feat: allow BGZ files for guess_sv_caller (#203)

src/annotate/strucvars/mod.rs

@@ -10,7 +10,7 @@ use std::path::Path;
 use std::str::FromStr;
 use std::{fs::File, io::BufWriter};
 
-use crate::common::GenomeRelease;
+use crate::common::{open_read_maybe_gz, GenomeRelease};
 use crate::ped::PedigreeByName;
 use annonars::common::cli::CANONICAL;
 use annonars::freqs::cli::import::reading::guess_assembly;
@@ -1631,7 +1631,8 @@ pub fn guess_sv_caller<P>(p: P) -> Result<SvCaller, anyhow::Error>
 where
     P: AsRef<Path>,
 {
-    let mut reader = noodles_vcf::reader::Builder.build_from_path(p)?;
+    let reader = open_read_maybe_gz(p)?;
+    let mut reader = noodles_vcf::reader::Builder.build_from_reader(reader)?;
     let header = reader.read_header()?;
     let mut records = reader.records(&header);
     let record = records

src/common.rs

@@ -1,10 +1,16 @@
 //! Commonly used code.
 
-use std::ops::Range;
+use std::{
+    fs::File,
+    io::{BufRead, BufReader},
+    ops::Range,
+    path::Path,
+};
 
 use byte_unit::Byte;
 use clap::Parser;
 use clap_verbosity_flag::{InfoLevel, Verbosity};
+use flate2::bufread::MultiGzDecoder;
 use hgvs::static_data::Assembly;
 
 /// Commonly used command line arguments.
@@ -92,6 +98,24 @@ pub fn version() -> &'static str {
     return VERSION;
 }
 
+/// Transparently open a file with gzip decoder.
+pub fn open_read_maybe_gz<P>(path: P) -> Result<Box<dyn BufRead>, anyhow::Error>
+where
+    P: AsRef<Path>,
+{
+    if path.as_ref().extension().map(|s| s.to_str()) == Some(Some("gz")) {
+        tracing::trace!("Opening {:?} as gzip for reading", path.as_ref());
+        let file = File::open(path)?;
+        let bufreader = BufReader::new(file);
+        let decoder = MultiGzDecoder::new(bufreader);
+        Ok(Box::new(BufReader::new(decoder)))
+    } else {
+        tracing::trace!("Opening {:?} as plain text for reading", path.as_ref());
+        let file = File::open(path).map(BufReader::new)?;
+        Ok(Box::new(BufReader::new(file)))
+    }
+}
+
 /// Version information that is returned by the HTTP server.
 #[derive(serde::Serialize, serde::Deserialize, Default, Debug, Clone)]
 #[serde_with::skip_serializing_none]
@@ -114,3 +138,37 @@ impl Version {
         }
     }
 }
+
+#[macro_export]
+macro_rules! set_snapshot_suffix {
+    ($($expr:expr),*) => {
+        let mut settings = insta::Settings::clone_current();
+        settings.set_snapshot_suffix(format!($($expr,)*));
+        let _guard = settings.bind_to_scope();
+    }
+}
+
+pub use set_snapshot_suffix;
+
+#[cfg(test)]
+mod test {
+    #[rstest::rstest]
+    #[case(true)]
+    #[case(false)]
+    fn open_read_maybe_gz(#[case] is_gzip: bool) -> Result<(), anyhow::Error> {
+        crate::common::set_snapshot_suffix!("{:?}", is_gzip);
+
+        let mut f = super::open_read_maybe_gz(if is_gzip {
+            "tests/common/test.txt.gz"
+        } else {
+            "tests/common/test.txt"
+        })?;
+
+        let mut buf = String::new();
+        f.read_to_string(&mut buf)?;
+
+        insta::assert_snapshot!(&buf);
+
+        Ok(())
+    }
+}

src/snapshots/mehari__common__test__open_read_maybe_gz@false.snap

@@ -0,0 +1,6 @@
+---
+source: src/common.rs
+expression: "&buf"
+---
+payload
+

src/snapshots/mehari__common__test__open_read_maybe_gz@true.snap

@@ -0,0 +1,6 @@
+---
+source: src/common.rs
+expression: "&buf"
+---
+payload
+

tests/common/test.txt

@@ -0,0 +1 @@
+payload