fix: using custom S3 endpoint (#362)

varfish-org · Jun 6, 2024 · 06334e6 · 06334e6
1 parent 6fe8f9f
commit 06334e6
Show file tree

Hide file tree

Showing 12 changed files with 444 additions and 297 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -4,19 +4,19 @@ version = "0.11.0"
 authors = ["Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>"]
 description = "Rust-based worker for varfish-server"
 license = "MIT"
-homepage = "https://github.com/bihealth/varfish-server-worker"
+repository = "https://github.com/bihealth/varfish-server-worker"
 edition = "2021"
 readme = "README.md"
-rust-version = "1.64.0"
+rust-version = "1.70.0"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
 annonars = "0.36"
 anyhow = "1.0"
 async-compression = { version = "0.4", features = ["tokio", "gzip"] }
-aws-sdk-s3 = "0.34"
-aws-config = "0.56"
+aws-sdk-s3 = { version = "1.33", features = ["behavior-version-latest"] }
+aws-config = { version = "1.5", features = ["behavior-version-latest"] }
 base16ct = "0.2"
 bio = "1.4"
 biocommons-bioutils = "0.1"

diff --git a/src/common/noodles.rs b/src/common/noodles.rs
@@ -101,19 +101,51 @@ pub async fn s3_open_read_maybe_gz<P>(path: P) -> Result<Pin<Box<dyn AsyncBufRea
 where
     P: AsRef<Path>,
 {
+    // Get configuration from environment variables.
+    let access_key = if let Ok(access_key) = std::env::var("AWS_ACCESS_KEY_ID") {
+        access_key
+    } else {
+        anyhow::bail!("could not access key from env AWS_ACCESS_KEY_ID")
+    };
+    let secret_key = if let Ok(secret_key) = std::env::var("AWS_SECRET_ACCESS_KEY") {
+        secret_key
+    } else {
+        anyhow::bail!("could not get secret key from env AWS_SECRET_ACCESS_KEY")
+    };
+    let endpoint_url = if let Ok(endpoint_url) = std::env::var("AWS_ENDPOINT_URL") {
+        endpoint_url
+    } else {
+        anyhow::bail!("could not get endpoint url from env AWS_ENDPOINT_URL")
+    };
+    let region = if let Ok(region) = std::env::var("AWS_REGION") {
+        region
+    } else {
+        anyhow::bail!("could not AWS region from env AWS_REGION")
+    };
+
+    let cred =
+        aws_sdk_s3::config::Credentials::new(access_key, secret_key, None, None, "loaded-from-env");
+    let s3_config = aws_sdk_s3::config::Builder::new()
+        .endpoint_url(&endpoint_url)
+        .credentials_provider(cred)
+        .region(aws_config::Region::new(region))
+        .force_path_style(true) // apply bucketname as path param instead of pre-domain
+        .build();
+
+    // Split bucket and path from input path.
     let path_string = format!("{}", path.as_ref().display());
     let (bucket, key) = if let Some((bucket, key)) = path_string.split_once('/') {
         (bucket.to_string(), key.to_string())
     } else {
         anyhow::bail!("invalid S3 path: {}", path.as_ref().display());
     };
 
-    let config = aws_config::load_from_env().await;
-    let client = aws_sdk_s3::Client::new(&config);
+    // Setup S3 client and access object.
+    let client = aws_sdk_s3::Client::from_conf(s3_config);
     let object = client.get_object().bucket(&bucket).key(&key).send().await?;
 
     let path_is_gzip = is_gz(path.as_ref());
-    tracing::trace!(
+    tracing::debug!(
         "Opening S3 object {} as {} for reading (async)",
         path.as_ref().display(),
         if path_is_gzip {
@@ -155,21 +187,19 @@ pub async fn open_vcf_readers(paths: &[String]) -> Result<Vec<AsyncVcfReader>, a
 /// The behaviour is as follows:
 ///
 /// - If `path_in` is "-" then open stdin and read as plain text.
-/// - If environment variable `AWS_PROFILE` is set to "varfish-s3" then enable S3 mode.
+/// - If environment variable `AWS_ACCESS_KEY_ID` is set then enable S3 mode.
 /// - If `path_in` is absolute or S3 mode is disabled then open `path_in` as local file
 /// - Otherwise, attempt to open `path_in` as S3 object.
 pub async fn open_vcf_reader(path_in: &str) -> Result<AsyncVcfReader, anyhow::Error> {
-    let s3_mode = match std::env::var("AWS_PROFILE") {
-        Ok(s) => s == "varfish-s3",
-        _ => false,
-    };
-    if s3_mode && !path_in.starts_with('/') {
+    if super::s3::s3_mode() && path_in != "-" && !path_in.starts_with('/') {
+        tracing::debug!("Opening S3 object {} for reading (async)", path_in);
         Ok(vcf::AsyncReader::new(
             s3_open_read_maybe_gz(path_in)
                 .await
                 .map_err(|e| anyhow::anyhow!("could not build VCF reader from S3 file: {}", e))?,
         ))
     } else {
+        tracing::debug!("Opening local file {} for reading (async)", path_in);
         Ok(vcf::AsyncReader::new(
             open_read_maybe_gz(path_in).await.map_err(|e| {
                 anyhow::anyhow!("could not build VCF reader from local file: {}", e)

