stop: 18277824 count: 12 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18278165 stop: 18278624 count: 47 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18283194 stop: 18283714 count: 2 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18285237 stop: 18293523 count: 40 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18289523 stop: 18349523 count: 15 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18289903 stop: 18289959 count: 8 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18296942 stop: 18296972 count: 31 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18297523 stop: 18309523 count: 3 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18299148 stop: 18299182 count: 24 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 5 +- chromNo: 13 + chromNo2: 13 + svType: Cnv start: 18301523 stop: 18306637 count: 36 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18305196 stop: 18305198 count: 27 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18307932 stop: 18307981 count: 73 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18307933 stop: 18307981 count: 8 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18309523 stop: 18316137 count: 33 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 1 +- chromNo: 13 + chromNo2: 13 + svType: Dup start: 18309523 stop: 18329523 count: 55605 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18310327 stop: 18311051 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18311392 stop: 18311408 count: 264 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 3 +- chromNo: 13 + chromNo2: 13 + svType: Ins start: 18312378 stop: 18312396 count: 1 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18318708 stop: 18324523 count: 45 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18319031 stop: 18319110 count: 30 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18322380 stop: 18330523 count: 4 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 5 +- chromNo: 13 + chromNo2: 13 + svType: Cnv start: 18328637 stop: 18335637 count: 45 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18328680 stop: 18510180 count: 21 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18334137 stop: 18339523 count: 3 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18334863 stop: 18334999 count: 2 -- chrom_no: 13 - chrom_no2: 13 - sv_type: 0 +- chromNo: 13 + chromNo2: 13 start: 18335624 stop: 18335821 count: 6 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17000000 stop: 17009625 count: 17973 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 5 +- chromNo: 14 + chromNo2: 14 + svType: Cnv start: 17000000 stop: 17009550 count: 28 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17003750 stop: 17022000 count: 1827 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17012000 stop: 17021500 count: 913 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 5 +- chromNo: 14 + chromNo2: 14 + svType: Cnv start: 17021000 stop: 17086000 count: 78 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17024450 stop: 17131825 count: 6170 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17041000 stop: 17046500 count: 17637 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17046500 stop: 17051600 count: 603 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17051600 stop: 17059000 count: 23066 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17087750 stop: 17098000 count: 62843 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17087750 stop: 17108150 count: 20 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17091000 stop: 17098500 count: 2 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17091000 stop: 17105000 count: 6 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17091050 stop: 17458700 count: 39198 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17094000 stop: 17100000 count: 10 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17094500 stop: 17100000 count: 248 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17096000 stop: 17181800 count: 41599 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17096000 stop: 17101075 count: 594 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 5 +- chromNo: 14 + chromNo2: 14 + svType: Cnv start: 17097500 stop: 17114550 count: 36 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17100800 stop: 17106000 count: 35 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17114000 stop: 17137050 count: 1 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17122700 stop: 17137000 count: 67 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17126600 stop: 17137000 count: 48157 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17127000 stop: 17136400 count: 774 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 5 +- chromNo: 14 + chromNo2: 14 + svType: Cnv start: 17128000 stop: 17166000 count: 45 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17138000 stop: 17156600 count: 40710 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17154000 stop: 17208000 count: 33663 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17154225 stop: 17203750 count: 239 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17156450 stop: 17180825 count: 33943 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17165250 stop: 17172000 count: 55 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17165900 stop: 17172800 count: 51451 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17169000 stop: 17180000 count: 248 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17171900 stop: 17177450 count: 23511 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17172000 stop: 17179400 count: 3969 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17187000 