rust-bio · Guelakais · Aug 5, 2024 · Aug 5, 2024 · Aug 5, 2024 · Aug 18, 2024
diff --git a/Cargo.toml b/Cargo.toml
@@ -22,40 +22,40 @@ phylogeny = ["pest", "pest_derive", "bio-types/phylogeny"]
 
 
 [dependencies]
-bytecount = "0.6"
-csv = "1.1"
-num-traits = "0.2"
-num-integer = "0.1"
+bytecount = "0.6.8"
+csv = "1.3"
+num-traits = "0.2.19"
+num-integer = "0.1.46"
 itertools = ">=0.8, <0.14"
-itertools-num = "0.1"
-bv = { version = "0.11", features = ["serde"] }
+itertools-num = "0.1.3"
+bv = { version = "0.11.1", features = ["serde"] }
 bit-set = "0.8"
 ndarray= ">=0.15, <0.16"
-lazy_static = "1.4"
-serde = "1.0"
-serde_derive = "1.0"
+lazy_static = "1.5"
+serde = "1.0.204"
+serde_derive = "1.0.204"
 approx = ">=0.3, <0.6"
-custom_derive = "0.1"
-newtype_derive = "0.1"
-ordered-float = "4.2"
-regex = { version = "1.3", default-features = false, features = ["std", "perf"] }
+custom_derive = "0.1.7"
+newtype_derive = "0.1.6"
+ordered-float = "4.2.2"
+regex = { version = "1.10.6", default-features = false, features = ["std", "perf"] }
 multimap = ">=0.6, <0.11"
-fxhash = "0.2"
+fxhash = "0.2.1"
 statrs = ">= 0.11, < 0.18"
 bio-types = ">=1.0.0"
-pest = { version = "2", optional = true }
-pest_derive = { version = "2", optional = true }
+pest = { version = "2.7.11", optional = true }
+pest_derive = { version = "2.7.11", optional = true }
 strum = ">= 0.16, < 0.27"
 strum_macros = ">= 0.16, < 0.27"
 enum-map = ">=0.6.4, <3"
 triple_accel = ">=0.3, <0.5"
-thiserror = "1"
-anyhow = "1"
+thiserror = "1.0.63"
+anyhow = "1.0.86"
 rand = ">=0.7.3, < 0.9"
 editdistancek = ">=1.0.1, <2"
 
 [dependencies.vec_map]
-version = "0.8"
+version = "0.8.2"
 features = ["eders"]
 
 [dependencies.petgraph]

diff --git a/benches/approximate_matching.rs b/benches/approximate_matching.rs
@@ -4,9 +4,13 @@ extern crate test;
 
 use test::Bencher;
 
-use bio::alignment::Alignment;
-use bio::pattern_matching::myers::{long, Myers};
-use bio::pattern_matching::ukkonen::*;
+use bio::{
+    alignment::Alignment,
+    pattern_matching::{
+        myers::{long, Myers},
+        ukkonen::*,
+    },
+};
 
 static TEXT: &[u8] = b"GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGC\
 ATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTAT\

diff --git a/benches/fasta_buffer_size.rs b/benches/fasta_buffer_size.rs
@@ -6,8 +6,7 @@ use test::Bencher;
 
 use bio::io::fasta;
 
-use std::io::Seek;
-use std::io::Write;
+use std::io::{Seek, Write};
 
 use rand::SeedableRng;
 

diff --git a/benches/fmindex.rs b/benches/fmindex.rs
@@ -2,10 +2,14 @@
 
 extern crate test;
 
-use bio::alphabets;
-use bio::data_structures::bwt::{bwt, less, Occ};
-use bio::data_structures::fmindex::{BackwardSearchResult, FMIndex, FMIndexable};
-use bio::data_structures::suffix_array::suffix_array;
+use bio::{
+    alphabets,
+    data_structures::{
+        bwt::{bwt, less, Occ},
+        fmindex::{BackwardSearchResult, FMIndex, FMIndexable},
+        suffix_array::suffix_array,
+    },
+};
 use test::Bencher;
 
 #[bench]

diff --git a/benches/interval_tree.rs b/benches/interval_tree.rs
@@ -4,10 +4,11 @@ extern crate test;
 
 use test::Bencher;
 
-use bio::data_structures::interval_tree::*;
-use bio::utils::Interval;
-use std::cmp::{max, min};
-use std::ops::Range;
+use bio::{data_structures::interval_tree::*, utils::Interval};
+use std::{
+    cmp::{max, min},
+    ops::Range,
+};
 
 #[bench]
 fn bench_interval_few_large_queries(b: &mut Bencher) {

diff --git a/benches/orf.rs b/benches/orf.rs
@@ -4,8 +4,7 @@ extern crate test;
 
 use test::Bencher;
 
