update code

Author: sharkLoc

src/cli/length.rs

@@ -3,6 +3,7 @@ use anyhow::{Error, Ok};
 use bio::io::fastq;
 use log::*;
 use std::collections::HashMap;
+use rayon::prelude::*;
 
 pub fn fq_length(
     file: Option<&String>,
@@ -30,9 +31,9 @@ pub fn fq_length(
 
     let mut sort_len: Vec<(&usize, &usize)> = reads_len.iter().collect();
     if rev {
-        sort_len.sort_by(|x, y| y.0.cmp(x.0));
+        sort_len.par_sort_by(|x, y| y.0.cmp(x.0));
     } else {
-        sort_len.sort_by_key(|x| x.0);
+        sort_len.par_sort_by_key(|x| x.0);
     }
 
     fo.write_all("lenth\tcount\n".as_bytes())?;

src/cli/search.rs

@@ -1,7 +1,7 @@
 use crate::utils::*;
 use anyhow::{Error, Ok};
 use bio::io::fastq;
-use crossbeam::channel::unbounded;
+use crossbeam::channel::bounded;
 use log::*;
 use regex::RegexBuilder;
 
@@ -67,7 +67,7 @@ pub fn search_fq(
         }
         fo.flush()?;
     } else {
-        let (tx, rx) = unbounded();
+        let (tx, rx) = bounded(5000);
         let mut fqiter = fq_reader.records();
         loop {
             let chunks: Vec<_> = fqiter.by_ref().take(chunk).map_while(Result::ok).collect();
@@ -79,7 +79,7 @@ pub fn search_fq(
         drop(tx);
 
         crossbeam::scope(|s| {
-            let (tx2, rx2) = unbounded();
+            let (tx2, rx2) = bounded(5000);
             let _handles: Vec<_> = (0..ncpu)
                 .map(|_| {
                     let tx_tmp = tx2.clone();

src/cli/stats.rs

@@ -199,55 +199,6 @@ pub fn stat_fq(
                     tf[4] += 1;
                 }
             }
-            /*if each.contains_key(&pos) {
-                let tf = each.get_mut(&pos).unwrap();
-                let gap = (idx + 5 + 1) as i32 - tf.len() as i32;
-                if gap > 0 {
-                    //tf.resize(gap+tf.len(), 0);           // error
-                    //tf.resize_with(gap+tf.len(), || 0);   // error
-                    //tf.append(&mut vec![0;gap]);          // error
-                    //for _ in 0..gap { tf.push(0); }       // error
-                    for _ in 0..gap {
-                        tf.insert(tf.len(), 0);
-                    } // WFK? ok:  add zero at vec![] tail in loop n
-                }
-                tf[idx + 5] += 1;
-                if sf == &b'A' {
-                    tf[0] += 1;
-                }
-                if sf == &b'T' {
-                    tf[1] += 1;
-                }
-                if sf == &b'G' {
-                    tf[2] += 1;
-                }
-                if sf == &b'C' {
-                    tf[3] += 1;
-                }
-                if sf == &b'N' {
-                    tf[4] += 1;
-                }
-            } else {
-                let cap = this_q as usize + 1 + 5;
-                let mut v_tmp = vec![0usize; cap];
-                v_tmp[idx + 5] += 1;
-                if sf == &b'A' {
-                    v_tmp[0] += 1;
-                }
-                if sf == &b'T' {
-                    v_tmp[1] += 1;
-                }
-                if sf == &b'G' {
-                    v_tmp[2] += 1;
-                }
-                if sf == &b'C' {
-                    v_tmp[3] += 1;
-                }
-                if sf == &b'N' {
-                    v_tmp[4] += 1;
-                }
-                each.insert(pos, v_tmp);
-            }*/
         }
     }
 

src/command.rs

@@ -34,7 +34,7 @@ pub struct Args {
     pub command: Subcli,
 
     /// threads number
-    #[arg(short = '@', long = "threads", default_value_t = 1, global = true, value_name = "INT", help_heading = Some("Global Arguments"))]
+    #[arg(short = '@', long = "threads", default_value_t = 4, global = true, value_name = "INT", help_heading = Some("Global Arguments"))]
     pub threads: usize,
 
     /// set gzip/bzip2/xz compression level 1 (compress faster) - 9 (compress better) for gzip/bzip2/xz output file, just work with option -o/--out