feat: transform "db mk-inhouse" to "strucvars aggregate" (#212) (#217)

src/common.rs

@@ -198,6 +198,49 @@ impl std::str::FromStr for GenomeRelease {
     }
 }
 
+/// Helper type for encoding genotypes in parsing.
+#[derive(Copy, Clone)]
+pub enum Genotype {
+    /// hom. ref.
+    HomRef,
+    /// het.
+    Het,
+    /// hom. alt.
+    HomAlt,
+}
+
+impl std::str::FromStr for Genotype {
+    type Err = anyhow::Error;
+
+    fn from_str(s: &str) -> Result<Self, Self::Err> {
+        Ok(match s {
+            "0/0" | "0|0" | "0" => Genotype::HomRef,
+            "0/1" | "1/0" | "0|1" | "1|0" => Genotype::Het,
+            "1/1" | "1|1" | "1" => Genotype::HomAlt,
+            _ => anyhow::bail!("invalid genotype value: {:?}", s),
+        })
+    }
+}
+
+#[derive(Copy, Clone)]
+pub enum Chrom {
+    Auto, // or chrMT, but does not matter for carrier computation
+    X,
+    Y,
+}
+
+impl std::str::FromStr for Chrom {
+    type Err = anyhow::Error;
+
+    fn from_str(s: &str) -> Result<Self, Self::Err> {
+        Ok(match s {
+            "X" => Chrom::X,
+            "Y" => Chrom::Y,
+            _ => Chrom::Auto,
+        })
+    }
+}
+
 /// The version of `varfish-server-worker` package.
 pub const VERSION: &str = env!("CARGO_PKG_VERSION");
 
@@ -293,6 +336,99 @@ pub fn add_contigs_37(
     Ok(builder)
 }
 
+/// Extract a PedigreeByName from the VCF header.
+pub fn extract_pedigree_and_case_uuid(
+    header: &vcf::Header,
+) -> Result<(mehari::ped::PedigreeByName, uuid::Uuid), anyhow::Error> {
+    let mut case_uuid = uuid::Uuid::nil();
+    let mut pedigree = mehari::ped::PedigreeByName::default();
+
+    if let vcf::header::record::value::Collection::Structured(sample_map) = header
+        .other_records()
+        .get("SAMPLE")
+        .ok_or_else(|| anyhow::anyhow!("no SAMPLE record in VCF header"))?
+    {
+        for (sample_name, sample_values) in sample_map.iter() {
+            let sex_value = sample_values
+                .other_fields()
+                .get("Sex")
+                .ok_or_else(|| anyhow::anyhow!("no Sex field in SAMPLE header?"))?
+                .as_ref();
+            let sex_value = match sex_value {
+                "Male" => mehari::ped::Sex::Male,
+                "Female" => mehari::ped::Sex::Female,
+                "Unknown" => mehari::ped::Sex::Unknown,
+                _ => anyhow::bail!("invalid value for Sex: {}", sex_value),
+            };
+
+            let disease_value = sample_values
+                .other_fields()
+                .get("Disease")
+                .ok_or_else(|| anyhow::anyhow!("no Disease field in SAMPLE header?"))?
+                .as_ref();
+            let disease_value = match disease_value {
+                "Affected" => mehari::ped::Disease::Affected,
+                "Unaffected" => mehari::ped::Disease::Unaffected,
+                "Unknown" => mehari::ped::Disease::Unknown,
+                _ => anyhow::bail!("invalid value for Disease: {}", disease_value),
+            };
+
+            pedigree.individuals.insert(
+                sample_name.clone(),
+                mehari::ped::Individual {
+                    family: "FAM".into(),
+                    name: sample_name.clone(),
+                    sex: sex_value,
+                    disease: disease_value,
+                    ..Default::default()
+                },
+            );
+        }
+    }
+
+    if let vcf::header::record::value::Collection::Structured(sample_map) = header
+        .other_records()
+        .get("PEDIGREE")
+        .ok_or_else(|| anyhow::anyhow!("no PEDIGREE record in VCF header"))?
+    {
+        for (sample_name, pedigree_values) in sample_map.iter() {
+            let father_value = pedigree_values.other_fields().get("Father");
+            let mother_value = pedigree_values.other_fields().get("Mother");
+
+            let individual = pedigree.individuals.get_mut(sample_name).ok_or_else(|| {
+                anyhow::anyhow!("individual {} not found in SAMPLE header", sample_name)
+            })?;
+            if let Some(father_value) = father_value {
+                individual.father = Some(father_value.clone());
+            }
+            if let Some(mother_value) = mother_value {
+                individual.mother = Some(mother_value.clone());
+            }
+        }
+    }
+
+    if let vcf::header::record::value::Collection::Unstructured(lines) = header
+        .other_records()
+        .get("x-varfish-case-uuid")
+        .ok_or_else(|| anyhow::anyhow!("no x-varfish-case-uuid record in VCF header"))?
+    {
+        case_uuid = lines
+            .first()
+            .ok_or_else(|| {
+                anyhow::anyhow!("no x-varfish-case-uuid record in VCF header, but expected one")
+            })?
+            .parse()
+            .map_err(|e| {
+                anyhow::anyhow!(
+                    "could not parse x-varfish-case-uuid record in VCF header: {}",
+                    e
+                )
+            })?;
+    }
+
+    Ok((pedigree, case_uuid))
+}
+
 /// Add contigs for GRCh38.
 pub fn add_contigs_38(
     builder: vcf::header::Builder,
@@ -377,6 +513,7 @@ where
 