stop: 17197250 count: 2769 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17187550 stop: 17202300 count: 26674 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17189000 stop: 17195000 count: 20533 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 5 +- chromNo: 14 + chromNo2: 14 + svType: Cnv start: 17193350 stop: 17320850 count: 21 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17196200 stop: 17202950 count: 42025 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17197350 stop: 17218550 count: 857 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17198000 stop: 17205000 count: 73 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17201900 stop: 17207000 count: 1 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17203000 stop: 17208250 count: 5 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17204000 stop: 17210800 count: 185 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17217950 stop: 17223000 count: 2974 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17218000 stop: 17224000 count: 262 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17220000 stop: 17245400 count: 42030 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17230700 stop: 17237000 count: 720 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17239175 stop: 17245475 count: 22948 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17243000 stop: 17264000 count: 41024 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17246000 stop: 17254250 count: 41540 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17254000 stop: 17287700 count: 30947 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17254000 stop: 17260000 count: 767 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17262900 stop: 17268000 count: 493 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17271350 stop: 17321000 count: 28162 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17273525 stop: 17285700 count: 25078 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17284850 stop: 17290850 count: 27066 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17285300 stop: 17299100 count: 28757 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17285675 stop: 17290925 count: 114 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17296250 stop: 17302000 count: 3 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17301500 stop: 17320850 count: 27795 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17313000 stop: 17319200 count: 644 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17321300 stop: 17327000 count: 66 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17325000 stop: 17331800 count: 1 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17327075 stop: 17340000 count: 71 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17327375 stop: 17344400 count: 23 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 0 +- chromNo: 14 + chromNo2: 14 start: 17330750 stop: 17339150 count: 31867 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17330900 stop: 17498450 count: 8 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17330950 stop: 17340000 count: 407 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17339950 stop: 17347000 count: 5 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17342000 stop: 17349100 count: 69 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 1 +- chromNo: 14 + chromNo2: 14 + svType: Dup start: 17344000 stop: 17358000 count: 69 -- chrom_no: 14 - chrom_no2: 14 - sv_type: 5 +- chromNo: 14 + chromNo2: 14 + svType: Cnv start: 17348825 stop: 17358100 count: 28 -- chrom_no: 14 - 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chrom_no2: 17 - sv_type: 1 +- chromNo: 17 + chromNo2: 17 + svType: Dup start: 71760 stop: 74950 count: 6 -- chrom_no: 17 - chrom_no2: 17 - sv_type: 0 +- chromNo: 17 + chromNo2: 17 start: 72094 stop: 72691 count: 1 -- chrom_no: 17 - chrom_no2: 17 - sv_type: 0 +- chromNo: 17 + chromNo2: 17 start: 72170 stop: 72253 count: 1 -- chrom_no: 17 - chrom_no2: 17 - sv_type: 1 +- chromNo: 17 + chromNo2: 17 + svType: Dup start: 72178 stop: 74930 count: 21 -- chrom_no: 17 - chrom_no2: 17 - sv_type: 0 +- chromNo: 17 + chromNo2: 17 start: 72220 stop: 72332 count: 3 -- chrom_no: 17 - chrom_no2: 17 - sv_type: 0 +- chromNo: 17 + chromNo2: 17 start: 72777 stop: 75278 count: 1 -- chrom_no: 17 - chrom_no2: 17 - sv_type: 0 +- chromNo: 17 + chromNo2: 17 start: 73187 stop: 76388 count: 1 -- chrom_no: 17 - chrom_no2: 17 - sv_type: 0 +- chromNo: 17 + chromNo2: 17 start: 73223 stop: 73993 count: 1 -- chrom_no: 18 - chrom_no2: 18 - sv_type: 1 +- chromNo: 18 + chromNo2: 18 + svType: Dup start: 60000 stop: 256000 count: 3792 -- chrom_no: 18 - 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chrom_no2: 19 - sv_type: 0 +- chromNo: 19 + chromNo2: 19 start: 73476 stop: 77723 count: 2 -- chrom_no: 19 - chrom_no2: 19 - sv_type: 0 +- chromNo: 19 + chromNo2: 19 start: 73504 stop: 84186 count: 2 -- chrom_no: 19 - chrom_no2: 19 - sv_type: 0 +- chromNo: 19 + chromNo2: 19 start: 76058 stop: 76708 count: 4 -- chrom_no: 19 - chrom_no2: 19 - sv_type: 3 +- chromNo: 19 + chromNo2: 19 + svType: Ins start: 76427 stop: 76478 count: 30 -- chrom_no: 19 - chrom_no2: 19 - sv_type: 0 +- chromNo: 19 + chromNo2: 19 start: 77186 stop: 77736 count: 6 -- chrom_no: 19 - chrom_no2: 19 - sv_type: 0 +- chromNo: 19 + chromNo2: 19 start: 77974 stop: 78113 count: 1 -- chrom_no: 19 - chrom_no2: 19 - sv_type: 4 +- chromNo: 19 + chromNo2: 19 + svType: Bnd start: 80842 stop: 80842 count: 2 -- chrom_no: 19 - chrom_no2: 19 - sv_type: 4 +- chromNo: 19 + chromNo2: 19 + svType: Bnd start: 80842 stop: 188556 count: 2 -- chrom_no: 19 - chrom_no2: 19 - sv_type: 0 +- chromNo: 19 + chromNo2: 19 start: 81225 stop: 93862 count: 3 -- chrom_no: 19 - 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chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10521000 stop: 10529250 count: 5714 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10525522 stop: 10526058 count: 950 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10525801 stop: 10526000 count: 3232 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10525831 stop: 10526029 count: 920 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10525993 stop: 10526058 count: 17 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10526361 stop: 10526438 count: 38 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10526375 stop: 10526530 count: 35 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10526487 stop: 10526995 count: 3364 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10526528 stop: 10526609 count: 99 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10526683 stop: 10527072 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10526958 stop: 10527086 count: 40 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10526998 stop: 10527095 count: 3 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10528174 stop: 10528753 count: 4 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10530530 stop: 10530683 count: 2 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10530538 stop: 10530702 count: 12 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10530548 stop: 10530689 count: 2 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10530551 stop: 10530690 count: 3 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10530587 stop: 10530625 count: 8 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10530660 stop: 10530851 count: 3 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10530698 stop: 10530855 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10530720 stop: 10530923 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10531088 stop: 10531577 count: 90 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10532165 stop: 10532216 count: 4 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10532550 stop: 10532563 count: 893 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10536516 stop: 10537104 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10559266 stop: 10559350 count: 5 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10562000 stop: 10568000 count: 35742 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10562000 stop: 10576500 count: 11272 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10571398 stop: 10571787 count: 429 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10571577 stop: 10571641 count: 16 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 4 +- chromNo: 21 + chromNo2: 21 + svType: Bnd start: 10571605 stop: 10571605 count: 179 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10571624 stop: 10571639 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10571661 stop: 10571738 count: 10 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10571676 stop: 10572728 count: 152 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10571685 stop: 10571742 count: 381 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10571705 stop: 10571792 count: 2 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10571709 stop: 10571788 count: 2 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10571709 stop: 10571776 count: 15 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10571737 stop: 10572037 count: 633 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10571750 stop: 10572048 count: 3020 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10571895 stop: 10571921 count: 632 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10571928 stop: 10572708 count: 1917 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10571952 stop: 10572007 count: 3266 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10572002 stop: 10572192 count: 96 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10572052 stop: 10572052 count: 10 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10572053 stop: 10572112 count: 6 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10572085 stop: 10572792 count: 5 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10572092 stop: 10572145 count: 6 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10572156 stop: 10572271 count: 157 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10572178 stop: 10572248 count: 7 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10572184 stop: 10572274 count: 132 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10572350 stop: 10572393 count: 2166 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10572536 stop: 10572619 count: 5 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10572608 stop: 10572728 count: 46 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10572628 stop: 10572960 count: 5 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10572642 stop: 10572745 count: 681 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10572686 stop: 10572798 count: 347 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10572737 stop: 10572758 count: 7256 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10577559 stop: 10577695 count: 3 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10577566 stop: 10577700 count: 3 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10577579 stop: 10577697 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10577579 stop: 10577683 count: 115 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10577580 stop: 10577691 count: 4 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10577612 stop: 10577689 count: 7 