diff --git a/src/seqvars/ingest/header.rs b/src/seqvars/ingest/header.rs index 28590822..1bc067b0 100644 --- a/src/seqvars/ingest/header.rs +++ b/src/seqvars/ingest/header.rs @@ -86,18 +86,30 @@ fn add_contigs_37(builder: vcf::header::Builder) -> Result<vcf::header::Builder, ("20", 63025520), ("21", 48129895), ("22", 51304566), - ("X ", 155270560), - ("Y ", 59373566), + ("X", 155270560), + ("Y", 59373566), ("MT", 16569), ]; for (contig, length) in specs { builder = builder.add_contig( - contig.parse()?, + contig + .parse() + .map_err(|_| anyhow::anyhow!("invalid contig: {}", contig))?, Map::<Contig>::builder() .set_length(*length) - .insert("assembly".parse()?, "GRCh37") - .insert("species".parse()?, "Homo sapiens") + .insert( + "assembly" + .parse() + .map_err(|_| anyhow::anyhow!("invalid key: assembly"))?, + "GRCh37", + ) + .insert( + "species" + .parse() + .map_err(|_| anyhow::anyhow!("invalid key: species"))?, + "Homo sapiens", + ) .build()?, ); } @@ -142,11 +154,23 @@ fn add_contigs_38(builder: vcf::header::Builder) -> Result<vcf::header::Builder, for (contig, length) in specs { builder = builder.add_contig( - contig.parse()?, + contig + .parse() + .map_err(|_| anyhow::anyhow!("invalid contig: {}", contig))?, Map::<Contig>::builder() .set_length(*length) - .insert("assembly".parse()?, "GRCh37") - .insert("species".parse()?, "Homo sapiens") + .insert( + "assembly" + .parse() + .map_err(|_| anyhow::anyhow!("invalid key: assembly"))?, + "GRCh38", + ) + .insert( + "species" + .parse() + .map_err(|_| anyhow::anyhow!("invalid key: species"))?, + "Homo sapiens", + ) .build()?, ); } @@ -310,7 +334,8 @@ pub fn build_output_header( let mut builder = match genomebuild { GenomeRelease::Grch37 => add_contigs_37(builder), GenomeRelease::Grch38 => add_contigs_38(builder), - }?; + } + .map_err(|e| anyhow::anyhow!("problem adding contigs: {}", e))?; if let Some(pedigree) = pedigree { let ped_idv = pedigree @@ -321,7 +346,7 @@ pub fn build_output_header( let input_idv = input_header .sample_names() .iter() - .map(|n| n.clone()) + .cloned() .collect::<HashSet<_>>(); if !ped_idv.eq(&input_idv) { anyhow::bail!( @@ -436,7 +461,7 @@ mod test { fn variant_caller_guess(#[case] path: &str) -> Result<(), anyhow::Error> { set_snapshot_suffix!("{}", path.split('/').last().unwrap()); - let vcf_header = noodles_vcf::reader::Builder::default() + let vcf_header = noodles_vcf::reader::Builder .build_from_path(path)? .read_header()?; @@ -454,12 +479,14 @@ mod test { set_snapshot_suffix!("{}", path.split('/').last().unwrap()); let tmpdir = temp_testdir::TempDir::default(); - let input_vcf_header = noodles_vcf::reader::Builder::default() + let pedigree = PedigreeByName::from_path(path.replace(".vcf", ".ped")).unwrap(); + + let input_vcf_header = noodles_vcf::reader::Builder .build_from_path(path)? .read_header()?; let output_vcf_header = super::build_output_header( &input_vcf_header, - &None, + &Some(pedigree), crate::common::GenomeRelease::Grch37, "x.y.z", )?; @@ -485,36 +512,10 @@ mod test { set_snapshot_suffix!("{}", path.split('/').last().unwrap()); let tmpdir = temp_testdir::TempDir::default(); - let input_vcf_header = noodles_vcf::reader::Builder::default() - .build_from_path(path)? - .read_header()?; - let output_vcf_header = super::build_output_header( - &input_vcf_header, - &None, - crate::common::GenomeRelease::Grch38, - "x.y.z", - )?; - - let out_path = tmpdir.join("out.vcf"); - let out_path_str = out_path.to_str().expect("invalid path"); - { - noodles_vcf::writer::Writer::new(std::fs::File::create(out_path_str)?) - .write_header(&output_vcf_header)?; - } - - insta::assert_snapshot!(std::fs::read_to_string(out_path_str)?); - - Ok(()) - } - - #[test] - fn build_output_header_ped() -> Result<(), anyhow::Error> { - let tmpdir = temp_testdir::TempDir::default(); - - let pedigree = PedigreeByName::from_path("tests/seqvars/ingest/example_gatk_hc.3.7-0.ped")?; + let pedigree = PedigreeByName::from_path(path.replace(".vcf", ".ped")).unwrap(); - let input_vcf_header = noodles_vcf::reader::Builder::default() - .build_from_path("tests/seqvars/ingest/example_gatk_hc.3.7-0.vcf")? + let input_vcf_header = noodles_vcf::reader::Builder + .build_from_path(path)? .read_header()?; let output_vcf_header = super::build_output_header( &input_vcf_header, diff --git a/src/seqvars/ingest/mod.rs b/src/seqvars/ingest/mod.rs index 30868f46..c0b37548 100644 --- a/src/seqvars/ingest/mod.rs +++ b/src/seqvars/ingest/mod.rs @@ -50,7 +50,7 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: let file = std::fs::File::open(&args.path_in) .map_err(|e| anyhow::anyhow!("could not open input file {}: {}", &args.path_in, e)) .map(std::io::BufReader::new)?; - vcf::reader::Builder::default() + vcf::reader::Builder .build_from_reader(file) .map_err(|e| anyhow::anyhow!("could not build VCF reader: {}", e))? }; @@ -64,7 +64,8 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: &Some(pedigree), args.genomebuild, worker_version(), - )?; + ) + .map_err(|e| anyhow::anyhow!("problem building output header: {}", e))?; let mut output_writer = { let writer = std::fs::File::create(&args.path_out).map_err(|e| { @@ -77,7 +78,9 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: let writer = std::io::BufWriter::new(writer); vcf::writer::Writer::new(writer) }; - output_writer.write_header(&output_header)?; + output_writer + .write_header(&output_header) + .map_err(|e| anyhow::anyhow!("problem writing header: {}", e))?; tracing::info!( "All of `seqvars ingest` completed in {:?}", @@ -105,14 +108,14 @@ mod test { #[case("tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.vcf")] #[case("tests/seqvars/ingest/example_gatk_hc.3.7-0.vcf")] #[case("tests/seqvars/ingest/example_gatk_hc.4.4.0.0.vcf")] - fn smoke_test_run(#[case] path: &str) { - set_snapshot_suffix!("{:?}", path.split('/').last().unwrap().replace(".", "_")); + fn smoke_test_run(#[case] path: &str) -> Result<(), anyhow::Error> { + set_snapshot_suffix!("{:?}", path.split('/').last().unwrap().replace('.', "_")); let tmpdir = temp_testdir::TempDir::default(); let args_common = Default::default(); let args = super::Args { - path_ped: "tests/seqvars/ingest/example_gatk_hc.3.7-0.ped".into(), + path_ped: path.replace(".vcf", ".ped"), genomebuild: GenomeRelease::Grch37, path_in: path.into(), path_out: tmpdir @@ -121,6 +124,6 @@ mod test { .expect("invalid path") .into(), }; - super::run(&args_common, &args).unwrap(); + super::run(&args_common, &args) } } diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.4.