Add support for auto-detecting interleaved FASTQ

Author: dagou

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "kun_peng"
-version = "0.7.5"
+version = "0.7.6"
 edition = "2021"
 authors = ["[email protected]"]
 description = "Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all"
@@ -19,7 +19,7 @@ double_hashing = []
 exact_counting = []
 
 [dependencies]
-seqkmer = "0.1.2"
+seqkmer = "0.1.3"
 clap = { version = "4.4.10", features = ["derive"] }
 hyperloglogplus = { version = "0.4.1", features = ["const-loop"] }
 seahash = "4.1.0"
@@ -38,8 +38,8 @@ num_cpus = "1.13.1"
 jemallocator = "0.5.4"
 
 [dev-dependencies]
-criterion = "0.5.1"
-twox-hash = "1.6.3"
+criterion = "0.7.0"
+twox-hash = "2.1.2"
 farmhash = { version = "1.1.5" }
 
 [profile.release]

data/test_interleaved.fastq

@@ -0,0 +1,24 @@
+@pair_A/1
+AGCAGAAGCGGAGCTTTAAGATGAATATAAATCCATATTTTCTTTCATAG
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@pair_A/2
+ATGACGTTGGCTAAAATTGAACTACTAAAGCAGCTGTTAAGGGACAATGA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@pair_B/1 This is the R1 read
+ATGGATACTTTTATTACAAAGAATTTCCAGACTACAATAATACAAAAGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@pair_B/2 This is the R2 read
+AGCAGAAGCGTTGCATTTTCTAATATCCACAAAATGAAGGCAATAATTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@pair_C/1
+GGCAGAAGCACAGCATTTTCTTGTGAGCTTCGAGCACTAATAAAACTGAA
++
+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+@pair_C/2
+AGCAGAAGCAGAGCATATTCTTAGAACTGAAGTGAACAGGCCAAAAATGA
++
+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH

examples/build_and_classify.rs

@@ -76,4 +76,46 @@ fn main() {
             String::from_utf8_lossy(&direct_output.stderr)
         );
     }
+
+    // --- Test 3: ./target/release/kun_peng direct --db test_database data/test_interleaved.fastq ---
+    println!("\n--- Testing Interleaved FASTQ Classification ---");
+
+    let interleaved_fq = data_dir.join("test_interleaved.fastq");
+    if !interleaved_fq.exists() {
+        println!(
+            "kun_peng error: fastq file {} does not exists",
+            interleaved_fq.to_string_lossy().to_string()
+        );
+        // 考虑在这里 panic，如果文件不存在，测试就没有意义
+        // panic!("Test FASTQ file not found!"); 
+    }
+    let direct_fastq_args = vec![
+        "direct".to_string(),
+        "--db".to_string(),
+        test_dir.to_string_lossy().to_string(),
+        interleaved_fq.to_string_lossy().to_string(),
+    ];
+
+    let direct_fastq_command_str = format!(
+        "{} {}",
+        kr2r_binary.to_string_lossy(),
+        direct_fastq_args.join(" ")
+    );
+    println!("Executing command: {}", direct_fastq_command_str);
+
+    let direct_fastq_output = Command::new(&kr2r_binary)
+        .args(&direct_fastq_args)
+        .output()
+        .expect("Failed to run kun_peng direct command with interleaved FASTQ");
+    
+    println!(
+        "kun_peng direct (fastq) output: {}",
+        String::from_utf8_lossy(&direct_fastq_output.stdout)
+    );
+    if !direct_fastq_output.stderr.is_empty() {
+        println!(
+            "kun_peng direct (fastq) error: {}",
+            String::from_utf8_lossy(&direct_fastq_output.stderr)
+        );
+    }
 }