refactor: improve grep example

Author: noamteyssier

examples/grep.rs

@@ -2,6 +2,7 @@ use std::sync::Arc;
 
 use anyhow::Result;
 use binseq::prelude::*;
+use clap::Parser;
 use memchr::memmem::Finder;
 use parking_lot::Mutex;
 
@@ -50,21 +51,26 @@ impl ParallelProcessor for GrepCounter {
     }
 }
 
-fn main() -> Result<()> {
-    let path = std::env::args()
-        .nth(1)
-        .unwrap_or("./data/subset.bq".to_string());
-    let pattern = std::env::args()
-        .nth(2)
-        .unwrap_or("ACGT".to_string())
-        .as_bytes()
-        .to_vec();
-    let n_threads = std::env::args().nth(3).unwrap_or("1".to_string()).parse()?;
+#[derive(Parser)]
+struct Args {
+    /// Input BINSEQ path to grep
+    #[clap(required = true)]
+    input: String,
 
-    let reader = BinseqReader::new(&path)?;
-    let counter = GrepCounter::new(&pattern);
-    reader.process_parallel(counter.clone(), n_threads)?;
-    counter.pprint();
+    /// Pattern to search for (either sseq or xseq)
+    #[clap(required = true)]
+    pattern: String,
+
+    /// Threads to use [0: auto]
+    #[clap(short = 'T', long, default_value_t = 0)]
+    threads: usize,
+}
 
+fn main() -> Result<()> {
+    let args = Args::parse();
+    let reader = BinseqReader::new(&args.input)?;
+    let counter = GrepCounter::new(args.pattern.as_bytes());
+    reader.process_parallel(counter.clone(), args.threads)?;
+    counter.pprint();
     Ok(())
 }