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.4.vcf.snap new file mode 100644 index 00000000..64a8c516 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.4.vcf.snap @@ -0,0 +1,54 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO=<ID=gnomad_exomes_an,Number=1,Type=Integer,Description="Number of samples in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_genomes_an,Number=1,Type=Integer,Description="Number of samples in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes"> +##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of samples in HelixMtDb"> +##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb"> +##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb"> +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> +##FILTER=<ID=PASS,Description="All filters passed"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##contig=<ID=1,length=249250621,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=2,length=243199373,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=3,length=198022430,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=4,length=191154276,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=5,length=180915260,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=6,length=171115067,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=7,length=159138663,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=8,length=146364022,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=9,length=141213431,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=10,length=135534747,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=11,length=135006516,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=12,length=133851895,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=13,length=115169878,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=14,length=107349540,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=15,length=102531392,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=16,length=90354753,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=17,length=81195210,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=18,length=78077248,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=19,length=59128983,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=20,length=63025520,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=21,length=48129895,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=22,length=51304566,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=X,length=155270560,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=Y,length=59373566,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=MT,length=16569,assembly="GRCh37",species="Homo sapiens"> +##SAMPLE=<ID=NA12878,Sex="Male",Disease="Affected"> +##PEDIGREE=<ID=NA12878> +##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z"> +##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.4, HW: 07.021.624"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.9.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.9.vcf.snap new file mode 100644 index 00000000..504e97b8 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.9.vcf.snap @@ -0,0 +1,54 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO=<ID=gnomad_exomes_an,Number=1,Type=Integer,Description="Number of samples in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_genomes_an,Number=1,Type=Integer,Description="Number of samples in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes"> +##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of samples in HelixMtDb"> +##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb"> +##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb"> +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> +##FILTER=<ID=PASS,Description="All filters passed"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##contig=<ID=1,length=249250621,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=2,length=243199373,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=3,length=198022430,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=4,length=191154276,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=5,length=180915260,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=6,length=171115067,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=7,length=159138663,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=8,length=146364022,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=9,length=141213431,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=10,length=135534747,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=11,length=135006516,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=12,length=133851895,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=13,length=115169878,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=14,length=107349540,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=15,length=102531392,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=16,length=90354753,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=17,length=81195210,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=18,length=78077248,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=19,length=59128983,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=20,length=63025520,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=21,length=48129895,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=22,length=51304566,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=X,length=155270560,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=Y,length=59373566,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=MT,length=16569,assembly="GRCh37",species="Homo sapiens"> +##SAMPLE=<ID=CASE,Sex="Male",Disease="Affected"> +##PEDIGREE=<ID=CASE> +##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z"> +##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.9, HW: 07.021.624"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.3.7-0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.3.7-0.vcf.snap new file mode 100644 index 00000000..606973d1 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.3.7-0.vcf.snap @@ -0,0 +1,58 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO=<ID=gnomad_exomes_an,Number=1,Type=Integer,Description="Number of samples in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_genomes_an,Number=1,Type=Integer,Description="Number of samples in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes"> +##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of samples in HelixMtDb"> +##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb"> +##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb"> +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> +##FILTER=<ID=PASS,Description="All filters passed"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##contig=<ID=1,length=249250621,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=2,length=243199373,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=3,length=198022430,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=4,length=191154276,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=5,length=180915260,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=6,length=171115067,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=7,length=159138663,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=8,length=146364022,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=9,length=141213431,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=10,length=135534747,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=11,length=135006516,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=12,length=133851895,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=13,length=115169878,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=14,length=107349540,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=15,length=102531392,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=16,length=90354753,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=17,length=81195210,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=18,length=78077248,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=19,length=59128983,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=20,length=63025520,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=21,length=48129895,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=22,length=51304566,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=X,length=155270560,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=Y,length=59373566,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=MT,length=16569,assembly="GRCh37",species="Homo