style: Fix clippy warnings

10XGenomics · Dec 4, 2024 · 728cf96 · 728cf96
1 parent 3b3e58c
commit 728cf96
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Showing 14 changed files with 92 additions and 113 deletions.
diff --git a/benches/array_bench.rs b/benches/array_bench.rs
@@ -7,13 +7,13 @@ use std::iter::FromIterator;
 fn run_benchmark(c: &mut Criterion) {
     let mut group = c.benchmark_group("bench-byte-array");
     group.bench_function("from-bytes", |b| {
-        b.iter(|| SSeq::from_bytes(b"AGTCCTCTGCATTTTG"))
+        b.iter(|| SSeq::from_bytes(b"AGTCCTCTGCATTTTG"));
     });
     group.bench_function("from-bytes-unchecked", |b| {
-        b.iter(|| SSeq::from_bytes_unchecked(b"AGTCCTCTGCATTTTG"))
+        b.iter(|| SSeq::from_bytes_unchecked(b"AGTCCTCTGCATTTTG"));
     });
     group.bench_function("from-iter", |b| {
-        b.iter(|| SSeq::from_iter(b"AGTCCTCTGCATTTTG"))
+        b.iter(|| SSeq::from_iter(b"AGTCCTCTGCATTTTG"));
     });
     group.finish();
 }

diff --git a/benches/benchmarks.rs b/benches/benchmarks.rs
@@ -115,12 +115,12 @@ fn run_fastq_lz4_benchmark(c: &mut Criterion) {
     c.bench_function("bench-lz4-wc", |b| {
         b.iter(
             || assert_eq!(lz4_count(INTERLEAVED_LZ4_FASTQ), 16000), // 16000 lines
-        )
+        );
     });
     c.bench_function("bench-lz4-read-pair-iter-count", |b| {
         b.iter(
             || assert_eq!(read_pair_count(INTERLEAVED_LZ4_FASTQ), 2000), // 2000 read pairs
-        )
+        );
     });
     // let chemistry: ChemistryDef =
     //     serde_json::from_reader(File::open("tests/rna_read/sc_vdj_chemistry.json").unwrap())
@@ -141,12 +141,12 @@ fn run_fastq_gz_benchmark(c: &mut Criterion) {
     c.bench_function("bench-gz-wc", |b| {
         b.iter(
             || assert_eq!(gz_count(INTERLEAVED_GZ_FASTQ), 16000), // 16000 lines
-        )
+        );
     });
     c.bench_function("bench-gz-read-pair-iter-count", |b| {
         b.iter(
             || assert_eq!(read_pair_count(INTERLEAVED_GZ_FASTQ), 2000), // 2000 read pairs
-        )
+        );
     });
     // let chemistry: ChemistryDef =
     //     serde_json::from_reader(File::open("tests/rna_read/sc_vdj_chemistry.json").unwrap())
@@ -167,12 +167,12 @@ fn run_fastq_benchmark(c: &mut Criterion) {
     c.bench_function("bench-fastq-wc", |b| {
         b.iter(
             || assert_eq!(simple_count(INTERLEAVED_FASTQ), 16000), // 16000 lines
-        )
+        );
     });
     c.bench_function("bench-fastq-read-pair-iter-count", |b| {
         b.iter(
             || assert_eq!(read_pair_count(INTERLEAVED_FASTQ), 2000), // 2000 read pairs
-        )
+        );
     });
     // let chemistry: ChemistryDef =
     //     serde_json::from_reader(File::open("tests/rna_read/sc_vdj_chemistry.json").unwrap())
@@ -222,7 +222,7 @@ fn sseq_serde_bincode(c: &mut Criterion) {
             let mut b = Vec::new();
             bincode::serialize_into(&mut b, &sseqs).unwrap();
             assert!(!b.is_empty());
-        })
+        });
     });
 }
 

