From 85baec9336c3e8e7936ab024321d2caee1352b1e Mon Sep 17 00:00:00 2001
From: Michael Hall <michael@mbh.sh>
Date: Mon, 22 Jul 2024 16:28:15 +1000
Subject: [PATCH] fix: IMPORTANT!! previous versions were emitting human reads
 [see #2]

---
 src/download.rs | 2 +-
 src/lib.rs      | 1 -
 src/main.rs     | 2 +-
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/download.rs b/src/download.rs
index 9ee0e17..95b7609 100644
--- a/src/download.rs
+++ b/src/download.rs
@@ -146,7 +146,7 @@ mod tests {
     use tempfile::TempDir;
 
     pub fn check_internet_connection(timeout: std::time::Duration) -> bool {
-        use std::net::{TcpStream, SocketAddr};
+        use std::net::{SocketAddr, TcpStream};
 
         let addr = "8.8.8.8:53".parse::<SocketAddr>().unwrap();
         TcpStream::connect_timeout(&addr, timeout).is_ok()
diff --git a/src/lib.rs b/src/lib.rs
index d8157ea..2eebf58 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -98,7 +98,6 @@ pub fn validate_db_directory(path: &Path) -> Result<PathBuf, String> {
     ))
 }
 
-
 #[cfg(test)]
 mod tests {
     use super::*;
diff --git a/src/main.rs b/src/main.rs
index 14c1ed8..ba34aaf 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -155,7 +155,7 @@ fn main() -> Result<()> {
         tmpdir.path().join("kraken_out.fq")
     };
     let outfile = outfile.to_string_lossy().to_string();
-    kraken_cmd.extend(&["--classified-out", &outfile]);
+    kraken_cmd.extend(&["--unclassified-out", &outfile]);
 
     kraken_cmd.extend(input.iter().map(|p| p.to_str().unwrap()));
     info!("Running kraken2...");