sapiens"> +##SAMPLE=<ID=Case_1_father-N1-DNA1-WGS1,Sex="Male",Disease="Unaffected"> +##SAMPLE=<ID=Case_1_index-N1-DNA1-WGS1,Sex="Female",Disease="Affected"> +##SAMPLE=<ID=Case_1_mother-N1-DNA1-WGS1,Sex="Male",Disease="Unaffected"> +##PEDIGREE=<ID=Case_1_father-N1-DNA1-WGS1> +##PEDIGREE=<ID=Case_1_index-N1-DNA1-WGS1,Father="Case_1_father-N1-DNA1-WGS1",Mother="Case_1_mother-N1-DNA1-WGS1"> +##PEDIGREE=<ID=Case_1_mother-N1-DNA1-WGS1> +##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z"> +##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.4.4.0.0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.4.4.0.0.vcf.snap new file mode 100644 index 00000000..e75108df --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.4.4.0.0.vcf.snap @@ -0,0 +1,54 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO=<ID=gnomad_exomes_an,Number=1,Type=Integer,Description="Number of samples in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_exomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD exomes"> +##INFO=<ID=gnomad_genomes_an,Number=1,Type=Integer,Description="Number of samples in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes"> +##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes"> +##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of samples in HelixMtDb"> +##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb"> +##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb"> +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> +##FILTER=<ID=PASS,Description="All filters passed"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##contig=<ID=1,length=249250621,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=2,length=243199373,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=3,length=198022430,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=4,length=191154276,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=5,length=180915260,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=6,length=171115067,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=7,length=159138663,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=8,length=146364022,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=9,length=141213431,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=10,length=135534747,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=11,length=135006516,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=12,length=133851895,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=13,length=115169878,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=14,length=107349540,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=15,length=102531392,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=16,length=90354753,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=17,length=81195210,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=18,length=78077248,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=19,length=59128983,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=20,length=63025520,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=21,length=48129895,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=22,length=51304566,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=X,length=155270560,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=Y,length=59373566,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=MT,length=16569,assembly="GRCh37",species="Homo sapiens"> +##SAMPLE=<ID=CASE,Sex="Male",Disease="Affected"> +##PEDIGREE=<ID=CASE> +##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z"> +##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="4.4.0.0"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap index 501f62ed..04ab2618 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap @@ -21,31 +21,33 @@ expression: "std::fs::read_to_string(out_path_str)?" ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> -##contig=<ID=chr1,length=248956422,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr2,length=242193529,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr3,length=198295559,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr4,length=190214555,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr5,length=181538259,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr6,length=170805979,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr7,length=159345973,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr8,length=145138636,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr9,length=138394717,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr10,length=133797422,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr11,length=135086622,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr12,length=133275309,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr13,length=114364328,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr14,length=107043718,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr15,length=101991189,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr16,length=90338345,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr17,length=83257441,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr18,length=80373285,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr19,length=58617616,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr20,length=64444167,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr21,length=46709983,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr22,length=50818468,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrX,length=156040895,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrY,length=57227415,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrM,length=16569,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=chr1,length=248956422,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr2,length=242193529,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr3,length=198295559,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr4,length=190214555,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr5,length=181538259,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr6,length=170805979,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr7,length=159345973,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr8,length=145138636,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr9,length=138394717,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr10,length=133797422,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr11,length=135086622,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr12,length=133275309,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr13,length=114364328,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr14,length=107043718,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr15,length=101991189,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr16,length=90338345,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr17,length=83257441,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr18,length=80373285,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr19,length=58617616,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr20,length=64444167,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr21,length=46709983,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr22,length=50818468,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrX,length=156040895,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrY,length=57227415,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrM,length=16569,assembly="GRCh38",species="Homo