feat: add standard derives to all public types (#505)

* feat: add standard derives to all public types

* fix(clippy): remove unnecessary clones

* fix(build): fix changes breaking tarpaulin

* fix(bench): removed unneeded derives from benches

src/alignment/pairwise/banded.rs

@@ -108,6 +108,7 @@ const DEFAULT_MATCH_SCORE: i32 = 2;
 /// in the band is less than MAX_CELLS (currently set to 10 million), otherwise it returns an
 /// empty alignment
 #[allow(non_snake_case)]
+#[derive(Default, Clone, Eq, PartialEq, Hash, Debug, Serialize, Deserialize)]
 pub struct Aligner<F: MatchFunc> {
     S: [Vec<i32>; 2],
     I: [Vec<i32>; 2],
@@ -1029,13 +1030,13 @@ trait MatchPair {
 impl MatchPair for (u32, u32) {
     fn continues(&self, p: Option<(u32, u32)>) -> bool {
         match p {
-            Some(_p) => (self.0 == _p.0 + 1 && self.1 == _p.1 + 1),
+            Some(_p) => self.0 == _p.0 + 1 && self.1 == _p.1 + 1,
             None => false,
         }
     }
 }
 
-#[derive(Clone, Debug)]
+#[derive(Default, Clone, Eq, PartialEq, Hash, Debug, Serialize, Deserialize)]
 struct Band {
     rows: usize,
     cols: usize,

src/alignment/pairwise/mod.rs

@@ -171,7 +171,9 @@ pub trait MatchFunc {
 
 /// A concrete data structure which implements trait MatchFunc with constant
 /// match and mismatch scores
-#[derive(Debug, Clone)]
+#[derive(
+    Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
+)]
 pub struct MatchParams {
     pub match_score: i32,
     pub mismatch_score: i32,
@@ -221,7 +223,9 @@ where
 /// An [affine gap score model](https://en.wikipedia.org/wiki/Gap_penalty#Affine)
 /// is used so that the gap score for a length `k` is:
 /// `GapScore(k) = gap_open + gap_extend * k`
-#[derive(Debug, Clone)]
+#[derive(
+    Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
+)]
 pub struct Scoring<F: MatchFunc> {
     pub gap_open: i32,
     pub gap_extend: i32,
@@ -455,6 +459,7 @@ impl<F: MatchFunc> Scoring<F> {
 ///
 /// `scoring` - see [`bio::alignment::pairwise::Scoring`](struct.Scoring.html)
 #[allow(non_snake_case)]
+#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
 pub struct Aligner<F: MatchFunc> {
     I: [Vec<i32>; 2],
     D: [Vec<i32>; 2],
@@ -1008,7 +1013,9 @@ impl<F: MatchFunc> Aligner<F> {
 /// Possible traceback moves include : start, insert, delete, match, substitute,
 /// prefix clip and suffix clip for x & y. So we need 4 bits each for matrices I, D, S
 /// to keep track of these 9 moves.
-#[derive(Copy, Clone, Default)]
+#[derive(
+    Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
+)]
 pub struct TracebackCell {
     v: u16,
 }
@@ -1100,6 +1107,7 @@ impl TracebackCell {
 }
 
 /// Internal traceback.
+#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
 struct Traceback {
     rows: usize,
     cols: usize,

src/alignment/poa.rs

@@ -53,20 +53,21 @@ pub type POAGraph = Graph<u8, i32, Directed, usize>;
 // traceback matrix. I have not yet figured out what the best level of
 // detail to store is, so Match and Del operations remember In and Out
 // nodes on the reference graph.
-#[derive(Debug, Clone)]
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
 pub enum AlignmentOperation {
     Match(Option<(usize, usize)>),
     Del(Option<(usize, usize)>),
     Ins(Option<usize>),
 }
 
+#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
 pub struct Alignment {
     pub score: i32,
     //    xstart: Edge,
     operations: Vec<AlignmentOperation>,
 }
 
-#[derive(Debug, Clone)]
+#[derive(Copy, Clone, Debug, Serialize, Deserialize)]
 pub struct TracebackCell {
     score: i32,
     op: AlignmentOperation,
@@ -94,6 +95,7 @@ impl PartialEq for TracebackCell {
 
 impl Eq for TracebackCell {}
 
+#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Debug)]
 pub struct Traceback {
     rows: usize,
     cols: usize,
@@ -196,7 +198,7 @@ impl Traceback {
         while i > 0 && j > 0 {
             // push operation and edge corresponding to (one of the) optimal
             // routes
-            ops.push(self.matrix[i][j].op.clone());
+            ops.push(self.matrix[i][j].op);
             match self.matrix[i][j].op {
                 AlignmentOperation::Match(Some((p, _))) => {
                     i = p + 1;
@@ -233,6 +235,7 @@ impl Traceback {
 /// A partially ordered aligner builder
 ///
 /// Uses consuming builder pattern for constructing partial order alignments with method chaining
+#[derive(Default, Clone, Debug)]
 pub struct Aligner<F: MatchFunc> {
     traceback: Traceback,
     query: Vec<u8>,
@@ -278,6 +281,7 @@ impl<F: MatchFunc> Aligner<F> {
 ///
 /// A directed acyclic graph datastructure that represents the topology of a
 /// traceback matrix.
+#[derive(Default, Clone, Debug)]
 pub struct Poa<F: MatchFunc> {
     scoring: Scoring<F>,
     pub graph: POAGraph,

src/alignment/sparse.rs

@@ -36,7 +36,7 @@ use std::hash::BuildHasherDefault;
 pub type HashMapFx<K, V> = HashMap<K, V, BuildHasherDefault<FxHasher>>;
 
