update docs and startup filepath handling

.gitignore

@@ -1,8 +1 @@
 /target
-cerevisiae.k21.hist.png
-freq.tsv.gz
-output.tsv
-output/
-reddit_feedback.txt
-revcomp_issue.txt
-.idea/

LICENSE

@@ -1,6 +1,6 @@
-MIT License
+# MIT License
 
-Copyright (c) 2021 suchapalaver
+Copyright (c) 2022 suchapalaver
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -5,23 +5,23 @@
 Run `krust` on the test data* in the [`krust` Github repo](https://github.com/suchapalaver/krust), searching for kmers of length 5, like this:
 
 ```bash
-    cargo run --release 5 cerevisae.pan.fa > output.tsv
+cargo run --release 5 your/local/path/to/cerevisae.pan.fa > output.tsv
 ```
 
 or, searching for kmers of length 21:  
 
 ```bash
-    cargo run --release 21 cerevisae.pan.fa > output.tsv
+cargo run --release 21 your/local/path/to/cerevisae.pan.fa > output.tsv
 ```
 
 `krust` prints to `stdout`, writing, on alternate lines:
 
 ```bash
-    >{frequency}  
-    {canonical k-mer}
-    >{frequency}  
-    {canonical k-mer}  
-    ...
+>{frequency}  
+{canonical k-mer}
+>{frequency}  
+{canonical k-mer}  
+...
 ```  
 
 `krust` uses the [`rust-bio`](https://docs.rs/bio/0.38.0/bio/), [`rayon`](https://docs.rs/rayon/1.5.1/rayon/), and [`dashmap`](https://docs.rs/crate/dashmap/4.0.2) Rust libraries.  

src/configuration.rs

@@ -1,28 +1,27 @@
-use std::env;
-use std::error::Error;
+use std::{env, error::Error, path::PathBuf};
 
 /// Parsing command line k-size and filepath arguments.
 pub struct Config {
-    pub kmer_len: usize,
-    pub filepath: String,
+    pub k: usize,
+    pub path: PathBuf,
 }
 
 impl Config {
     pub fn new(mut args: env::Args) -> Result<Config, Box<dyn Error>> {
-        let kmer_len: usize = match args.nth(1) {
+        let k: usize = match args.nth(1) {
             Some(arg) => match arg.parse() {
-                Ok(kmer_len) if kmer_len > 0 && kmer_len < 33 => kmer_len,
+                Ok(k) if k > 0 && k < 33 => k,
                 Ok(_) => return Err("k-mer length needs to be larger than zero and, for `krust` in its current working form, no more than 32".into()),
                 Err(_) => return Err(format!("issue with k-mer length argument: {}", arg).into()),
             },
             None => return Err("k-mer length input required".into()),
         };
 
-        let filepath = match args.next() {
-            Some(arg) => arg,
+        let path = match args.next() {
+            Some(arg) => PathBuf::from(arg),
             None => return Err("filepath argument needed".into()),
         };
 
-        Ok(Config { kmer_len, filepath })
+        Ok(Config { k, path })
     }
 }

src/kmer.rs

@@ -3,7 +3,7 @@ custom_error::custom_error! { pub ValidityError
 }
 
 /// Creating a valid k-mer bytestring.
-#[derive(Debug, PartialEq)]
+#[derive(Debug, Eq, PartialEq)]
 pub struct Kmer(pub Vec<u8>);
 
 /// Find the canonical kmer

src/main.rs

@@ -6,7 +6,7 @@ fn main() {
         process::exit(1);
     });
 
-    if let Err(e) = krust::startup::run(config.filepath, config.kmer_len) {
+    if let Err(e) = krust::startup::run(config.path, config.k) {
         eprintln!("Application error: {}", e);
         drop(e);
         process::exit(1);

src/startup.rs

@@ -12,12 +12,13 @@ use std::{
     error::Error,
     hash::BuildHasherDefault,
     io::{BufWriter, Stdout, Write},
+    path::Path,
 };
 
-pub fn run(filepath: String, k: usize) -> Result<(), Box<dyn Error>> {
+pub fn run<P: AsRef<Path> + std::fmt::Debug>(path: P, k: usize) -> Result<(), Box<dyn Error>> {
     let mut buf = BufWriter::new(std::io::stdout());
 
-    let _print_results = build_kmer_map(filepath, k)?
+    build_kmer_map(path, k)?
         .into_iter()
         .par_bridge()
         .map(|(bitpacked_kmer, freq)| (UnpackedKmer::from_kmer_data(bitpacked_kmer, k).0, freq))
@@ -40,9 +41,12 @@ pub fn run(filepath: String, k: usize) -> Result<(), Box<dyn Error>> {
 /// using a customized [`dashmap`](https://docs.rs/dashmap/4.0.2/dashmap/struct.DashMap.html)
 /// with [`FxHasher`](https://docs.rs/fxhash/0.2.1/fxhash/struct.FxHasher.html) to update in parallel a
 /// hashmap of canonical k-mers (keys) and their frequency in the data (values).
-fn build_kmer_map(filepath: String, k: usize) -> Result<DashFx, Box<dyn Error>> {
+fn build_kmer_map<P: AsRef<Path> + std::fmt::Debug>(
+    path: P,
+    k: usize,
+) -> Result<DashFx, Box<dyn Error>> {
     let kmer_map: DashFx = DashMap::with_hasher(BuildHasherDefault::<FxHasher>::default());
-    let _ = fasta::Reader::from_file(&filepath)?
+    fasta::Reader::from_file(path)?
         .records()
         .into_iter()
         .par_bridge()

tests/find_invalid.rs

@@ -39,4 +39,3 @@ fn find_invalid_works5() {
     assert_eq!(0, ans);
     assert_eq!(&b'N', dna.iter().collect::<Vec<_>>()[ans]);
 }
-