sapiens"> +##SAMPLE=<ID=NA12878,Sex="Male",Disease="Affected"> +##PEDIGREE=<ID=NA12878> ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z"> ##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.4, HW: 07.021.624"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap index 217a78b5..ffb1a8fa 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap @@ -21,31 +21,33 @@ expression: "std::fs::read_to_string(out_path_str)?" ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> -##contig=<ID=chr1,length=248956422,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr2,length=242193529,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr3,length=198295559,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr4,length=190214555,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr5,length=181538259,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr6,length=170805979,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr7,length=159345973,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr8,length=145138636,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr9,length=138394717,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr10,length=133797422,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr11,length=135086622,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr12,length=133275309,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr13,length=114364328,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr14,length=107043718,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr15,length=101991189,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr16,length=90338345,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr17,length=83257441,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr18,length=80373285,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr19,length=58617616,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr20,length=64444167,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr21,length=46709983,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr22,length=50818468,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrX,length=156040895,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrY,length=57227415,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrM,length=16569,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=chr1,length=248956422,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr2,length=242193529,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr3,length=198295559,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr4,length=190214555,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr5,length=181538259,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr6,length=170805979,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr7,length=159345973,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr8,length=145138636,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr9,length=138394717,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr10,length=133797422,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr11,length=135086622,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr12,length=133275309,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr13,length=114364328,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr14,length=107043718,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr15,length=101991189,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr16,length=90338345,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr17,length=83257441,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr18,length=80373285,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr19,length=58617616,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr20,length=64444167,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr21,length=46709983,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr22,length=50818468,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrX,length=156040895,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrY,length=57227415,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrM,length=16569,assembly="GRCh38",species="Homo sapiens"> +##SAMPLE=<ID=CASE,Sex="Male",Disease="Affected"> +##PEDIGREE=<ID=CASE> ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z"> ##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.9, HW: 07.021.624"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap index 8c6ecc4f..98f14248 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap @@ -21,31 +21,37 @@ expression: "std::fs::read_to_string(out_path_str)?" ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> -##contig=<ID=chr1,length=248956422,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr2,length=242193529,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr3,length=198295559,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr4,length=190214555,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr5,length=181538259,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr6,length=170805979,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr7,length=159345973,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr8,length=145138636,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr9,length=138394717,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr10,length=133797422,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr11,length=135086622,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr12,length=133275309,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr13,length=114364328,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr14,length=107043718,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr15,length=101991189,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr16,length=90338345,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr17,length=83257441,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr18,length=80373285,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr19,length=58617616,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr20,length=64444167,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr21,length=46709983,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr22,length=50818468,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrX,length=156040895,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrY,length=57227415,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrM,length=16569,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=chr1,length=248956422,