diff --git a/src/adapter_trimmer.rs b/src/adapter_trimmer.rs
@@ -1,11 +1,9 @@
 //! Trim adapters from reads using a combination of
 //! k-mer matches, sparse alignment and banded alignment.
-//! Inspired by the [cutadapt](https://cutadapt.readthedocs.io/)
-//! tool.
+//! Inspired by the [cutadapt](https://cutadapt.readthedocs.io/) tool.
 //!
 //! # Features/Limitations
-//! * Supports regular, anchored and non-internal, 3' and 5'
-//! adapter trimming
+//! * Supports regular, anchored and non-internal, 3' and 5' adapter trimming
 //! * Linked adapters are not supported as of now
 //! * Allowed error rate for the adapter is 10%
 //!
@@ -23,13 +21,10 @@ use bio::alignment::pairwise::{self, MatchParams, Scoring};
 use bio::alignment::sparse;
 use bio::alignment::sparse::HashMapFx;
 use serde::{Deserialize, Serialize};
-use std::cmp::Ordering;
-use std::cmp::{max, min};
-use std::collections::HashMap;
-use std::collections::HashSet;
+use std::cmp::{max, min, Ordering};
+use std::collections::{HashMap, HashSet};
 use std::fmt::Debug;
 use std::hash::BuildHasher;
-use std::i32;
 use std::ops::Range;
 
 type Aligner = pairwise::banded::Aligner<MatchParams>;
@@ -122,7 +117,7 @@ pub enum AdapterLoc {
 /// * `end`: whether it's a `FivePrime` adapter or a `ThreePrime` adapter
 /// * `location`: Specify the location of the adapter (See [`AdapterLoc`](enum.AdapterLoc.html))
 /// * `seq`: The sequence of the adapter as a `String`. One could use a `Vec<u8>` here, but
-/// chose a String for the ease of auto (de)serialization from a json file.
+///   choose a String for the ease of auto (de)serialization from a json file.
 ///
 /// # Example
 /// The example below shows how you can create an `Adapter` from a JSON string
@@ -270,7 +265,7 @@ impl<'a> AdapterTrimmer<'a> {
     ///
     /// Ouput:
     /// * `Option<TrimResult>`: `None` if the adapter is not found,
-    /// otherwise `Some(TrimResult)` (See [`TrimResult`](struct.TrimResult.html))
+    ///   otherwise `Some(TrimResult)` (See [`TrimResult`](struct.TrimResult.html))
     pub fn find(&mut self, read: &[u8]) -> Option<TrimResult> {
         use bio::alignment::AlignmentOperation::{Del, Ins, Match, Subst};
 
@@ -642,7 +637,7 @@ fn compute_path(
     {
         let mut max_l_score = pairwise::MIN_SCORE;
         let mut max_r_score = pairwise::MIN_SCORE;
-        for &this_match in matches.iter() {
+        for &this_match in matches {
             max_l_score = max(max_l_score, l_score(this_match));
             max_r_score = max(max_r_score, r_score(this_match));
         }

diff --git a/src/array.rs b/src/array.rs
@@ -106,12 +106,11 @@ where
             *l = *r.borrow();
             len += 1;
         }
-        if src.next().is_some() {
-            panic!(
-                "Error: Input iter exceeds capacity of {} bytes.",
-                bytes.len()
-            );
-        }
+        assert!(
+            src.next().is_none(),
+            "Error: Input iter exceeds capacity of {} bytes.",
+            bytes.len()
+        );
 
         ByteArray {
             length: len,
@@ -200,9 +199,7 @@ where
     type Output = u8;
 
     fn index(&self, index: usize) -> &Self::Output {
-        if index >= self.length as usize {
-            panic!("index out of bounds")
-        }
+        assert!(index < self.length as usize, "index out of bounds");
 
         &self.bytes[index]
     }
@@ -213,9 +210,7 @@ where
     T: ArrayContent,
 {
     fn index_mut(&mut self, index: usize) -> &mut Self::Output {
-        if index >= self.length as usize {
-            panic!("index out of bounds")
-        }
+        assert!(index < self.length as usize, "index out of bounds");
         &mut self.bytes[index]
     }
 }

diff --git a/src/background_iterator.rs b/src/background_iterator.rs
@@ -93,9 +93,7 @@ mod test {
         let v = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9];
 
         let iter = (0..11usize).map(move |i| {
-            if v[i] == 5 {
-                panic!("simulated panic");
-            }
+            assert!(!(v[i] == 5), "simulated panic");
             v[i]
         });
 

diff --git a/src/filenames/bcl2fastq.rs b/src/filenames/bcl2fastq.rs
@@ -495,7 +495,7 @@ mod tests_from_tenkit {
     #[test]
     fn test_sample_name_verification() -> Result<()> {
         let path = "tests/filenames/tenkit91";
-        for &s in ["test_sample", "test_sample_suffix"].iter() {
+        for &s in &["test_sample", "test_sample_suffix"] {
             let query = Bcl2FastqDef {
                 fastq_path: path.to_string(),
                 sample_name_spec: s.into(),

diff --git a/src/filenames/bcl_processor.rs b/src/filenames/bcl_processor.rs
@@ -75,7 +75,7 @@ impl FindFastqs for BclProcessorFastqDef {
             if self.sample_index_spec.matches(&bcl_proc.si)
                 && self.lane_spec.contains(bcl_proc.lane_mode())
             {
-                res.push(fastqs)
+                res.push(fastqs);
             }
         }
 

diff --git a/src/filenames/fastq_dir.rs b/src/filenames/fastq_dir.rs
@@ -37,21 +37,20 @@ impl Bcl2FastqDir {
             });
         }
 
