Improve compression rate with zlip compression

Author: marshallku

Cargo.lock

@@ -8,3 +8,4 @@ license = "MIT"
 repository = "https://github.com/marshallku/base-sequence-compression"
 
 [dependencies]
+flate2 = "1.0.35"

Cargo.toml

@@ -1,3 +1,9 @@
+use std::io::{self, Read, Write};
+
+use flate2::read::ZlibDecoder;
+use flate2::write::ZlibEncoder;
+use flate2::Compression;
+
 /// The bit pattern for the base 'A' (00).
 pub const A_BITS: u8 = 0b00;
 /// The bit pattern for the base 'C' (01).
@@ -28,12 +34,12 @@ pub fn compress_sequence(sequence: &str) -> Vec<u8> {
     for base in sequence.chars() {
         let bits = match base {
             'A' => A_BITS,
-            'C' => C_BITS,
-            'T' => T_BITS,
-            'G' => G_BITS,
             'a' => A_BITS,
+            'C' => C_BITS,
             'c' => C_BITS,
+            'T' => T_BITS,
             't' => T_BITS,
+            'G' => G_BITS,
             'g' => G_BITS,
             _ => continue,
         };
@@ -53,7 +59,10 @@ pub fn compress_sequence(sequence: &str) -> Vec<u8> {
         compressed.push(current_byte);
     }
 
-    compressed
+    // Apply ZLIB compression
+    let mut encoder = ZlibEncoder::new(Vec::new(), Compression::best());
+    encoder.write_all(&compressed).unwrap();
+    encoder.finish().unwrap()
 }
 
 /// Decompresses a vector of bytes into a DNA sequence string.
@@ -69,10 +78,14 @@ pub fn compress_sequence(sequence: &str) -> Vec<u8> {
 /// # Returns
 ///
 /// A string containing the decompressed DNA sequence.
-pub fn decompress_sequence(compressed: &[u8], sequence_length: usize) -> String {
+pub fn decompress_sequence(compressed: &[u8], sequence_length: usize) -> io::Result<String> {
+    let mut decoder = ZlibDecoder::new(compressed);
+    let mut decompressed_data = Vec::new();
+    decoder.read_to_end(&mut decompressed_data)?;
+
     let mut sequence = String::new();
 
-    for &byte in compressed {
+    for &byte in &decompressed_data {
         let mut current_byte = byte;
         for _ in 0..4 {
             if sequence.len() >= sequence_length {
@@ -90,5 +103,5 @@ pub fn decompress_sequence(compressed: &[u8], sequence_length: usize) -> String
         }
     }
 
-    sequence
+    Ok(sequence)
 }

src/lib.rs

@@ -9,7 +9,7 @@ mod tests {
         let dna_sequence = "ACGTACGTACGT";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
 
         assert_eq!(dna_sequence, decompressed);
     }
@@ -19,7 +19,7 @@ mod tests {
         let dna_sequence = "";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
         assert_eq!(dna_sequence, decompressed);
     }
 
@@ -28,7 +28,7 @@ mod tests {
         let dna_sequence = "A";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
         assert_eq!(dna_sequence, decompressed);
     }
 
@@ -37,7 +37,7 @@ mod tests {
         let dna_sequence = "C";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
         assert_eq!(dna_sequence, decompressed);
     }
 
@@ -46,7 +46,7 @@ mod tests {
         let dna_sequence = "T";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
         assert_eq!(dna_sequence, decompressed);
     }
 
@@ -55,7 +55,7 @@ mod tests {
         let dna_sequence = "G";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
         assert_eq!(dna_sequence, decompressed);
     }
 
@@ -64,7 +64,7 @@ mod tests {
         let dna_sequence = "ACGTACGTA";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
         assert_eq!(dna_sequence, decompressed);
     }
 
@@ -73,7 +73,7 @@ mod tests {
         let dna_sequence = "ACGTACGTAC";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
         assert_eq!(dna_sequence, decompressed);
     }
 
@@ -82,7 +82,7 @@ mod tests {
         let dna_sequence = "ACGTACGTACG";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
         assert_eq!(dna_sequence, decompressed);
     }
 
@@ -91,7 +91,7 @@ mod tests {
         let dna_sequence = "acgt";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
 
         assert_eq!(dna_sequence.to_uppercase(), decompressed);
     }
@@ -101,7 +101,7 @@ mod tests {
         let dna_sequence = "ACXGT";
         let compressed = compress_sequence(dna_sequence);
         let sequence_length = dna_sequence.len();
-        let decompressed = decompress_sequence(&compressed, sequence_length);
+        let decompressed = decompress_sequence(&compressed, sequence_length).unwrap();
 
         assert_eq!("ACGT", decompressed);
     }