feat: remove gene regions from "strucvars query" database enhancement (…

…#221) (#222)

src/common.rs

@@ -514,30 +514,6 @@ where
     Ok(buffer)
 }
 
-/// Enum for the supported gene/transcript databases.
-#[derive(
-    serde::Serialize,
-    serde::Deserialize,
-    enum_map::Enum,
-    PartialEq,
-    Eq,
-    Clone,
-    Copy,
-    Debug,
-    Default,
-    strum::EnumString,
-    strum::Display,
-)]
-#[serde(rename_all = "lowercase")]
-#[strum(serialize_all = "lowercase")]
-pub enum Database {
-    /// RefSeq
-    #[default]
-    RefSeq,
-    /// ENSEMBL
-    Ensembl,
-}
-
 /// Enum for the supported TADs.
 #[derive(
     serde::Serialize,

src/main.rs

@@ -35,7 +35,7 @@ enum Commands {
     Seqvars(Seqvars),
 }
 
-/// Parsing of "sv *" sub commands.
+/// Parsing of "strucvars *" sub commands.
 #[derive(Debug, Args)]
 #[command(args_conflicts_with_subcommands = true)]
 struct Strucvars {
@@ -44,7 +44,7 @@ struct Strucvars {
     command: StrucvarsCommands,
 }
 
-/// Enum supporting the parsing of "sv *" sub commands.
+/// Enum supporting the parsing of "strucvars *" sub commands.
 #[derive(Debug, Subcommand)]
 enum StrucvarsCommands {
     Aggregate(strucvars::aggregate::cli::Args),
@@ -62,7 +62,7 @@ struct Seqvars {
     command: SeqvarsCommands,
 }
 
-/// Enum supporting the parsing of "sv *" sub commands.
+/// Enum supporting the parsing of "strucvars *" sub commands.
 #[derive(Debug, Subcommand)]
 enum SeqvarsCommands {
     Aggregate(seqvars::aggregate::Args),

src/proto/varfish/v1/sv.proto

@@ -56,24 +56,6 @@ message MaskedDatabase {
     repeated MaskedDbRecord records = 1;
 }
 
-// Record for the gene region database.
-message GeneRegionRecord {
-    // Numeric chromosome number.
-    int32 chrom_no = 1;
-    // 1-based start position.
-    int32 start = 2;
-    // 1-based stop position.
-    int32 stop = 3;
-    // Numeric gene identifier.
-    uint32 gene_id = 4;
-}
-
-// Gene region database.
-message GeneRegionDatabase {
-    // List of gene region records.
-    repeated GeneRegionRecord records = 1;
-}
-
 // Record for the gene cross-link database.
 message XlinkRecord {
     // HGNC ID (e.g., "HGNC:123")

src/strucvars/aggregate/cli.rs

@@ -279,7 +279,7 @@ pub struct Args {
     pub slack_ins: i32,
 }
 
-/// Main entry point for the `sv bg-db-to-bin` command.
+/// Main entry point for the `strucvars txt-to-bin` command.
 pub fn run(common_args: &crate::common::Args, args: &Args) -> Result<(), anyhow::Error> {
     tracing::info!("Starting `strucvars aggregate`");
     tracing::info!("  common_args = {:?}", &common_args);

src/strucvars/query/bgdbs.rs

@@ -133,7 +133,7 @@ impl BeginEnd for BgDbRecord {
     }
 }
 
-/// Load background database from a `.bin` file as created by `sv convert-bgdb`.
+/// Load background database from a `.bin` file as created by `strucvar txt-to-bin`.
 #[tracing::instrument]
 pub fn load_bg_db_records(path: &Path) -> Result<BgDb, anyhow::Error> {
     tracing::debug!("loading binary bg db records from {:?}", path);

src/strucvars/query/genes.rs

@@ -1,90 +1,13 @@
 //! Code for supporting annotation with overlapping genes.
 
-use std::{collections::HashSet, ops::Range, path::Path, time::Instant};
+use std::{collections::HashSet, path::Path, time::Instant};
 
-use bio::data_structures::interval_tree::ArrayBackedIntervalTree;
 use mehari::common::open_read_maybe_gz;
 use prost::Message;
 use serde::Deserialize;
 use tracing::info;
 