 #[cfg(test)]
 mod test {
+    use noodles_vcf as vcf;
     use std::io::Read;
 
     #[test]
@@ -510,4 +647,15 @@ mod test {
 
         Ok(())
     }
+
+    #[test]
+    fn extract_pedigree_snapshot() {
+        let path = "tests/seqvars/aggregate/ingest.vcf";
+        let mut vcf_reader = vcf::reader::Builder.build_from_path(path).unwrap();
+        let header = vcf_reader.read_header().unwrap();
+
+        let (pedigree, case_uuid) = super::extract_pedigree_and_case_uuid(&header).unwrap();
+        insta::assert_debug_snapshot!(pedigree);
+        insta::assert_debug_snapshot!(case_uuid);
+    }
 }

src/db/mod.rs

@@ -1,6 +1,5 @@
 //! Code supporting the `db *` sub commands.
 
 pub mod conf;
-pub mod mk_inhouse;
 pub mod pbs;
 pub mod to_bin;

src/db/to_bin/vardbs/input.rs

@@ -4,7 +4,7 @@
 use serde::Deserialize;
 use tracing::error;
 
-use crate::db::mk_inhouse::output::Record as InhouseDbRecord;
+use crate::strucvars::aggregate::output::Record as InhouseDbRecord;
 use crate::strucvars::query::schema::SvType;
 
 /// dbVar database record as read from TSV file.

src/db/to_bin/vardbs/mod.rs

@@ -12,8 +12,8 @@ use thousands::Separable;
 
 use crate::common::{build_chrom_map, trace_rss_now};
 use crate::db;
-use crate::db::mk_inhouse::output::Record as InhouseDbRecord;
 use crate::db::pbs::{BackgroundDatabase, BgDbRecord};
+use crate::strucvars::aggregate::output::Record as InhouseDbRecord;
 use crate::strucvars::query::schema::SvType;
 
 use self::input::InputRecord;

src/main.rs

@@ -52,7 +52,6 @@ struct Db {
 #[derive(Debug, Subcommand)]
 enum DbCommands {
     ToBin(db::to_bin::cli::Args),
-    MkInhouse(db::mk_inhouse::cli::Args),
 }
 
 /// Parsing of "sv *" sub commands.
@@ -67,6 +66,7 @@ struct Strucvars {
 /// Enum supporting the parsing of "sv *" sub commands.
 #[derive(Debug, Subcommand)]
 enum StrucvarsCommands {
+    Aggregate(strucvars::aggregate::cli::Args),
     Ingest(strucvars::ingest::Args),
     Query(strucvars::query::Args),
 }
@@ -112,9 +112,6 @@ fn main() -> Result<(), anyhow::Error> {
     tracing::subscriber::with_default(collector, || {
         match &cli.command {
             Commands::Db(db) => match &db.command {
-                DbCommands::MkInhouse(args) => {
-                    db::mk_inhouse::cli::run(&cli.common, args)?;
-                }
                 DbCommands::ToBin(args) => {
                     db::to_bin::cli::run(&cli.common, args)?;
                 }
@@ -131,6 +128,9 @@ fn main() -> Result<(), anyhow::Error> {
                 }
             },
             Commands::Strucvars(strucvars) => match &strucvars.command {
+                StrucvarsCommands::Aggregate(args) => {
+                    strucvars::aggregate::cli::run(&cli.common, args)?;
+                }
                 StrucvarsCommands::Ingest(args) => {
                     strucvars::ingest::run(&cli.common, args)?;
                 }