update log in each subcmd

Cargo.toml

@@ -2,7 +2,7 @@
 
 [package]
 name = "fqkit"
-version = "0.4.10"
+version = "0.4.11"
 edition = "2021"
 authors = ["sharkLoc <[email protected]>"]
 rust-version = "1.77.2"

README.md

@@ -40,7 +40,7 @@ cargo install --git https://github.com/sharkLoc/fqkit.git
 ```bash
 FqKit -- A simple and cross-platform program for fastq file manipulation
 
-Version: 0.4.10
+Version: 0.4.11
 
 Authors: sharkLoc <[email protected]>
 Source code: https://github.com/sharkLoc/fqkit.git

example/summary.txt

@@ -0,0 +1,18 @@
+read average length:	126
+read min length:	126
+read max length:	126
+total gc content(%):	57.52
+total read count:	2000
+total base count:	252000
+
+base A count:	53864	(21.37%)
+base T count:	53136	(21.09%)
+base G count:	70989	(28.17%)
+base C count:	73967	(29.35%)
+base N count:	44	(0.02%)
+
+Number of base calls with quality value of 5 or higher (Q5+) (%)	251956	(99.98%)
+Number of base calls with quality value of 10 or higher (Q10+) (%)	251956	(99.98%)
+Number of base calls with quality value of 15 or higher (Q15+) (%)	244768	(97.13%)
+Number of base calls with quality value of 20 or higher (Q20+) (%)	237670	(94.31%)
+Number of base calls with quality value of 30 or higher (Q30+) (%)	223461	(88.67%)

src/cli/barcode.rs

@@ -6,7 +6,6 @@ use log::*;
 use std::collections::HashMap;
 use std::io::BufRead;
 use std::path::{Path, PathBuf};
-use std::time::Instant;
 
 fn barcode_list(file: &String, rev_comp: bool) -> Result<HashMap<String, String>> {
     let mut maps = HashMap::new();
@@ -97,7 +96,7 @@ pub fn split_fq(
     xz: bool,
     compression_level: u32,
 ) -> Result<()> {
-    let start = Instant::now();
+
 
     if !Path::new(outdir).try_exists().unwrap() {
         error!("{}", FqkitError::InvalidOutputDir(outdir.to_string()));
@@ -229,6 +228,5 @@ pub fn split_fq(
         );
     }
 
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }

src/cli/check.rs

@@ -2,7 +2,6 @@ use crate::utils::*;
 use anyhow::Result;
 use bio::io::fastq;
 use log::*;
-use std::time::Instant;
 
 pub fn check_fastq(
     file: Option<&String>,
@@ -11,7 +10,6 @@ pub fn check_fastq(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<()> {
-    let start = Instant::now();
 
     let (mut total, mut ok_read, mut err_read) = (0, 0, 0);
     let fp_reader = file_reader(file).map(fastq::Reader::new)?;
@@ -57,7 +55,6 @@ pub fn check_fastq(
         "total reads num: {}, ok reads number: {}, error reads number: {}",
         total, ok_read, err_read
     );
-    info!("time elapsed is: {:?}", start.elapsed());
 
     Ok(())
 }

src/cli/concat.rs

@@ -2,7 +2,7 @@ use crate::utils::*;
 use anyhow::{Error, Ok};
 use bio::io::fastq;
 use log::*;
-use std::{io::BufRead, time::Instant};
+use std::io::BufRead;
 
 pub fn concat_fqstq_lane(
     r1_list: &String,
@@ -12,7 +12,6 @@ pub fn concat_fqstq_lane(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<(), Error> {
-    let start = Instant::now();
 
     let mut vec1 = vec![];
     let mut vec2 = vec![];
@@ -65,7 +64,6 @@ pub fn concat_fqstq_lane(
         pe_read,
         vec1.len()
     );
-    info!("time elapsed is: {:?}", start.elapsed());
 
     Ok(())
 }

src/cli/cutadapter.rs

@@ -4,7 +4,6 @@ use anyhow::{Error, Ok, Result};
 use bio::io::{fasta, fastq};
 use log::*;
 use std::collections::HashMap;
-use std::time::Instant;
 
 pub fn cut_adapter(
     input: Option<&String>,
@@ -15,7 +14,6 @@ pub fn cut_adapter(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<(), Error> {
-    let start = Instant::now();
 
     let seqfile_reader = file_reader(Some(seqfile)).map(fasta::Reader::new)?;
     if let Some(file) = input {
@@ -99,6 +97,5 @@ pub fn cut_adapter(
     }
     fq_writer.flush()?;
 
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }

src/cli/filter.rs

@@ -3,7 +3,6 @@ use anyhow::{Ok, Result};
 use bio::io::fastq;
 use crossbeam::channel::unbounded;
 use log::*;
-use std::time::Instant;
 
 #[allow(clippy::too_many_arguments)]
 pub fn filter_fastq(
@@ -22,7 +21,6 @@ pub fn filter_fastq(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<()> {
