clippy

Cargo.toml

@@ -42,6 +42,8 @@ spin = "0.9.8"
 tch = {version = "0.14.0", optional = true}
 tempfile = "3.3.0"
 derive_builder = "0.12.0"
+gzp = "0.11.3"
+niffler = {version = "2.5.0", default-features = false, features = ["gz"]}
 
 [features]
 cli = ["dep:clap", "dep:clap_complete", "dep:clap_mangen", "dep:console"]

src/bamlift/mod.rs

@@ -20,7 +20,7 @@ where
 /// Normal sort is supposed to be very fast on two sorted lists
 /// <https://doc.rust-lang.org/std/vec/struct.Vec.html#current-implementation-6>
 /// ```
-/// use bamlift::*;
+/// use fibertools_rs::bamlift::*;
 /// let x = vec![1,3];
 /// let x_q = vec!["a","b"];
 /// let y = vec![2,4];
@@ -76,7 +76,7 @@ pub fn positions_on_complimented_sequence(
 /// get positions on the complimented sequence in the cigar record
 pub fn positions_on_complimented_sequence_in_place(
     record: &bam::Record,
-    input_positions: &mut Vec<i64>,
+    input_positions: &mut [i64],
     part_of_range: bool,
 ) {
     if !record.is_reverse() {
@@ -107,7 +107,7 @@ where
 /// a\[i-1\] <= v < a\[i\]
 /// <https://numpy.org/doc/stable/reference/generated/numpy.searchsorted.html>
 /// ```
-/// use bamlift::*;
+/// use fibertools_rs::bamlift::*;
 /// let a = vec![1, 2, 3, 5, 6, 7, 8, 9, 10];
 /// let v = vec![0, 1, 3, 4, 11, 11];
 /// let indexes = search_sorted(&a, &v);
@@ -187,22 +187,22 @@ fn liftover_closest(
             // get the previous closest position
             let (best_r_pos, best_diff) = pos_mapping.get_mut(cur_pos).unwrap();
             // exact match found
-            if cur_pos >= &q_st && cur_pos < &q_en {
+            if cur_pos >= q_st && cur_pos < q_en {
                 let dist_from_start = cur_pos - q_st;
                 *best_diff = 0;
                 *best_r_pos = r_st + dist_from_start;
                 break;
             }
             // we are before the start of the block
-            else if cur_pos < &q_st {
+            else if cur_pos < q_st {
                 let diff = (q_st - cur_pos).abs();
                 if diff < *best_diff {
                     *best_diff = diff;
                     *best_r_pos = *r_st;
                 }
             }
             // we are past the end of the block
-            else if cur_pos >= &q_en {
+            else if cur_pos >= q_en {
                 let diff = (q_en - cur_pos).abs();
                 if diff < *best_diff {
                     *best_diff = diff;
@@ -237,7 +237,7 @@ pub fn lift_reference_positions(
 
 /// find the closest query positions for a list of reference positions
 pub fn lift_query_positions(
-    aligned_block_pairs: &Vec<([i64; 2], [i64; 2])>,
+    aligned_block_pairs: &[([i64; 2], [i64; 2])],
     reference_positions: &[i64],
 ) -> Vec<Option<i64>> {
     // if lifting to the query, we need to reverse the pairs
@@ -266,7 +266,7 @@ fn lift_range(
     assert_eq!(ref_starts.len(), ref_ends.len());
     let rtn = ref_starts
         .into_iter()
-        .zip(ref_ends.into_iter())
+        .zip(ref_ends)
         .map(|(start, end)| match (start, end) {
             (Some(start), Some(end)) => {
                 if start == end {

src/basemods/mod.rs

@@ -1,6 +1,6 @@
-use bamlift::*;
+use super::bamlift::*;
+use super::bio_io::*;
 use bio::alphabets::dna::revcomp;
-use bio_io::*;
 use itertools::{izip, multiunzip};
 use lazy_static::lazy_static;
 use regex::Regex;

src/bio_io/mod.rs

@@ -43,8 +43,7 @@ pub fn no_length_progress_bar() -> ProgressBar {
     let bar = ProgressBar::new(0);
     bar.set_style(style);
     let finish = indicatif::ProgressFinish::AndLeave;
-    let bar = bar.with_finish(finish);
-    bar
+    bar.with_finish(finish)
 }
 
 /*
@@ -98,12 +97,12 @@ pub fn write_to_file(out: &str, buffer: &mut Box<dyn Write>) {
 
 /// a reader that can read compressed files but also stdin (indicated by -)
 /// ```
-/// use bio_io::buffer_from;
+/// use fibertools_rs::bio_io::buffer_from;
 /// use std::io;
-/// let reader = buffer_from("../tests/data/test.txt.gz").expect("Error: cannot open file");
+/// let reader = buffer_from("tests/data/test.txt.gz").expect("Error: cannot open file");
 /// let msg = io::read_to_string(reader).unwrap();
 /// assert_eq!(msg, "Hello World!\n");
-/// let reader = buffer_from("../tests/data/test.txt").expect("Error: cannot open file");
+/// let reader = buffer_from("tests/data/test.txt").expect("Error: cannot open file");
 /// let msg = io::read_to_string(reader).unwrap();
 /// assert_eq!(msg, "Hello World!\n");
 /// ```
@@ -321,8 +320,9 @@ pub fn find_pb_polymerase(header: &bam::Header) -> PbChem {
 
 ///```
 /// use rust_htslib::{bam, bam::Read};
+/// use fibertools_rs::bio_io;
 /// use log;
-/// let mut bam = bam::Reader::from_path(&"../tests/data/all.bam").unwrap();
+/// let mut bam = bam::Reader::from_path(&"tests/data/all.bam").unwrap();
 /// for record in bam.records() {
 ///     let record = record.unwrap();
 ///     let n_s = bio_io::get_u32_tag(&record, b"ns");

src/fiber.rs

@@ -1,8 +1,8 @@
+use super::bamlift::*;
 use super::basemods::BaseMods;
+use super::bio_io::*;
 use super::center::CenterPosition;
 use super::center::CenteredFiberData;
-use bamlift::*;
-use bio_io::*;
 use rayon::prelude::*;
 use rust_htslib::bam::Read;
 use rust_htslib::{bam, bam::ext::BamRecordExtensions, bam::record::Aux, bam::HeaderView};

src/footprint.rs

@@ -1,6 +1,7 @@
 use crate::center::CenterPosition;
 
 use super::bam_writer;
+use super::bio_io;
 use super::cli::FootprintOptions;
 use super::fiber::*;
 use anyhow;

tests/extract_test.rs

@@ -1,3 +1,4 @@
+use fibertools_rs::bio_io;
 use rust_htslib::bam::Read;
 
 fn get_fiber_data_from_test_bam(bam_file: &str) -> Vec<fibertools_rs::fiber::FiberseqData> {