-use bio::seq_analysis::gc::*;
-use bio::seq_analysis::orf::Finder;
+use bio::seq_analysis::{gc::*, orf::Finder};
 
 // 5,000 random nucleotides, GC content = .55
 static STR_1: &[u8] = b"ATCTAACTATTCCCTGTGCCTTATGGGGGCCTGCGCTATCTGCCTGT\

diff --git a/benches/pairhmm.rs b/benches/pairhmm.rs
@@ -2,8 +2,7 @@
 
 extern crate test;
 
-use bio::stats::pairhmm::*;
-use bio::stats::{LogProb, Prob};
+use bio::stats::{pairhmm::*, LogProb, Prob};
 use test::Bencher;
 
 static TEXT: &[u8] = b"GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGC\

diff --git a/benches/pattern_matching.rs b/benches/pattern_matching.rs
@@ -2,11 +2,9 @@
 
 extern crate test;
 
-use bio::pattern_matching::bndm::BNDM;
-use bio::pattern_matching::bom::BOM;
-use bio::pattern_matching::horspool::Horspool;
-use bio::pattern_matching::kmp::KMP;
-use bio::pattern_matching::shift_and::ShiftAnd;
+use bio::pattern_matching::{
+    bndm::BNDM, bom::BOM, horspool::Horspool, kmp::KMP, shift_and::Shift
F438
And,
+};
 use test::Bencher;
 
 static TEXT: &[u8] = b"GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGC\

diff --git a/src/alignment/pairwise/banded.rs b/src/alignment/pairwise/banded.rs
@@ -18,10 +18,11 @@
 //! # Example
 //!
 //! ```
-//! use bio::alignment::pairwise::banded::*;
-//! use bio::alignment::pairwise::{Scoring, MIN_SCORE};
-//! use bio::alignment::sparse::hash_kmers;
-//! use bio::alignment::AlignmentOperation::*;
+//! use bio::alignment::{
+//!     pairwise::{banded::*, Scoring, MIN_SCORE},
+//!     sparse::hash_kmers,
+//!     AlignmentOperation::*,
+//! };
 //! use std::iter::repeat;
 //!
 //! let x = b"AGCACACGTGTGCGCTATACAGTAAGTAGTAGTACACGTGTCACAGTTGTACTAGCATGAC";
@@ -80,16 +81,17 @@
 //! // aligner.custom_with_prehash(x, y, &y_kmers_hash) is also supported
 //! ```
 
-use crate::alignment::{Alignment, AlignmentOperation};
-use crate::utils::TextSlice;
-use std::cmp::{max, min, Ordering};
-use std::i32;
-use std::ops::Range;
+use crate::{
+    alignment::{Alignment, AlignmentOperation},
+    utils::TextSlice,
+};
+use std::{
+    cmp::{max, min, Ordering},
+    ops::Range,
+};
 
 use super::*;
-use crate::alignment::pairwise::Scoring;
-use crate::alignment::sparse;
-use crate::alignment::sparse::HashMapFx;
+use crate::alignment::{pairwise::Scoring, sparse, sparse::HashMapFx};
 
 const MAX_CELLS: usize = 5_000_000;
 const DEFAULT_MATCH_SCORE: i32 = 2;
@@ -323,7 +325,7 @@ impl<F: MatchFunc> Aligner<F> {
     /// * `y` - Textslice
     /// * `matches` - Vector of kmer matching pairs (xpos, ypos)
     /// * `allowed_mismatches` - Extend the matches diagonally allowing upto
-    /// the specified number of mismatches (Option<usize>)
+    ///   the specified number of mismatches (Option<usize>)
     /// * `use_lcskpp_union` - Extend the results from sdpkpp using lcskpp
     pub fn custom_with_expanded_matches(
         &mut self,
@@ -377,7 +379,7 @@ impl<F: MatchFunc> Aligner<F> {
     /// * `y` - Textslice
     /// * `matches` - Vector of kmer matching pairs (xpos, ypos)
     /// * `path` - Vector of indices pointing to `matches` vector
-    /// which defines a path. The validity of the path is not checked.
+    ///   which defines a path. The validity of the path is not checked.
     pub fn custom_with_match_path(
         &mut self,
         x: TextSlice,
@@ -1407,9 +1409,13 @@ impl Band {
 
 #[cfg(test)]
 mod banded {
-    use crate::alignment::pairwise::{self, banded, Scoring};
-    use crate::alignment::sparse::hash_kmers;
-    use crate::utils::TextSlice;
+    use crate::{
+        alignment::{
+            pairwise::{self, banded, Scoring},
+            sparse::hash_kmers,
+        },
+        utils::TextSlice,
+    };
 