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10577843 stop: 10577881 count: 44 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10590000 stop: 10616100 count: 3719 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10590750 stop: 10596275 count: 5410 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10593176 stop: 10593227 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10598229 stop: 10598336 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10612000 stop: 10618000 count: 5162 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10613100 stop: 10613627 count: 11 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10619979 stop: 10620029 count: 5 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10628504 stop: 10628670 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10628790 stop: 10628906 count: 20 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 3 +- chromNo: 21 + chromNo2: 21 + svType: Ins start: 10628791 stop: 10628801 count: 10 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10628826 stop: 10628926 count: 3483 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10628856 stop: 10628957 count: 4 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10628875 stop: 10628932 count: 6 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10633162 stop: 10633704 count: 8 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10633675 stop: 10634286 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10637101 stop: 10637620 count: 3 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10639737 stop: 10640383 count: 4 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10639746 stop: 10640189 count: 49 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10640864 stop: 10641437 count: 72 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10640951 stop: 10641122 count: 7 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10641151 stop: 10641675 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10641897 stop: 10641996 count: 1 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 4 +- chromNo: 21 + chromNo2: 21 + svType: Bnd start: 10647109 stop: 10647109 count: 8 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10657198 stop: 10657273 count: 4 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 1 +- chromNo: 21 + chromNo2: 21 + svType: Dup start: 10658000 stop: 10950572 count: 12 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 5 +- chromNo: 21 + chromNo2: 21 + svType: Cnv start: 10660000 stop: 10729950 count: 325 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10663191 stop: 10663879 count: 13 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10663268 stop: 10663878 count: 258 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10663386 stop: 10663443 count: 2 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10664354 stop: 10664969 count: 14 -- chrom_no: 21 - chrom_no2: 21 - sv_type: 0 +- chromNo: 21 + chromNo2: 21 start: 10665537 stop: 10665633 count: 123 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 10000 stop: 28874000 count: 1 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 10000 stop: 43825 count: 40310 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 1 +- chromNo: 22 + chromNo2: 22 + svType: Dup start: 10000 stop: 24000 count: 78 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 5 +- chromNo: 22 + chromNo2: 22 + svType: Cnv start: 10000 stop: 16150 count: 36 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 10020 stop: 10020 count: 527 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 10037 stop: 10561 count: 151 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 10040 stop: 10230 count: 60 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 10279 stop: 10329 count: 1 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 10536 stop: 10953 count: 5 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 12440 stop: 12440 count: 6 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 12504 stop: 16544 count: 105 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 12810 stop: 16459 count: 2049 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 13025 stop: 13025 count: 66 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 13076 stop: 13174 count: 2 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 13101 stop: 13101 count: 37 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 1 +- chromNo: 22 + chromNo2: 22 + svType: Dup start: 13421 stop: 13487 count: 1 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 13545 stop: 13545 count: 316 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 1 +- chromNo: 22 + chromNo2: 22 + svType: Dup start: 13559 stop: 13759 count: 20794 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 13559 stop: 13559 count: 10 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 13608 stop: 13820 count: 341 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 3 +- chromNo: 22 + chromNo2: 22 + svType: Ins start: 13679 stop: 13720 count: 79 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 13713 stop: 13816 count: 2228 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 1 +- chromNo: 22 + chromNo2: 22 + svType: Dup start: 13723 stop: 13857 count: 13 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 1 +- chromNo: 22 + chromNo2: 22 + svType: Dup start: 13781 stop: 13902 count: 1 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 1 +- chromNo: 22 + chromNo2: 22 + svType: Dup start: 13789 stop: 13981 count: 7104 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 1 +- chromNo: 22 + chromNo2: 22 + svType: Dup start: 13820 stop: 13949 count: 23 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 3 +- chromNo: 22 + chromNo2: 22 + svType: Ins start: 