-        let is_lane_split = match fastq_data
+        let Ok(is_lane_split) = fastq_data
             .iter()
             .map(|(g, _)| match g.lane_mode {
                 LaneMode::NoLaneSplitting => false,
                 LaneMode::SingleLane(_) => true,
             })
             .dedup()
             .exactly_one()
-        {
-            Ok(val) => val,
-            Err(_) => bail!(
+        else {
+            bail!(
                 "Some files in the fastq path {} are split by lane, while some are not. \
                  This is not supported.",
                 fastq_path.display()
-            ),
+            );
         };
 
         let samples = fastq_data.iter().map(|(g, _)| g.sample.clone()).collect();
@@ -230,7 +229,7 @@ impl FastqChecker {
 
         let lane_spec = match lanes {
             None => LaneSpec::Any,
-            Some(ref l) => LaneSpec::Lanes(l.iter().cloned().collect()),
+            Some(l) => LaneSpec::Lanes(l.iter().copied().collect()),
         };
 
         if bcl_dir
@@ -243,7 +242,7 @@ impl FastqChecker {
 
         Ok(match sample_name_spec {
             SampleNameSpec::Names(names) => names,
-            _ => unreachable!(),
+            SampleNameSpec::Any => unreachable!(),
         })
     }
 

diff --git a/src/illumina_header_info.rs b/src/illumina_header_info.rs
@@ -36,7 +36,7 @@ impl InputFastqs {
             .ok_or_else(|| anyhow!("No Read1 in FASTQ data"))?;
 
         let header = std::str::from_utf8(header)?;
-        let header_prefix = header.split(|x: char| x == ' ' || x == '/').next();
+        let header_prefix = header.split([' ', '/']).next();
         if header_prefix.is_none() {
             return Ok(None);
         }

diff --git a/src/lib.rs b/src/lib.rs
@@ -4,9 +4,10 @@
 //! Major functionality includes:
 //! * Find groups FASTQs (R1/R2/I1/I2) following Illumina filename conventions
 //! * Parsing flowcell information from Illumina FASTQ headers
-//! * High-speed FASTQ I/O (via the `fastq` crate), with careful validation of FASTQ correctness and good error message.
-//! * Containers for FASTQ read-pairs (along with index reads), providing access to 'technical' read components like cell barcode and
-//! UMI sequences.
+//! * High-speed FASTQ I/O (via the `fastq` crate), with careful validation of
+//!   FASTQ correctness and good error message.
+//! * Containers for FASTQ read-pairs (along with index reads), providing access
+//!   to 'technical' read components like cell barcode and UMI sequences.
 //! * Flexible read trimming inspired by `cutadapt`
 
 #![deny(warnings, unused)]
@@ -35,8 +36,7 @@ use crate::read_pair_iter::{AnyReadPairIter, InputFastqs, ReadPairIter};
 pub use crate::squality::SQuality;
 pub use crate::sseq::SSeq;
 use anyhow::Error;
-pub use fastq::OwnedRecord;
-pub use fastq::Record;
+pub use fastq::{OwnedRecord, Record};
 pub use read_pair::WhichRead;
 use read_pair_iter::FastqError;
 use serde::{Deserialize, Serialize};

diff --git a/src/read_pair.rs b/src/read_pair.rs
@@ -4,7 +4,7 @@
 //! including the primary 'R1' and 'R2' and index 'I1' and 'I2' reads.
 
