cargo fmt

gtars/src/common/utils.rs

@@ -39,8 +39,8 @@ pub fn get_dynamic_reader(path: &Path) -> Result<BufReader<Box<dyn Read>>> {
 ///
 /// - file_path: path to the file to read, or '-' for stdin
 ///
-/// # Returns 
-/// 
+/// # Returns
+///
 /// A `BufReader` object for a given file path or stdin.
 pub fn get_dynamic_reader_w_stdin(file_path_str: &str) -> Result<BufReader<Box<dyn Read>>> {
     if file_path_str == "-" {
@@ -51,7 +51,6 @@ pub fn get_dynamic_reader_w_stdin(file_path_str: &str) -> Result<BufReader<Box<d
     }
 }
 
-
 ///
 /// Create a region-to-id hash-map from a list of regions
 ///

gtars/src/digests/mod.rs

@@ -13,21 +13,21 @@
 //! # Usage
 //!
 //! The `sha512t24u` function can be used to compute the GA4GH sha512t24 checksum of a string.
-//! 
+//!
 //! ```rust
 //! use gtars::digests::sha512t24u;
 //!
 //! let digest = sha512t24u("hello world");
 //! ```
-use std::io::prelude::{Read, Write};
-use std::io;
 use std::fs::File;
+use std::io;
+use std::io::prelude::{Read, Write};
 use std::path::Path;
 
 use anyhow::Result;
 use md5::Md5;
+use seq_io::fasta::{Reader, Record, RefRecord};
 use sha2::{Digest, Sha512};
-use seq_io::fasta::{Reader, RefRecord, Record};
 
 use crate::common::utils::get_dynamic_reader;
 
@@ -75,7 +75,6 @@ pub fn md5(string: &str) -> String {
     format!("{:x}", result)
 }
 
-
 /// Processes a FASTA file to compute the digests of each sequence in the file.
 ///
 /// This function reads a FASTA file, computes the SHA-512 and MD5 digests for each sequence,
@@ -103,7 +102,8 @@ pub fn digest_fasta(file_path: &str) -> Result<Vec<DigestResult>> {
     let file_reader = get_dynamic_reader(&path)?;
     let mut fasta_reader = Reader::new(file_reader);
     let mut results = Vec::new();
-    while let Some(record) = fasta_reader.next() {  // returns a RefRecord object
+    while let Some(record) = fasta_reader.next() {
+        // returns a RefRecord object
         let record = record.expect("Error found when retrieving next record.");
         let id = record.id().expect("No ID found for the FASTA record");
         let mut sha512_hasher = Sha512::new();
@@ -123,7 +123,7 @@ pub fn digest_fasta(file_path: &str) -> Result<Vec<DigestResult>> {
             id: id.to_string(),
             length: length,
             sha512t24u: sha512,
-            md5: md5
+            md5: md5,
         });
     }
     Ok(results)
@@ -169,10 +169,10 @@ mod tests {
         assert_eq!(results[0].sha512t24u, "iYtREV555dUFKg2_agSJW6suquUyPpMw");
         assert_eq!(results[0].md5, "5f63cfaa3ef61f88c9635fb9d18ec945");
     }
-    
+
     #[test]
     fn bogus_fasta_file() {
         let result = digest_fasta("tests/data/bogus.fa");
         assert!(result.is_err(), "Expected an error for a bogus fasta file");
     }
-}
+}

gtars/src/uniwig/counting.rs

@@ -35,7 +35,6 @@ pub fn start_end_counts(
     smoothsize: i32,
     stepsize: i32,
 ) -> (Vec<u32>, Vec<i32>) {
-
     let mut v_coordinate_positions: Vec<i32> = Vec::new(); // these are the final coordinates after any adjustments
     let mut v_coord_counts: Vec<u32> = Vec::new(); // u8 stores 0:255 This may be insufficient. u16 max is 65535
 

gtars/src/uniwig/mod.rs

@@ -191,7 +191,7 @@ pub fn run_uniwig(matches: &ArgMatches) {
 }
 
 /// Ensures that the start position is at a minimum equal to `1`
-fn clamped_start_position(start: i32, smoothsize: i32, wig_shift:i32) -> i32 {
+fn clamped_start_position(start: i32, smoothsize: i32, wig_shift: i32) -> i32 {
     std::cmp::max(1, start - smoothsize + wig_shift)
 }
 /// Ensure that the start position is at a minimum equal to `0`
@@ -222,7 +222,6 @@ pub fn uniwig_main(
         .build()
         .unwrap();
 
