fix clippy

Author: nh13

fg-stitch-lib/src/align/aligners/constants.rs

@@ -16,7 +16,6 @@ pub const DEFAULT_ALIGNER_CAPACITY: usize = 200;
 /// value associated with the clipping operations are the lengths clipped. In case
 /// of standard modes like Global, Semi-Global and Local alignment, the clip operations
 /// are filtered out.
-#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
 #[derive(Eq, PartialEq, Debug, Copy, Clone, Hash)]
 pub enum AlignmentOperation {
     Match,               // Consumes one x and one y base
@@ -93,7 +92,6 @@ impl AlignmentOperation {
 /// appropriately set.
 ///
 /// The default alignment mode is Global.
-#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
 #[derive(Default, Debug, PartialEq, Eq, Copy, Clone)]
 pub enum AlignmentMode {
     /// Aligns a sub-sequence of the read versus a sub-sequence of the reference

fg-stitch-lib/src/align/aligners/mod.rs

@@ -618,7 +618,7 @@ fn header_to_name(header: &[u8]) -> Result<String> {
         .context("empty read name")
 }
 
-impl<'a, F: MatchFunc> SamRecordFormatter<'a, F> {
+impl<F: MatchFunc> SamRecordFormatter<'_, F> {
     pub fn format(
         &self,
         fastq: &FastxOwnedRecord,

fg-stitch-lib/src/align/aligners/single_contig_aligner.rs

@@ -5,7 +5,7 @@
 // This file may not be copied, modified, or distributed
 // except according to those terms.
 
-use std::{cmp::max, i32, iter::repeat};
+use std::{cmp::max, iter::repeat};
 
 use crate::align::{aligners::constants::AlignmentMode, scoring::Scoring, traceback::TB_XJUMP};
 use bio::{

fg-stitch-lib/src/align/alignment.rs

@@ -12,7 +12,6 @@ use crate::align::aligners::constants::{
 /// lengths of sequences x and y, and the alignment edit operations. The start position
 /// and end position of the alignment does not include the clipped regions. The length
 /// of clipped regions are already encapsulated in the Alignment Operation.
-#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
 #[derive(Debug, Eq, PartialEq, Clone, Default)]
 pub struct Alignment {
     // FIXME: rename to Alignment

fg-stitch-lib/src/align/io.rs

@@ -106,7 +106,7 @@ pub struct InputMessage {
 /// The output result of a single pairwise alignment as a triple:
 /// 1. the FASTQ record that was aligned
 /// 2. None if no alignment was found, otherwise some tuple of pairwise alignment and the target
-///   strand to which the alignment was made.
+///    strand to which the alignment was made.
 /// 3. The alignment score, if aligned.
 pub type OutputResult = (FastxOwnedRecord, Vec<Alignment>, Option<i32>);
 

fg-stitch-lib/src/align/traceback/mod.rs

@@ -60,7 +60,7 @@ pub mod packed_length_cell;
 pub mod simple_cell;
 
 cfg_if::cfg_if! {
-    if #[cfg(low_mem)] {
+    if #[cfg(feature = "low_mem")] {
         pub type Cell = simple_cell::SimpleCell;
     } else {
         pub type Cell = packed_length_cell::PackedLengthCell;

fg-stitch-lib/src/align/traceback/packed_length_cell.rs

@@ -15,10 +15,10 @@ use super::{SValue, TracebackCell};
 /// - bits 0-3 are reserved for *_POS
 /// - bits 4-31 are reserved for alignment length (27 bits each)
 /// - bit 31 for each of s/i/d is reserved for the upper 3-bits of the jump contig index (i.e. which contig did we jump from)
-/// The `aux` field is packed as follows:
+///   The `aux` field is packed as follows:
 /// - bits 0-4 are for the lower 5-bits of the jump contig index (i.e. which contig did we jump from)
 /// - bits 5-31 are for the "from" jump index in the contig (i.e. where in the given contig did we jump from)
-/// Also contains s_from (u32), so we have a totoal of u32 * 4 = 128 bits
+///   Also contains s_from (u32), so we have a totoal of u32 * 4 = 128 bits
 #[derive(
     Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
 )]

fg-stitch-lib/src/align/traceback/simple_cell.rs

@@ -15,7 +15,7 @@ use serde::{Deserialize, Serialize};
 /// - bits 4-7 are for deletion traceback (D_POS)
 /// - bits 8-11 are for S matrix traceback (S_POS)
 /// - bit 12-15 are for the upper 4-bits of the jump contig index (i.e. which contig did we jump from)
-/// The `aux` field is packed as follows:
+///   The `aux` field is packed as follows:
 /// - bits 0-3 are for the lower 4-bits of the jump contig index (i.e. which contig did we jump from)
 /// - bits 4-31 are for the "from" jump index in the contig (i.e. where in the given contig did we jump from)
 #[derive(