From bb0d35d4b1b0a19ba790aae2044f8cd342575330 Mon Sep 17 00:00:00 2001
From: sharkLoc <mmtinfo@163.com>
Date: Thu, 19 Dec 2024 22:20:41 +0800
Subject: [PATCH] remove duplicate thread option

---
 src/cli/filter.rs | 5 -----
 src/cli/search.rs | 5 -----
 src/cli/size.rs   | 2 --
 src/command.rs    | 9 ---------
 src/main.rs       | 9 +++------
 5 files changed, 3 insertions(+), 27 deletions(-)

diff --git a/src/cli/filter.rs b/src/cli/filter.rs
index 8ca8e2d..4e1ee3d 100644
--- a/src/cli/filter.rs
+++ b/src/cli/filter.rs
@@ -27,11 +27,6 @@ pub fn filter_fastq(
         error!("{}", FqkitError::InvalidPhredValue);
         std::process::exit(1);
     }
-    if ncpu <= 1 {
-        info!("thread num is: {}", ncpu);
-    } else {
-        info!("additional thread num is: {}", ncpu);
-    }
     info!("output clean read1 file: {}", out1);
     info!("output clean read2 file: {}", out2);
 
diff --git a/src/cli/search.rs b/src/cli/search.rs
index 57b8301..8519142 100644
--- a/src/cli/search.rs
+++ b/src/cli/search.rs
@@ -26,11 +26,6 @@ pub fn search_fq(
     }
 
     info!("regex pattern is: {}", pat);
-    if ncpu == 1 || ncpu == 0 {
-        info!("thread num is: {}", ncpu);
-    } else {
-        info!("additional thread num is: {}", ncpu);
-    }
 
     let mut chunk = chunk;
     if chunk == 0 {
diff --git a/src/cli/size.rs b/src/cli/size.rs
index c0a66bd..32e4a95 100644
--- a/src/cli/size.rs
+++ b/src/cli/size.rs
@@ -1,7 +1,6 @@
 use crate::utils::*;
 use anyhow::Result;
 use bio::io::fastq;
-//use crossbeam::channel::unbounded;
 use crossbeam::channel::bounded;
 use log::*;
 
@@ -43,7 +42,6 @@ pub fn size_fastq(
     } else {
         info!("reading from stdin");
     }
-    info!("additional worker threads is: {}", ncpu);
 
     let mut chunk = chunk;
     if chunk == 0 {
diff --git a/src/command.rs b/src/command.rs
index 41cb62c..08ebead 100644
--- a/src/command.rs
+++ b/src/command.rs
@@ -217,9 +217,6 @@ pub enum Subcli {
         /// the number of reads in the chunk on each thread
         #[arg(short, long, default_value_t = 5000, value_name = "INT")]
         chunk: usize,
-        /// number of additional worker threads to use
-        #[arg(short = '@', long = "thread", default_value_t = 4, value_name = "INT")]
-        thread: usize,
         /// specify the file to store reads(interleaved) that cannot pass the filters, file ending in .gz/.bz2/.xz will be compressed automatically
         #[arg(short = 'u', long = "failed", value_name = "FILE")]
         failed: String,
@@ -260,9 +257,6 @@ pub enum Subcli {
         /// the number of reads in the chunk on each thread
         #[arg(short, long, default_value_t = 5000, value_name = "INT")]
         chunk: usize,
-        /// number of additional worker threads to use
-        #[arg(short = '@', long = "thread", default_value_t = 1, value_name = "INT")]
-        thread: usize,
         /// output contain pattern/motif reads result fastq file or write to stdout, file ending in .gz/.bz2/.xz will be compressed automatically
         #[arg(short = 'o', long = "out", value_name = "FILE")]
         out: Option<String>,
@@ -334,9 +328,6 @@ pub enum Subcli {
         /// the number of reads in the chunk on each thread
         #[arg(short, long, default_value_t = 5000, value_name = "INT")]
         chunk: usize,
-        /// number of additional worker threads to use
-        #[arg(short = '@', long = "thread", default_value_t = 3, value_name = "INT")]
-        thread: usize,
         /// output file name or write to stdout, file ending in .gz/.bz2/.xz will be compressed automatically
         #[arg(short = 'o', long = "out", value_name = "FILE")]
         out: Option<String>,
diff --git a/src/main.rs b/src/main.rs
index de294db..3c0fcbd 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -140,7 +140,6 @@ fn main() -> Result<(), Error> {
             case,
             invert,
             chunk,
-            thread,
             out,
         } => {
             search_fq(
@@ -150,7 +149,7 @@ fn main() -> Result<(), Error> {
                 invert,
                 chunk,
                 out.as_ref(),
-                thread,
+                arg.threads,
                 arg.compression_level,
                 arg.stdout_type,
             )?;
@@ -283,13 +282,12 @@ fn main() -> Result<(), Error> {
         }
         Subcli::size {
             input,
-            thread,
             chunk,
             out,
         } => {
             size_fastq(
                 input.as_ref(),
-                thread,
+                arg.threads,
                 chunk,
                 out.as_ref(),
                 arg.compression_level,
@@ -369,7 +367,6 @@ fn main() -> Result<(), Error> {
             average_qual,
             phred,
             chunk,
-            thread,
             failed,
             out1,
             out2,
@@ -383,7 +380,7 @@ fn main() -> Result<(), Error> {
                 average_qual,
                 phred,
                 chunk,
-                thread,
+                arg.threads,
                 &failed,
                 &out1,
                 &out2,