-use crate::{
-    common::{Database, GenomeRelease, CHROMS},
-    strucvars::pbs,
-};
-
-/// Alias for the interval tree that we use.
-type IntervalTree = ArrayBackedIntervalTree<i32, u32>;
-
-/// Information to store for a TAD set entry.
-#[derive(Default, Clone, Debug)]
-pub struct GeneRegionRecord {
-    /// 0-based begin position.
-    pub begin: i32,
-    /// End position.
-    pub end: i32,
-    /// gene ID
-    pub gene_id: u32,
-}
-
-/// Gene region overlapping information.
-#[derive(Default, Debug)]
-pub struct GeneRegionDb {
-    /// Records, stored by chromosome.
-    pub records: Vec<Vec<GeneRegionRecord>>,
-    /// Interval trees, stored by chromosome.
-    pub trees: Vec<IntervalTree>,
-}
-
-impl GeneRegionDb {
-    /// Return IDs of overlapping genes.
-    pub fn overlapping_gene_ids(&self, chrom_no: u32, query: Range<i32>) -> Vec<u32> {
-        self.trees[chrom_no as usize]
-            .find(query)
-            .iter()
-            .map(|cursor| self.records[chrom_no as usize][*cursor.data() as usize].gene_id)
-            .collect()
-    }
-}
-
-#[tracing::instrument]
-fn load_gene_regions_db(path: &Path) -> Result<GeneRegionDb, anyhow::Error> {
-    tracing::debug!("loading binary gene region records from {:?}...", path);
-
-    let before_loading = Instant::now();
-    let mut result = GeneRegionDb::default();
-    for _ in CHROMS {
-        result.records.push(Vec::new());
-        result.trees.push(IntervalTree::new());
-    }
-
-    let fcontents =
-        std::fs::read(path).map_err(|e| anyhow::anyhow!("error reading {:?}: {}", &path, e))?;
-    let gene_region_db = pbs::GeneRegionDatabase::decode(std::io::Cursor::new(fcontents))
-        .map_err(|e| anyhow::anyhow!("error decoding {:?}: {}", &path, e))?;
-
-    let mut total_count = 0;
-    for record in gene_region_db.records.into_iter() {
-        let chrom_no = record.chrom_no as usize;
-        let key = (record.start - 1)..record.stop;
-        result.trees[chrom_no].insert(key, result.records[chrom_no].len() as u32);
-        result.records[chrom_no].push(GeneRegionRecord {
-            begin: record.start - 1,
-            end: record.stop,
-            gene_id: record.gene_id,
-        });
-
-        total_count += 1;
-    }
-    result.trees.iter_mut().for_each(|tree| tree.index());
-    tracing::debug!(
-        "... done loading {} records and building trees in {:?}",
-        total_count,
-        before_loading.elapsed(),
-    );
-
-    Ok(result)
-}
+use crate::{common::GenomeRelease, strucvars::pbs};
 
 /// Information to store for the interlink table.
 #[derive(Default, Debug)]
@@ -108,43 +31,6 @@ pub struct XlinkDb {
     pub from_hgnc: multimap::MultiMap<String, u32>,
 }
 
-impl XlinkDb {
-    fn entrez_id_to_symbols(&self, entrez_id: u32) -> Vec<String> {
-        let mut tmp = self
-            .from_entrez
-            .get_vec(&entrez_id)
-            .map_or(Vec::new(), |idxs| {
-                idxs.iter()
-                    .map(|idx| self.records[*idx as usize].symbol.clone())
-                    .collect::<Vec<String>>()
-            });
-        tmp.sort();
-        tmp.dedup();
-        tmp
-    }
-
-    fn ensembl_to_symbols(&self, ensembl_id: u32) -> Vec<String> {
-        let mut tmp = self
-            .from_ensembl
-            .get_vec(&ensembl_id)
-            .map_or(Vec::new(), |idxs| {
-                idxs.iter()
-                    .map(|idx| self.records[*idx as usize].symbol.clone())
-                    .collect::<Vec<String>>()
-            });
-        tmp.sort();
-        tmp.dedup();
-        tmp
-    }
-
-    pub fn gene_id_to_symbols(&self, database: Database, gene_id: u32) -> Vec<String> {
-        match database {
-            Database::RefSeq => self.entrez_id_to_symbols(gene_id),
-            Database::Ensembl => self.ensembl_to_symbols(gene_id),
-        }
-    }
-}
-
 #[tracing::instrument]
 fn load_xlink_db(path: &Path) -> Result<XlinkDb, anyhow::Error> {
     tracing::debug!("loading binary xlink records from {:?}...", path);
@@ -287,44 +173,17 @@ fn load_mim2gene_db(path: &Path) -> Result<OmimDb, anyhow::Error> {
 /// Bundle of gene region DBs and the xlink info packaged with VarFish.
 #[derive(Default, Debug)]
 pub struct GeneDb {
-    pub refseq: GeneRegionDb,
-    pub ensembl: GeneRegionDb,
     pub xlink: XlinkDb,
     pub acmg: AcmgDb,
     pub mim2gene: OmimDb,
 }
 
-impl GeneDb {
-    /// Return IDs of overlapping genes.
-    pub fn overlapping_gene_ids(
-        &self,
-        database: Database,
-        chrom_no: u32,
-        query: Range<i32>,
-    ) -> Vec<u32> {
-        match database {
-            Database::RefSeq => self.refseq.overlapping_gene_ids(chrom_no, query),
-            Database::Ensembl => self.ensembl.overlapping_gene_ids(chrom_no, query),
-        }
-    }
-}
-
 // Load all gene information, such as region, id mapping and symbols.
 #[tracing::instrument]
 pub fn load_gene_db(path_db: &str, genome_release: GenomeRelease) -> Result<GeneDb, anyhow::Error> {
     info!("Loading gene dbs");
 
     let result = GeneDb {
-        refseq: load_gene_regions_db(
-            Path::new(path_db)
-                .join(format!("{}/genes/refseq_regions.bin", genome_release))
-                .as_path(),
-        )?,
-        ensembl: load_gene_regions_db(
-            Path::new(path_db)
-                .join(format!("{}/genes/ensembl_regions.bin", genome_release))
-                .as_path(),
-        )?,
         xlink: load_xlink_db(Path::new(path_db).join("noref/genes/xlink.bin").as_path())?,
         acmg: load_acmg_db(Path::new(path_db).join("noref/genes/acmg.tsv").as_path())?,
         mim2gene: load_mim2gene_db(