 /// Result of a sparse alignment
-#[derive(Debug, PartialEq, Eq)]
+#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
 pub struct SparseAlignmentResult {
     /// LCSk++ path, represented as vector of indices into the input matches vector.
     pub path: Vec<usize>,

src/alphabets/mod.rs

@@ -27,7 +27,7 @@ pub mod rna;
 pub type SymbolRanks = VecMap<u8>;
 
 /// Representation of an alphabet.
-#[derive(Debug, PartialEq, Eq)]
+#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug)]
 pub struct Alphabet {
     pub symbols: BitSet,
 }
@@ -217,7 +217,7 @@ impl Alphabet {
 ///
 /// `RankTransform` can be used in to perform bit encoding for texts over a
 /// given alphabet via `bio::data_structures::bitenc`.
-#[derive(Serialize, Deserialize)]
+#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
 pub struct RankTransform {
     pub ranks: SymbolRanks,
 }
@@ -384,6 +384,7 @@ impl RankTransform {
 }
 
 /// Iterator over q-grams.
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize)]
 pub struct QGrams<'a, C, T>
 where
     C: Borrow<u8>,

src/data_structures/annot_map.rs

@@ -47,7 +47,7 @@ use bio_types::annot::loc::Loc;
 ///
 /// Thus, the overlapping annotations identified by querying a
 /// `AnnotMap` may need further filtering.
-#[derive(Debug, Clone)]
+#[derive(Clone, Eq, PartialEq, Debug, Serialize, Deserialize)]
 pub struct AnnotMap<R, T>
 where
     R: Hash + Eq,
@@ -180,7 +180,7 @@ where
 }
 
 /// A view of one annotation in a `AnnotMap` container.
-#[derive(Debug, Clone)]
+#[derive(Copy, Clone, Eq, PartialEq, Hash, Debug, Serialize)]
 pub struct Entry<'a, R, T>
 where
     R: Eq + Hash,
@@ -213,6 +213,7 @@ where
 /// `AnnotMap`.
 ///
 /// This struct is created by the `find` function on `AnnotMap`.
+#[derive(Clone, Eq, PartialEq, Hash, Debug, Serialize)]
 pub struct AnnotMapIterator<'a, R, T>
 where
     R: Eq + Hash,

src/data_structures/bit_tree.rs

@@ -41,6 +41,7 @@ pub trait PrefixOp<T> {
 /// a smaller element at the same index.
 /// Time Complexity: O(n) to build a new tree or O(log n) for get() and set() operations,
 /// where `n = tree.len()`.
+#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
 pub struct FenwickTree<T: Default + Ord, Op: PrefixOp<T>> {
     tree: Vec<T>,
     phantom: PhantomData<Op>,
@@ -84,6 +85,9 @@ impl<T: Ord + Default + Copy, Op: PrefixOp<T>> FenwickTree<T, Op> {
     }
 }
 
+#[derive(
+    Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
+)]
 pub struct MaxOp;
 impl<T: Copy + Ord> PrefixOp<T> for MaxOp {
     fn operation(t1: T, t2: T) -> T {
@@ -94,6 +98,9 @@ impl<T: Copy + Ord> PrefixOp<T> for MaxOp {
 /// Fenwick tree specialized for prefix-max
 pub type MaxBitTree<T> = FenwickTree<T, MaxOp>;
 
+#[derive(
+    Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
+)]
 pub struct SumOp;
 impl<T: Copy + Add> PrefixOp<T> for SumOp
 where

src/data_structures/bitenc.rs

@@ -46,7 +46,7 @@
 /// For values that are not a divider of 32, some bits will remain unused.
 /// For example for `width = 7` only `4 * 7 = 28` bits are used.
 /// Five 7-bit values are stored in 2 blocks.
-#[derive(Serialize, Deserialize, PartialEq, Eq, Hash)]
+#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
 pub struct BitEnc {
     storage: Vec<u32>,
     width: usize,
@@ -385,7 +385,7 @@ impl BitEnc {
     /// // Add another 2 to create a second block
     /// bitenc.push(2);
     /// assert_eq!(bitenc.nr_blocks(), 2);
-    /// ```    
+    /// ```
     pub fn nr_blocks(&self) -> usize {
         self.storage.len()
     }
@@ -408,7 +408,7 @@ impl BitEnc {
     /// assert_eq!(bitenc.nr_symbols(), 4);
     /// bitenc.push(2);
     /// assert_eq!(bitenc.nr_symbols(), 5);
-    /// ```    
+    /// ```
     pub fn nr_symbols(&self) -> usize {
         self.len
     }
@@ -436,6 +436,7 @@ impl BitEnc {
 