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr2,length=242193529,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr3,length=198295559,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr4,length=190214555,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr5,length=181538259,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr6,length=170805979,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr7,length=159345973,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr8,length=145138636,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr9,length=138394717,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr10,length=133797422,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr11,length=135086622,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr12,length=133275309,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr13,length=114364328,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr14,length=107043718,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr15,length=101991189,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr16,length=90338345,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr17,length=83257441,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr18,length=80373285,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr19,length=58617616,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr20,length=64444167,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr21,length=46709983,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr22,length=50818468,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrX,length=156040895,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrY,length=57227415,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrM,length=16569,assembly="GRCh38",species="Homo sapiens"> +##SAMPLE=<ID=Case_1_father-N1-DNA1-WGS1,Sex="Male",Disease="Unaffected"> +##SAMPLE=<ID=Case_1_index-N1-DNA1-WGS1,Sex="Female",Disease="Affected"> +##SAMPLE=<ID=Case_1_mother-N1-DNA1-WGS1,Sex="Male",Disease="Unaffected"> +##PEDIGREE=<ID=Case_1_father-N1-DNA1-WGS1> +##PEDIGREE=<ID=Case_1_index-N1-DNA1-WGS1,Father="Case_1_father-N1-DNA1-WGS1",Mother="Case_1_mother-N1-DNA1-WGS1"> +##PEDIGREE=<ID=Case_1_mother-N1-DNA1-WGS1> ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z"> ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap index b3876668..76a3c2f3 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap @@ -21,31 +21,33 @@ expression: "std::fs::read_to_string(out_path_str)?" ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> -##contig=<ID=chr1,length=248956422,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr2,length=242193529,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr3,length=198295559,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr4,length=190214555,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr5,length=181538259,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr6,length=170805979,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr7,length=159345973,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr8,length=145138636,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr9,length=138394717,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr10,length=133797422,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr11,length=135086622,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr12,length=133275309,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr13,length=114364328,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr14,length=107043718,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr15,length=101991189,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr16,length=90338345,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr17,length=83257441,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr18,length=80373285,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr19,length=58617616,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr20,length=64444167,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr21,length=46709983,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chr22,length=50818468,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrX,length=156040895,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrY,length=57227415,assembly="GRCh37",species="Homo sapiens"> -##contig=<ID=chrM,length=16569,assembly="GRCh37",species="Homo sapiens"> +##contig=<ID=chr1,length=248956422,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr2,length=242193529,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr3,length=198295559,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr4,length=190214555,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr5,length=181538259,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr6,length=170805979,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr7,length=159345973,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr8,length=145138636,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr9,length=138394717,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr10,length=133797422,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr11,length=135086622,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr12,length=133275309,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr13,length=114364328,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr14,length=107043718,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr15,length=101991189,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr16,length=90338345,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr17,length=83257441,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr18,length=80373285,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr19,length=58617616,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr20,length=64444167,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr21,length=46709983,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chr22,length=50818468,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrX,length=156040895,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrY,length=57227415,assembly="GRCh38",species="Homo sapiens"> +##contig=<ID=chrM,length=16569,assembly="GRCh38",species="Homo sapiens"> +##SAMPLE=<ID=CASE,Sex="Male",Disease="Affected"> +##PEDIGREE=<ID=CASE> ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z"> ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="4.4.0.0"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE diff --git a/tests/seqvars/ingest/example_dragen.07.021.624.3.10.4.ped b/tests/seqvars/ingest/example_dragen.07.021.624.3.10.4.ped new file mode 100644 index 00000000..38609565 --- /dev/null +++ b/tests/seqvars/ingest/example_dragen.07.021.624.3.10.4.ped @@ -0,0 +1 @@ +FAM NA12878 0 0 1 2 diff --git a/tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.ped b/tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.ped new file mode 100644 index 00000000..aff8cffb --- /dev/null +++ b/tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.ped @@ -0,0 +1 @@ +FAM CASE 0 0 1 2 diff --git a/tests/seqvars/ingest/example_gatk_hc.4.4.0.0.ped b/tests/seqvars/ingest/example_gatk_hc.4.4.0.0.ped new file mode 100644 index 00000000..aff8cffb --- /dev/null +++ b/tests/seqvars/ingest/example_gatk_hc.4.4.0.0.ped @@ -0,0 +1 @@ +FAM CASE 0 0 1 2