diff --git a/src/common/s3.rs b/src/common/s3.rs
@@ -4,7 +4,9 @@ use mehari::common::io::std::is_gz;
 
 /// Helper that returns whether S3 mode has been enabled via `AWS_ACCESS_KEY_ID`.
 pub fn s3_mode() -> bool {
-    std::env::var("AWS_ACCESS_KEY_ID").is_ok()
+    let result = std::env::var("AWS_ACCESS_KEY_ID").is_ok();
+    tracing::trace!("S3 mode is {}", if result { "enabled" } else { "disabled" });
+    result
 }
 
 /// Return the S3 configuration from environment variables.

diff --git a/src/seqvars/ingest/mod.rs b/src/seqvars/ingest/mod.rs
@@ -2,14 +2,15 @@
 
 use std::sync::{Arc, OnceLock};
 
+use crate::common::noodles::open_vcf_reader;
 use crate::{
     common::{self, worker_version, GenomeRelease},
     flush_and_shutdown,
 };
 use futures::TryStreamExt;
 use mehari::{
     annotate::seqvars::provider::Provider as MehariProvider,
-    common::noodles::{open_vcf_reader, open_vcf_writer, AsyncVcfReader, AsyncVcfWriter},
+    common::noodles::{open_vcf_writer, AsyncVcfReader, AsyncVcfWriter},
 };
 use noodles_vcf as vcf;
 use thousands::Separable;
@@ -427,7 +428,7 @@ async fn process_variants(
                         &mut output_record,
                     )?;
                 } else {
-                    tracing::trace!(
+                    tracing::debug!(
                         "Record @{:?} on non-canonical chromosome, skipping.",
                         &vcf_var
                     );

diff --git a/src/seqvars/prefilter/mod.rs b/src/seqvars/prefilter/mod.rs
@@ -2,13 +2,11 @@
 
 use std::io::BufRead;
 
+use crate::common::noodles::open_vcf_reader;
 use futures::TryStreamExt;
 use mehari::{
     annotate::seqvars::ann::AnnField,
-    common::{
-        io::std::is_gz,
-        noodles::{open_vcf_reader, open_vcf_writer, AsyncVcfReader, AsyncVcfWriter},
-    },
+    common::noodles::{open_vcf_writer, AsyncVcfReader, AsyncVcfWriter},
 };
 use noodles_vcf as vcf;
 use thousands::Separable;
@@ -20,7 +18,7 @@ use crate::{common, flush_and_shutdown};
 #[derive(Debug, Clone, serde::Deserialize, serde::Serialize)]
 struct PrefilterParams {
     /// Path to output file.
-    pub path_out: String,
+    pub prefilter_path: String,
     /// Maximal allele population frequency.
     pub max_freq: f64,
     /// Maximal distance to exon.
@@ -216,9 +214,10 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
     {
         tracing::info!("opening output files...");
         let mut output_writers = Vec::new();
+        let mut out_path_helpers = Vec::new();
         for params in params_list.iter() {
             let header_params = PrefilterParams {
-                path_out: "<stripped>".into(),
+                prefilter_path: "<stripped>".into(),
                 ..params.clone()
             };
             let mut header = header.clone();
@@ -232,9 +231,17 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
                 ),
             )?;
 
-            let mut writer = open_vcf_writer(&params.path_out).await?;
+            out_path_helpers.push(crate::common::s3::OutputPathHelper::new(
+                &params.prefilter_path,
+            )?);
+            let mut writer =
+                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 {}: {}", &params.path_out, e)
+                anyhow::anyhow!(
+                    "could not write header to {}: {}",
+                    &params.prefilter_path,
+                    e
+                )
             })?;
             output_writers.push(writer);
         }
@@ -248,28 +255,14 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
         for output_writer in output_writers.drain(..) {
             flush_and_shutdown!(output_writer);
         }
-    }
-
-    for params in params_list.iter() {
-        if is_gz(&params.path_out) {
-            tracing::info!("writing TBI index for {}...", &params.path_out);
-            crate::common::noodles::build_tbi(
-                &params.path_out,
-                &format!("{}.tbi", &params.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 {}",
-                &params.path_out
-            );
+        for out_path_helper in out_path_helpers.drain(..) {
+            out_path_helper.create_tbi_for_bgzf().await?;
+            out_path_helper.upload_for_s3().await?;
         }
     }
 
