fixing simple things like removing unused code and imports before I t…

…ry to merge encode/decode kmers and reverse_comp between the ska and skalo code

src/cli.rs

@@ -358,6 +358,7 @@ pub enum Commands {
         #[arg(long, default_value_t = DEFAULT_STRAND)]
         single_strand: bool,
     },
+    /// Finds 'left out' SNPs and INDELs using a graph
     Lo {
         /// input SKA2 file
         #[arg(short = 'i', long, help_heading = "input")]

src/ska_dict/bit_encoding.rs

@@ -135,7 +135,7 @@ pub trait UInt<'a>:
     fn hash_val(self, hash_fn: &RandomState) -> u64;
 }
 
-impl<'a> UInt<'a> for u64 {
+impl UInt<'_> for u64 {
     #[inline(always)]
     fn rev_comp(mut self, k_size: usize) -> Self {
         // This part reverses the bases by shuffling them using an on/off pattern
@@ -327,7 +327,7 @@ impl<'a> UInt<'a> for u64 {
     }
 }
 
-impl<'a> UInt<'a> for u128 {
+impl UInt<'_> for u128 {
     #[inline(always)]
     fn rev_comp(mut self, k_size: usize) -> u128 {
         // This part reverses the bases by shuffling them using an on/off pattern
@@ -397,7 +397,7 @@ impl<'a> UInt<'a> for u128 {
             result = (result << 2) | (nucleotide_to_bits[index] as Self);
         }
 
-        result
+        result as Self
     }
 
     #[inline(always)]

src/skalo/utils.rs

@@ -36,101 +36,6 @@ pub fn rev_compl(seq: &str) -> String {
     complemented_seq
 }
 
-// pub fn rev_compl_u128(kmer: u128, k: usize) -> u128 {
-//     // mask for the last 2 bits (representing one nucleotide)
-//     let mask = 0b11u128;
-
-//     // initialize reverse complement result
-//     let mut rc_u128 = 0u128;
-
-//     // for each nucleotide in the k-mer
-//     for i in 0..k {
-//         // get the last 2 bits (current nucleotide)
-//         let nucleotide = (kmer >> (2 * i)) & mask;
-
-//         // complement the nucleotide:
-//         let complement = match nucleotide {
-//             0b00 => 0b11, // A -> T
-//             0b01 => 0b10, // C -> G
-//             0b10 => 0b01, // G -> C
-//             0b11 => 0b00, // T -> A
-//             _ => unreachable!(),
-//         };
-
-//         // shift the complemented nucleotide to its reverse position
-//         rc_u128 |= complement << (2 * (k - i - 1));
-//     }
-//     rc_u128
-// }
-
-// pub fn encode_kmer<IntT: for<'a> UInt<'a>>(kmer: &str) -> IntT {
-//     let nucleotide_to_bits: [u8; 4] = [
-//         0b00, // A
-//         0b01, // C
-//         0b10, // G
-//         0b11, // T
-//     ];
-
-//     let mut result: IntT = 0 as InT;
-
-//     for nucleotide in kmer.chars() {
-//         let index = match nucleotide {
-//             'A' => 0,
-//             'C' => 1,
-//             'G' => 2,
-//             'T' => 3,
-//             _ => panic!("Invalid nucleotide"),
-//         };
-//         result = (result << 2) | (nucleotide_to_bits[index] as u128);
-//     }
-//     result
-// }
-
-pub fn encode_u8_kmer(dna: &[u8]) -> u128 {
-    let mut encoded: u128 = 0;
-    for &nucleotide in dna {
-        encoded <<= 2; // Shift left by 2 bits
-        encoded |= match nucleotide {
-            b'A' => 0b00,
-            b'C' => 0b01,
-            b'G' => 0b10,
-            b'T' => 0b11,
-            _ => panic!("Invalid nucleotide: {}", nucleotide as char),
-        };
-    }
-    encoded
-}
-
-pub fn decode_kmer(encoded: u128, k: usize) -> String {
-    let bits_to_nucleotide: [char; 4] = ['A', 'C', 'G', 'T'];
-    let mut kmer = String::with_capacity(k);
-
-    let mask = (1u128 << (2 * k)) - 1;
-    let mut value = encoded & mask;
-
-    for _ in 0..k {
-        let index = (value & 0b11) as usize;
-        let nucleotide = bits_to_nucleotide[index];
-        kmer.insert(0, nucleotide);
-        value >>= 2;
-    }
-    kmer
-}
-
-// extract last nucleotide from an encoded k-mer
-// pub fn get_last_nucl<IntT: for<'a> UInt<'a>>(encoded_kmer: IntT) -> char {
-//     // mask the last 2 bits to get the encoded nucleotide
-//     let last_bits = (encoded_kmer & 0b11) as u8;
-//     // decode the nucleotide based on the 2-bit pattern
-//     match last_bits {
-//         0b00 => 'A',
-//         0b01 => 'C',
-//         0b10 => 'G',
-//         0b11 => 'T',
-//         _ => unreachable!(),
-//     }
-// }
-
 #[derive(Clone)]
 pub struct VariantInfo {
     pub sequence: DnaSequence,