13824 stop: 13845 count: 2 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 1 +- chromNo: 22 + chromNo2: 22 + svType: Dup start: 13884 stop: 13959 count: 4 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 13925 stop: 14384 count: 5 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 13936 stop: 13936 count: 1 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 1 +- chromNo: 22 + chromNo2: 22 + svType: Dup start: 13944 stop: 13999 count: 58 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 13946 stop: 13946 count: 1 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 14000 stop: 14000 count: 4511 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 0 +- chromNo: 22 + chromNo2: 22 start: 14077 stop: 18273 count: 576 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 14078 stop: 14078 count: 1 -- chrom_no: 22 - chrom_no2: 22 - sv_type: 4 +- chromNo: 22 + chromNo2: 22 + svType: Bnd start: 14078 stop: 544696 count: 1 -- chrom_no: 22 - 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chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2817388 stop: 2822788 count: 4 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 2817388 stop: 2913388 count: 16 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2817884 stop: 2822824 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2835989 stop: 2836144 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2839672 stop: 2840370 count: 28 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2845099 stop: 2846474 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 2850988 stop: 2873388 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2851388 stop: 2871388 count: 34 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2853485 stop: 2854115 count: 44 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2872828 stop: 2873061 count: 190 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2879982 stop: 2911961 count: 36 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2887388 stop: 2894388 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 3 +- chromNo: 23 + chromNo2: 23 + svType: Ins start: 2891940 stop: 2891976 count: 8906 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2894920 stop: 2895713 count: 12 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2899686 stop: 2900290 count: 52 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2904986 stop: 2905650 count: 38 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2908236 stop: 2908400 count: 30 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 4 +- chromNo: 23 + chromNo2: 23 + svType: Bnd start: 2913342 stop: 2913342 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2916783 stop: 2919593 count: 126 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2919388 stop: 2927388 count: 26 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2921697 stop: 2925901 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2924388 stop: 2933388 count: 30 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2926910 stop: 2926962 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2937450 stop: 2938167 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2938376 stop: 2939009 count: 12 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2946862 stop: 2946941 count: 102 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 3 +- chromNo: 23 + chromNo2: 23 + svType: Ins start: 2953688 stop: 2953738 count: 40 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 2953738 stop: 2953824 count: 16 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 3 +- chromNo: 23 + chromNo2: 23 + svType: Ins start: 2953824 stop: 2953834 count: 48 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2955016 stop: 2956603 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2957388 stop: 2967388 count: 26 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2969388 stop: 2975388 count: 34 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 4 +- chromNo: 23 + chromNo2: 23 + svType: Bnd start: 2973372 stop: 2973372 count: 6 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 2973388 stop: 3021388 count: 4 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 3 +- chromNo: 23 + chromNo2: 23 + svType: Ins start: 2980742 stop: 2980749 count: 24 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2983388 stop: 2991388 count: 24 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 2987388 stop: 3212388 count: 14 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2987502 stop: 2989746 count: 4 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2987567 stop: 2989883 count: 1404 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2990176 stop: 2990248 count: 40 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2992437 stop: 2992943 count: 44 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2994410 stop: 2994650 count: 62 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 2997388 stop: 3003388 count: 22 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 3 +- chromNo: 23 + chromNo2: 23 + svType: Ins start: 2998156 stop: 2998178 count: 4 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 4 +- chromNo: 23 + chromNo2: 23 + svType: Bnd start: 2998176 stop: 2998176 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 4 +- chromNo: 23 + chromNo2: 23 + svType: Bnd start: 2998880 stop: 2998880 count: 18 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 4 +- chromNo: 23 + chromNo2: 23 + svType: Bnd start: 2999003 stop: 2999003 count: 4 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3007161 stop: 3012282 count: 26 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3007388 stop: 3017388 count: 8 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3010710 stop: 3011274 