     tracing::info!(
-        "All of `seqvars ingest` completed in {:?}",
+        "All of `seqvars prefilter` completed in {:?}",
         before_anything.elapsed()
     );
     Ok(())
@@ -285,7 +278,7 @@ mod test {
             path_in: "tests/seqvars/prefilter/ingest.vcf".into(),
             params: vec![format!(
                 r#"{{
-                    "path_out": "{}/out-1.vcf",
+                    "prefilter_path": "{}/out-1.vcf",
                     "max_freq": 0.01,
                     "max_exon_dist": 200
                 }}"#,
@@ -301,7 +294,7 @@ mod test {
         ))
         .exists());
 
-        insta::assert_snapshot!(std::fs::read_to_string(&format!(
+        insta::assert_snapshot!(std::fs::read_to_string(format!(
             "{}/out-1.vcf",
             tmpdir.to_path_buf().to_str().unwrap()
         ))?);
@@ -314,7 +307,7 @@ mod test {
         let tmpdir = temp_testdir::TempDir::default();
 
         let params_json = format!(
-            r#"{{"path_out": "{}/out-1.vcf", "max_freq": 0.01, "max_exon_dist": 200}}"#,
+            r#"{{"prefilter_path": "{}/out-1.vcf", "max_freq": 0.01, "max_exon_dist": 200}}"#,
             tmpdir.to_path_buf().to_str().unwrap()
         );
 
@@ -334,7 +327,7 @@ mod test {
         ))
         .exists());
 
-        insta::assert_snapshot!(std::fs::read_to_string(&format!(
+        insta::assert_snapshot!(std::fs::read_to_string(format!(
             "{}/out-1.vcf",
             tmpdir.to_path_buf().to_str().unwrap()
         ))?);
@@ -351,15 +344,15 @@ mod test {
             params: vec![
                 format!(
                     r#"{{
-                        "path_out": "{}/out-1.vcf",
+                        "prefilter_path": "{}/out-1.vcf",
                         "max_freq": 0.01,
                         "max_exon_dist": 200
                     }}"#,
                     tmpdir.to_path_buf().to_str().unwrap()
                 ),
                 format!(
                     r#"{{
-                        "path_out": "{}/out-2.vcf",
+                        "prefilter_path": "{}/out-2.vcf",
                         "max_freq": 0,
                         "max_exon_dist": 20
                     }}"#,
@@ -381,11 +374,11 @@ mod test {
         ))
         .exists());
 
-        insta::assert_snapshot!(std::fs::read_to_string(&format!(
+        insta::assert_snapshot!(std::fs::read_to_string(format!(
             "{}/out-1.vcf",
             tmpdir.to_path_buf().to_str().unwrap()
         ))?);
-        insta::assert_snapshot!(std::fs::read_to_string(&format!(
+        insta::assert_snapshot!(std::fs::read_to_string(format!(
             "{}/out-2.vcf",
             tmpdir.to_path_buf().to_str().unwrap()
         ))?);