     // Check that the banded alignment is equivalent to the exhaustive SW alignment
     fn compare_to_full_alignment_local(x: TextSlice<'_>, y: TextSlice<'_>) {
@@ -1752,8 +1758,7 @@ mod banded {
     //     compare_to_full_alignment_semiglobal(x, y);
     // }
 
-    use crate::alignment::AlignmentOperation::*;
-    use crate::scores::blosum62;
+    use crate::{alignment::AlignmentOperation::*, scores::blosum62};
     use std::iter::repeat;
 
     #[test]

diff --git a/src/alignment/pairwise/mod.rs b/src/alignment/pairwise/mod.rs
@@ -11,9 +11,10 @@
 //! # Example
 //!
 //! ```
-//! use bio::alignment::pairwise::*;
-//! use bio::alignment::AlignmentOperation::*;
-//! use bio::scores::blosum62;
+//! use bio::{
+//!     alignment::{pairwise::*, AlignmentOperation::*},
+//!     scores::blosum62,
+//! };
 //!
 //! let x = b"ACCGTGGAT";
 //! let y = b"AAAAACCGTTGAT";
@@ -150,12 +151,12 @@
 //! );
 //! ```
 
-use std::cmp::max;
-use std::i32;
-use std::iter::repeat;
+use std::{cmp::max, iter::repeat};
 
-use crate::alignment::{Alignment, AlignmentMode, AlignmentOperation};
-use crate::utils::TextSlice;
+use crate::{
+    alignment::{Alignment, AlignmentMode, AlignmentOperation},
+    utils::TextSlice,
+};
 
 pub mod banded;
 
@@ -1163,8 +1164,7 @@ impl Traceback {
 #[cfg(test)]
 mod tests {
     use super::*;
-    use crate::alignment::AlignmentOperation::*;
-    use crate::scores::blosum62;
+    use crate::{alignment::AlignmentOperation::*, scores::blosum62};
 
     #[test]
     fn traceback_cell() {

diff --git a/src/alignment/poa.rs b/src/alignment/poa.rs
@@ -9,18 +9,17 @@
 //!
 //! For the original concept and theory, see:
 //! * Lee, Christopher, Catherine Grasso, and Mark F. Sharlow. "Multiple sequence alignment using
-//! partial order graphs." Bioinformatics 18.3 (2002): 452-464.
+//!   partial order graphs." Bioinformatics 18.3 (2002): 452-464.
 //! * Lee, Christopher. "Generating consensus sequences from partial order multiple sequence
-//! alignment graphs." Bioinformatics 19.8 (2003): 999-1008.
+//!   alignment graphs." Bioinformatics 19.8 (2003): 999-1008.
 //!
 //! For a modern reference implementation, see poapy:
 //! https://github.com/ljdursi/poapy
 //!
 //! # Example
 //!
 //! ```
-//! use bio::alignment::pairwise::Scoring;
-//! use bio::alignment::poa::*;
+//! use bio::alignment::{pairwise::Scoring, poa::*};
 //!
 //! let x = b"AAAAAAA";
 //! let y = b"AABBBAA";
@@ -41,8 +40,7 @@ use crate::utils::TextSlice;
 
 use crate::alignment::pairwise::{MatchFunc, Scoring};
 
-use petgraph::graph::NodeIndex;
-use petgraph::visit::Topo;
+use petgraph::{graph::NodeIndex, visit::Topo};
 
 use petgraph::{Directed, Graph, Incoming};
 
@@ -921,8 +919,7 @@ impl<F: MatchFunc> Poa<F> {
 mod tests {
     use super::*;
     use crate::alignment::pairwise::Scoring;
-    use petgraph::dot::Dot;
-    use petgraph::graph::NodeIndex;
+    use petgraph::{dot::Dot, graph::NodeIndex};
 
     #[test]
     fn test_init_graph() {

diff --git a/src/alignment/sparse.rs b/src/alignment/sparse.rs
@@ -29,9 +29,11 @@
 
 use crate::data_structures::bit_tree::MaxBitTree;
 use fxhash::FxHasher;
-use std::cmp::{max, min};
-use std::collections::HashMap;
-use std::hash::BuildHasherDefault;
+use std::{
+    cmp::{max, min},
+    collections::HashMap,
+    hash::BuildHasherDefault,
+};
 
 pub type HashMapFx<K, V> = HashMap<K, V, BuildHasherDefault<FxHasher>>;
 

diff --git a/src/alphabets/mod.rs b/src/alphabets/mod.rs
@@ -14,8 +14,7 @@
 //! assert!(!alphabet.is_word(b"AXYZ"));
 //! ```
 
-use std::borrow::Borrow;
-use std::mem;
+use std::{borrow::Borrow, mem};
 
 use bit_set::BitSet;
 use vec_map::VecMap;