-
     // Determine Input File Type
     let input_filetype = FileType::from_str(filetype.to_lowercase().as_str());
     // Set up output file names
@@ -319,7 +318,7 @@ pub fn uniwig_main(
                                                     clamped_start_position(
                                                         primary_start.0,
                                                         smoothsize,
-                                                        1 //must shift wiggle starts and core by 1 since it is 1 based
+                                                        1, //must shift wiggle starts and core by 1 since it is 1 based
                                                     ),
                                                     stepsize,
                                                     current_chrom_size,
@@ -449,7 +448,7 @@ pub fn uniwig_main(
                                                     clamped_start_position(
                                                         primary_end.0,
                                                         smoothsize,
-                                                        0
+                                                        0,
                                                     ),
                                                     stepsize,
                                                     meta_data_file_names[1].clone(),
@@ -468,7 +467,7 @@ pub fn uniwig_main(
                                                     clamped_start_position(
                                                         primary_end.0,
                                                         smoothsize,
-                                                        0
+                                                        0,
                                                     ),
                                                     stepsize,
                                                     meta_data_file_names[1].clone(),
@@ -520,7 +519,7 @@ pub fn uniwig_main(
                                                     &core_results.0,
                                                     file_name.clone(),
                                                     chrom_name.clone(),
-                                                    clamped_start_position(primary_start.0, 0,1), //starts are 1 based must be shifted by 1
+                                                    clamped_start_position(primary_start.0, 0, 1), //starts are 1 based must be shifted by 1
                                                     stepsize,
                                                     current_chrom_size,
                                                 );
@@ -589,9 +588,9 @@ pub fn uniwig_main(
                         );
                     }
                 }
-                "npy" =>{
+                "npy" => {
                     // populate hashmap for the npy meta data
-                    for chromosome in final_chromosomes.iter(){
+                    for chromosome in final_chromosomes.iter() {
                         let chr_name = chromosome.chrom.clone();
                         let current_chrom_size =
                             *chrom_sizes.get(&chromosome.chrom).unwrap() as i32;
@@ -605,42 +604,46 @@ pub fn uniwig_main(
                     }
 
                     for location in vec_count_type.iter() {
-
-                        let temp_meta_file_name = format!("{}{}.{}", bwfileheader, *location, "meta");
+                        let temp_meta_file_name =
+                            format!("{}{}.{}", bwfileheader, *location, "meta");
 
                         if let Ok(file) = File::open(&temp_meta_file_name) {
-
                             let reader = BufReader::new(file);
 
                             for line in reader.lines() {
                                 let line = line.unwrap();
                                 let parts: Vec<&str> = line.split_whitespace().collect();
                                 if parts.len() >= 3 {
-                                    let chrom = parts[1].split('=')
-                                        .nth(1)
-                                        .expect("Processing npy metadata file: Missing chromosome in line");
+                                    let chrom = parts[1].split('=').nth(1).expect(
+                                        "Processing npy metadata file: Missing chromosome in line",
+                                    );
                                     let start_str = parts[2].split('=')
                                         .nth(1)
                                         .expect("Processing npy metadata file: Missing start position in line");
-                                    let starting_position: i32 = start_str.parse().expect("Processing npy metadata file: Invalid start position");
+                                    let starting_position: i32 = start_str.parse().expect(
+                                        "Processing npy metadata file: Invalid start position",
+                                    );
 
-                                    if let Some(current_chr_data) = npy_meta_data_map.get_mut(chrom) {
-                                        current_chr_data.insert((*location.to_string()).parse().unwrap(), starting_position);
+                                    if let Some(current_chr_data) = npy_meta_data_map.get_mut(chrom)
+                                    {
+                                        current_chr_data.insert(
+                                            (*location.to_string()).parse().unwrap(),
+                                            starting_position,
+                                        );
                                     }
                                 }
                             }
                             // Remove the file after it is used.
                             let path = std::path::Path::new(&temp_meta_file_name);
                             let _ = remove_file(path).unwrap();
                         }
-
                     }
                     //write combined metadata as json
                     let json_string = serde_json::to_string_pretty(&npy_meta_data_map).unwrap();
-                    let combined_npy_meta_file_path = format!("{}{}.{}", bwfileheader, "npy_meta", "json");
+                    let combined_npy_meta_file_path =
+                        format!("{}{}.{}", bwfileheader, "npy_meta", "json");
                     let mut file = File::create(combined_npy_meta_file_path).unwrap();
                     file.write_all(json_string.as_bytes()).unwrap();
-
                 }
                 _ => {}
             }