 /// Iterator over values of a bitencoded sequence (values will be unpacked into bytes).
 /// Used to implement the `iter` method of `BitEnc`.
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize)]
 pub struct BitEncIter<'a> {
     bitenc: &'a BitEnc,
     i: usize,

src/data_structures/bwt.rs

@@ -73,7 +73,7 @@ pub fn invert_bwt(bwt: &BWTSlice) -> Vec<u8> {
 }
 
 /// An occurrence array implementation.
-#[derive(Clone, Serialize, Deserialize)]
+#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
 pub struct Occ {
     occ: Vec<Vec<usize>>,
     k: u32,

src/data_structures/fmindex.rs

@@ -63,7 +63,9 @@ use crate::data_structures::suffix_array::SuffixArray;
 use std::mem::swap;
 
 /// A suffix array interval.
-#[derive(Clone, Copy, Debug, PartialEq, Eq, Hash)]
+#[derive(
+    Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
+)]
 pub struct Interval {
     pub lower: usize,
     pub upper: usize,
@@ -86,7 +88,7 @@ impl Interval {
 /// The interval returned is the range of suffix array indices for the maximal
 /// matching suffix, and the `usize` is the length of the maximal matching suffix.
 /// Absent - None suffix of the pattern matched in the text.
-#[derive(Clone, Copy, Debug, PartialEq, Eq, Hash)]
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
 pub enum BackwardSearchResult {
     Complete(Interval),
     Partial(Interval, usize),
@@ -201,7 +203,9 @@ pub trait FMIndexable {
 
 /// The Fast Index in Minute space (FM-Index, Ferragina and Manzini, 2000) for finding suffix array
 /// intervals matching a given pattern.
-#[derive(Serialize, Deserialize)]
+#[derive(
+    Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
+)]
 pub struct FMIndex<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> {
     bwt: DBWT,
     less: DLess,
@@ -237,7 +241,9 @@ impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> FMIndex<DBWT, DL
 }
 
 /// A bi-interval on suffix array of the forward and reverse strand of a DNA text.
-#[derive(Clone, Copy, Debug, PartialEq, Eq, Hash)]
+#[derive(
+    Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
+)]
 pub struct BiInterval {
     lower: usize,
     lower_rev: usize,
@@ -271,7 +277,9 @@ impl BiInterval {
 
 /// The FMD-Index for linear time search of supermaximal exact matches on forward and reverse
 /// strand of DNA texts (Li, 2012).
-#[derive(Serialize, Deserialize)]
+#[derive(
+    Default, Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize,
+)]
 pub struct FMDIndex<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> {
     fmindex: FMIndex<DBWT, DLess, DOcc>,
 }

src/data_structures/interpolation_table.rs

@@ -36,6 +36,7 @@ pub fn interpolate(a: f64, b: f64, fraction: f64) -> f64 {
 /// Input values are sampled with a given precision and results are stored in a vector.
 /// During lookup, infimum and supremum of a given value are calculated and the result is
 /// interpolated.
+#[derive(Default, Clone, PartialEq, PartialOrd, Debug, Serialize, Deserialize)]
 pub struct InterpolationTable<F: Fn(f64) -> f64> {
     inner: Vec<f64>,
     func: F,

src/data_structures/interval_tree/array_backed_interval_tree.rs

@@ -39,7 +39,7 @@ use std::iter::FromIterator;
 
 /// A `find` query on the interval tree does not directly return references to the intervals in the
 /// tree but wraps the fields `interval` and `data` in an `Entry`.
-#[derive(PartialEq, Eq, Debug, Clone)]
+#[derive(Clone, Eq, PartialEq, Hash, Debug, Serialize, Deserialize)]
 struct InternalEntry<N: Ord + Clone + Copy, D> {
     data: D,
     interval: Interval<N>,
@@ -48,7 +48,7 @@ struct InternalEntry<N: Ord + Clone + Copy, D> {
 
 /// A `find` query on the interval tree does not directly return references to the nodes in the tree, but
 /// wraps the fields `interval` and `data` in an `Entry`.
-#[derive(PartialEq, Eq, Debug, Clone)]
+#[derive(Copy, Clone, Eq, PartialEq, Hash, Debug, Serialize)]
 pub struct Entry<'a, N: Ord + Clone, D> {
     data: &'a D,
     interval: &'a Interval<N>,
@@ -76,6 +76,7 @@ impl<N: Ord + Clone + Copy, D> Default for ArrayBackedIntervalTree<N, D> {
     }
 }
 
+#[derive(Clone, Eq, PartialEq, Hash, Debug, Serialize, Deserialize)]
 pub struct ArrayBackedIntervalTree<N: Ord + Clone + Copy, D> {
     entries: Vec<InternalEntry<N, D>>,
     max_level: usize,