 use crate::WhichEnd;
-use anyhow::{bail, Result};
+use anyhow::{bail, ensure, Result};
 use bytes::{Bytes, BytesMut};
 use fastq::{OwnedRecord, Record};
 use serde::{Deserialize, Serialize};
@@ -186,9 +186,9 @@ impl RpRange {
     /// # Args
     /// * `read` - Specify `WhichRead`
     /// * `offset` - Start of the interval. Must be less than 2^15 (=32,768)
-    /// * `len` - Optional length that determines the end of the interval. A
-    /// value `None` indicates everything from `offset` until the end of the
-    /// `read`. Must be less than 2^15 (=32,768)
+    /// * `len` - Optional length that determines the end of the interval.
+    ///    A value `None` indicates everything from `offset` until the end of the `read`.
+    ///    Must be less than 2^15 (=32,768)
     ///
     /// # Panics
     /// * If `offset` or `len` is >= `2^15`
@@ -205,11 +205,11 @@ impl RpRange {
     ///
     /// # Tests
     /// * `test_rprange_invalid_offset()` - Test that this function panics with
-    /// an offset that is too large
+    ///   an offset that is too large
     /// * `test_rprange_invalid_len()` - Test that this function panics with
-    /// a length that is too large
+    ///   a length that is too large
     /// * `prop_test_rprange_representation()` - Test that arbitrary construction of RpRange
-    /// stores the values correctly.
+    ///   stores the values correctly.
     pub fn new(read: WhichRead, offset: usize, len: Option<usize>) -> RpRange {
         assert!(offset < (1 << 15));
         let len_bits = match len {
@@ -296,7 +296,7 @@ impl RpRange {
     ///
     /// # Tests
     /// * `test_rprange_intersect_panic()` - Make sure that this function panics
-    /// if the reads do not match
+    ///   if the reads do not match
     /// * `test_rprange_intersect_both_open()` - Test a case when both lengths are not set
     /// * `test_rprange_intersect_self_open()` - Test a case when only self length is set
     /// * `test_rprange_intersect_other_open()` - Test a case when only other length is set
@@ -363,7 +363,7 @@ impl RpRange {
     /// * `test_shrink_invalid_range_3()`: Test for panic if shrink range start > end
     /// * `test_rprange_trivial_shrink()`: Test shrink to an empty range.
     /// * `prop_test_rprange_shrink()`: Test shrink for arbitrary values of
-    /// `RpRange` and valid `shrink_range`
+    ///   `RpRange` and valid `shrink_range`
     pub fn shrink(&mut self, shrink_range: &ops::Range<usize>) {
         assert!(
             shrink_range.start <= shrink_range.end,
@@ -496,14 +496,12 @@ impl<'a> MutReadPair<'a> {
 
     pub fn new<R: Record>(buffer: &'a mut BytesMut, rr: &[Option<R>; 4]) -> MutReadPair<'a> {
         let mut rp = MutReadPair::empty(buffer);
-
-        for (_rec, which) in rr.iter().zip(WhichRead::read_types().iter()) {
-            if let Some(ref rec) = *_rec {
-                rp.push_read(rec, *which)
+        for (rec, which) in rr.iter().zip(WhichRead::read_types()) {
+            if let Some(rec) = rec {
+                rp.push_read(rec, which);
             }
             // default ReadOffsets is exists = false
         }
-
         rp
     }
 
@@ -600,32 +598,26 @@ impl ReadPair {
 
     pub fn check_range(&self, range: &RpRange, region_name: &str) -> Result<()> {
         let req_len = range.offset() + range.len().unwrap_or(0);
-
-        match self.get(range.read(), ReadPart::Seq) {
-            Some(read) => {
-                if read.len() < req_len {
-                    bail!(
-                        "{} is expected in positions {}-{} in Read {}, but read is {} bp long.",
-                        region_name,
-                        range.offset(),
-                        req_len,
-                        range.read(),
-                        read.len()
-                    );
-                } else {
-                    Ok(())
-                }
-            }
-            None => bail!(
+        let Some(read) = self.get(range.read(), ReadPart::Seq) else {
+            bail!(
                 "{region_name} is missing from FASTQ. Read {} is not present.",
                 range.read()
-            ),
-        }
+            );
+        };
+        ensure!(
+            read.len() >= req_len,
+            "{region_name} is expected in positions {}-{} in Read {}, but read is {} bp long.",
+            range.offset(),
+            req_len,
+            range.read(),
+            read.len()
+        );
+        Ok(())
     }
 
     pub fn to_owned_record(&self) -> HashMap<WhichRead, OwnedRecord> {
         let mut result = HashMap::new();
-        for &which in WhichRead::read_types().iter() {
+        for &which in &WhichRead::read_types() {
             if self.offsets[which as usize].exists {
                 let w = self.offsets[which as usize];
                 let rec = OwnedRecord {