count: 50 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 3010953 stop: 3041103 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3012169 stop: 3028778 count: 30 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3019913 stop: 3021206 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3020300 stop: 3030123 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3020508 stop: 3020646 count: 8 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 3 +- chromNo: 23 + chromNo2: 23 + svType: Ins start: 3020514 stop: 3020564 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3020553 stop: 3020652 count: 880 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3020570 stop: 3036845 count: 8 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 4 +- chromNo: 23 + chromNo2: 23 + svType: Bnd start: 3020575 stop: 3020575 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 4 +- chromNo: 23 + chromNo2: 23 + svType: Bnd start: 3020603 stop: 3020603 count: 6 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3020647 stop: 3031417 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 3 +- chromNo: 23 + chromNo2: 23 + svType: Ins start: 3020705 stop: 3020705 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3023900 stop: 3023985 count: 10 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 3023904 stop: 3024039 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3029388 stop: 3049388 count: 36 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3032903 stop: 3033282 count: 76 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3041363 stop: 3041808 count: 90 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3046826 stop: 3047241 count: 82 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 3049388 stop: 3105388 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3052187 stop: 3052288 count: 488 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3059388 stop: 3069388 count: 6 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3065388 stop: 3083388 count: 8 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3078388 stop: 3127588 count: 8 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3079125 stop: 3079318 count: 40 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3083388 stop: 3089388 count: 18 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 3 +- chromNo: 23 + chromNo2: 23 + svType: Ins start: 3084373 stop: 3084410 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3099388 stop: 3115388 count: 14 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3107388 stop: 3113388 count: 4 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3116411 stop: 3116909 count: 4 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3122048 stop: 3147332 count: 18 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3151387 stop: 26673214 count: 30 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3153388 stop: 3159388 count: 4 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 3155388 stop: 3163388 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3163388 stop: 3169388 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 3167388 stop: 3223388 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 3167388 stop: 3177388 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 1 +- chromNo: 23 + chromNo2: 23 + svType: Dup start: 3174227 stop: 5791687 count: 6 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3178703 stop: 3194987 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3201771 stop: 3202308 count: 8 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3201771 stop: 3202117 count: 18 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3213820 stop: 3236800 count: 2 -- chrom_no: 23 - chrom_no2: 23 - sv_type: 0 +- chromNo: 23 + chromNo2: 23 start: 3217338 stop: 3225488 count: 6 diff --git a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@InhouseDb-inhouse.snap b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@InhouseDb-inhouse.snap index 5a8f7a23..c063b7c9 100644 --- a/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@InhouseDb-inhouse.snap +++ b/src/strucvars/txt_to_bin/vardbs/snapshots/varfish_server_worker__strucvars__txt_to_bin__vardbs__test__deserialize_branch@InhouseDb-inhouse.snap @@ -2,9 +2,6 @@ source: src/strucvars/txt_to_bin/vardbs/mod.rs expression: records --- -- chrom_no: 0 - chrom_no2: 0 - sv_type: 0 - start: 849999 +- start: 849999 stop: 860000 count: 1 diff --git a/src/strucvars/txt_to_bin/xlink.rs b/src/strucvars/txt_to_bin/xlink.rs index cd3bb6b4..d2b57b7a 100644 --- a/src/strucvars/txt_to_bin/xlink.rs +++ b/src/strucvars/txt_to_bin/xlink.rs @@ -8,7 +8,7 @@ use thousands::Separable; use crate::{ common::{numeric_gene_id, trace_rss_now}, - strucvars::pbs::{XlinkDatabase, XlinkRecord}, + pbs::svs::{XlinkDatabase, XlinkRecord}, }; /// Module with code for parsing the TSVs. diff --git a/tests/seqvars/ingest/Case_1.custom_id.ped b/tests/seqvars/ingest/Case_1.custom_id.ped new file mode 100644 index 00000000..2855cb64 --- /dev/null +++ b/tests/seqvars/ingest/Case_1.custom_id.ped @@ -0,0 +1,3 @@ +FAM Case_1_index Case_1_father Case_1_mother 2 2 +FAM Case_1_father 0 0 1 1 +FAM Case_1_mother 0 0 2 1 diff --git a/tests/seqvars/ingest/NA12878_dragen.custom_id.ped b/tests/seqvars/ingest/NA12878_dragen.custom_id.ped new file mode 100644 index 00000000..2bc44360 --- /dev/null +++ b/tests/seqvars/ingest/NA12878_dragen.custom_id.ped @@ -0,0 +1 @@ +FAM my-custom-id 0 0 2 2 diff --git a/tests/strucvars/ingest/dragen-cnv-min.custom_id.ped b/tests/strucvars/ingest/dragen-cnv-min.custom_id.ped new file mode 100644 index 00000000..e2ffadc3 --- /dev/null +++ b/tests/strucvars/ingest/dragen-cnv-min.custom_id.ped @@ -0,0 +1 @@ +FAM my-custom-id 0 0 1 2