diff --git a/...efilter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_arg.snap b/...efilter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_arg.snap
@@ -1,6 +1,6 @@
 ---
 source: src/seqvars/prefilter/mod.rs
-expression: "std::fs::read_to_string(&format!(\"{}/out-1.vcf\",\n                tmpdir.to_path_buf().to_str().unwrap()))?"
+expression: "std::fs::read_to_string(format!(\"{}/out-1.vcf\",\n            tmpdir.to_path_buf().to_str().unwrap()))?"
 ---
 ##fileformat=VCFv4.4
 ##INFO=<ID=gnomad_exomes_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD exomes">
@@ -54,8 +54,7 @@ expression: "std::fs::read_to_string(&format!(\"{}/out-1.vcf\",\n
 ##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">
-##x-varfish-prefilter-params={"path_out":"<stripped>","max_freq":0.01,"max_exon_dist":200}
+##x-varfish-prefilter-params={"prefilter_path":"<stripped>","max_freq":0.01,"max_exon_dist":200}
 #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
 17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|	GT:AD:DP:GQ	0/0:29:29:87	0/1:23:36:99	0/1:15:32:99
 MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	1/1:0:2757:99	1/1:0:2392:99	1/1:0:1621:99
-
diff --git a/...filter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_file.snap b/...filter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_file.snap
@@ -1,6 +1,6 @@
 ---
 source: src/seqvars/prefilter/mod.rs
-expression: "std::fs::read_to_string(&format!(\"{}/out-1.vcf\",\n                tmpdir.to_path_buf().to_str().unwrap()))?"
+expression: "std::fs::read_to_string(format!(\"{}/out-1.vcf\",\n            tmpdir.to_path_buf().to_str().unwrap()))?"
 ---
 ##fileformat=VCFv4.4
 ##INFO=<ID=gnomad_exomes_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD exomes">
@@ -54,8 +54,7 @@ expression: "std::fs::read_to_string(&format!(\"{}/out-1.vcf\",\n
 ##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">
-##x-varfish-prefilter-params={"path_out":"<stripped>","max_freq":0.01,"max_exon_dist":200}
+##x-varfish-prefilter-params={"prefilter_path":"<stripped>","max_freq":0.01,"max_exon_dist":200}
 #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
 17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|	GT:AD:DP:GQ	0/0:29:29:87	0/1:23:36:99	0/1:15:32:99
 MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	1/1:0:2757:99	1/1:0:2392:99	1/1:0:1621:99
-
diff --git a/...refilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg-2.snap b/...refilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg-2.snap
@@ -1,6 +1,6 @@
 ---
 source: src/seqvars/prefilter/mod.rs
-expression: "std::fs::read_to_string(&format!(\"{}/out-2.vcf\",\n                tmpdir.to_path_buf().to_str().unwrap()))?"
+expression: "std::fs::read_to_string(format!(\"{}/out-2.vcf\",\n            tmpdir.to_path_buf().to_str().unwrap()))?"
 ---
 ##fileformat=VCFv4.4
 ##INFO=<ID=gnomad_exomes_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD exomes">
@@ -54,7 +54,6 @@ expression: "std::fs::read_to_string(&format!(\"{}/out-2.vcf\",\n
 ##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">
-##x-varfish-prefilter-params={"path_out":"<stripped>","max_freq":0.0,"max_exon_dist":20}
+##x-varfish-prefilter-params={"prefilter_path":"<stripped>","max_freq":0.0,"max_exon_dist":20}
 #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
 MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	1/1:0:2757:99	1/1:0:2392:99	1/1:0:1621:99
-
diff --git a/.../prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg.snap b/.../prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg.snap
@@ -1,6 +1,6 @@
 ---
 source: src/seqvars/prefilter/mod.rs
-expression: "std::fs::read_to_string(&format!(\"{}/out-1.vcf\",\n                tmpdir.to_path_buf().to_str().unwrap()))?"
+expression: "std::fs::read_to_string(format!(\"{}/out-1.vcf\",\n            tmpdir.to_path_buf().to_str().unwrap()))?"
 ---
 ##fileformat=VCFv4.4
 ##INFO=<ID=gnomad_exomes_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD exomes">
@@ -54,8 +54,7 @@ expression: "std::fs::read_to_string(&format!(\"{}/out-1.vcf\",\n
 ##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">
-##x-varfish-prefilter-params={"path_out":"<stripped>","max_freq":0.01,"max_exon_dist":200}
+##x-varfish-prefilter-params={"prefilter_path":"<stripped>","max_freq":0.01,"max_exon_dist":200}
 #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
 17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|	GT:AD:DP:GQ	0/0:29:29:87	0/1:23:36:99	0/1:15:32:99
 MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	1/1:0:2757:99	1/1:0:2392:99	1/1:0:1621:99
-
diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs
@@ -97,11 +97,11 @@ fn passes_for_gene(
         .iter()
         .for_each(|(sample_name, genotype_choice)| match genotype_choice {
             Some(GenotypeChoice::ComphetIndex) => {
-                index_name = sample_name.clone();
+                index_name.clone_from(sample_name);
                 mode = Mode::ComphetRecessive;
             }
             Some(GenotypeChoice::RecessiveIndex) => {
-                index_name = sample_name.clone();
+                index_name.clone_from(sample_name);
                 mode = Mode::Recessive;
             }
             Some(GenotypeChoice::RecessiveParent) => {

diff --git a/src/strucvars/ingest/mod.rs b/src/strucvars/ingest/mod.rs
@@ -1,11 +1,12 @@
 //! Implementation of `strucvars ingest` subcommand.
 
+use crate::common::noodles::open_vcf_readers;
 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_readers, open_vcf_writer, AsyncVcfReader, AsyncVcfWriter};
+use mehari::common::noodles::{open_vcf_writer, AsyncVcfReader, AsyncVcfWriter};
 use noodles_vcf as vcf;
 use rand_core::SeedableRng;
 use tokio::io::AsyncWriteExt;