-    let start = Instant::now();
     info!("read forward reads from file: {}", read1);
     info!("read reverse reads from file: {}", read2);
     if ![33u8, 64u8].contains(&phred) {
@@ -210,7 +208,6 @@ pub fn filter_fastq(
 
     info!("total clean pe reads number (r1+r2): {}", pe_ok * 2);
     info!("total failed pe reads number (r1+r2): {}", pe_fail * 2);
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }
 

src/cli/flatten.rs

@@ -2,7 +2,6 @@ use crate::utils::*;
 use anyhow::{Error, Ok};
 use bio::io::fastq;
 use log::*;
-use std::time::Instant;
 
 #[allow(clippy::too_many_arguments)]
 pub fn flatten_fq(
@@ -16,7 +15,6 @@ pub fn flatten_fq(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<(), Error> {
-    let start = Instant::now();
 
     let fq_reader = file_reader(file).map(fastq::Reader::new)?;
     if let Some(file) = file {
@@ -62,7 +60,6 @@ pub fn flatten_fq(
     }
     out_writer.flush()?;
 
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }
 

src/cli/fq2fa.rs

@@ -3,7 +3,6 @@ use anyhow::{Error, Ok};
 use bio::io::fasta;
 use bio::io::fastq;
 use log::*;
-use std::time::Instant;
 
 pub fn fq2fa(
     file: Option<&String>,
@@ -12,7 +11,6 @@ pub fn fq2fa(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<(), Error> {
-    let start = Instant::now();
 
     let mut num = 0usize;
     let fq_reader = fastq::Reader::new(file_reader(file)?);
@@ -37,6 +35,5 @@ pub fn fq2fa(
     fo.flush()?;
 
     info!("total reads number: {}", num);
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }

src/cli/fq2sam.rs

@@ -2,7 +2,6 @@ use crate::utils::*;
 use anyhow::{Error, Ok};
 use bio::io::fastq;
 use log::*;
-use std::time::Instant;
 
 #[allow(clippy::too_many_arguments)]
 pub fn fastq2sam(
@@ -16,7 +15,6 @@ pub fn fastq2sam(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<(), Error> {
-    let start = Instant::now();
     if let Some(r2) = r2 {
         info!("read file1 from: {}", r1);
         info!("read file2 from: {}", r2);
@@ -105,7 +103,5 @@ pub fn fastq2sam(
         }
     }
     sam.flush()?;
-
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }

src/cli/fqscore.rs

@@ -2,7 +2,6 @@ use crate::utils::*;
 use anyhow::{Ok, Result};
 use bio::io::{fastq, fastq::Record};
 use log::*;
-use std::time::Instant;
 
 pub fn phred_score(
     file: Option<&String>,
@@ -12,8 +11,7 @@ pub fn phred_score(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<()> {
-    let start = Instant::now();
-
+
     let fq_reader = file_reader(file).map(fastq::Reader::new)?;
     if let Some(r) = file {
         info!("read file from: {}", r);
@@ -55,6 +53,5 @@ pub fn phred_score(
     }
     fq_writer.flush()?;
 
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }

src/cli/gcplot.rs

@@ -6,7 +6,6 @@ use log::*;
 use lowcharts::plot;
 use plotters::prelude::*;
 use std::collections::HashMap;
-use std::time::Instant;
 
 #[allow(clippy::too_many_arguments)]
 pub fn gc_content(
@@ -21,7 +20,6 @@ pub fn gc_content(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<(), Error> {
-    let start = Instant::now();
 
     let fq_reader = file_reader(fqin).map(fastq::Reader::new)?;
     if let Some(inp) = fqin {
@@ -76,7 +74,6 @@ pub fn gc_content(
     }
     plot_gc(df_ret, prefix, width, height, ylim, types)?;
 
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }
 

src/cli/grep.rs

@@ -4,7 +4,6 @@ use anyhow::{Ok, Result};
 use bio::io::fastq;
 use log::*;
 use std::io::BufRead;
-use std::time::Instant;
 
 pub fn grep_fastq(
     fq: Option<&String>,
@@ -14,7 +13,6 @@ pub fn grep_fastq(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<()> {
-    let start = Instant::now();
 
     let fq_reader = file_reader(fq).map(fastq::Reader::new)?;
     if let Some(file) = fq {
@@ -59,6 +57,5 @@ pub fn grep_fastq(
     fo.flush()?;
 
     info!("total reads matched number: {}", num);
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }

src/cli/kmer.rs

@@ -3,7 +3,7 @@ use anyhow::Error;
 use bio::io::fastq;
 use log::*;
 use nthash::nthash;
-use std::{collections::HashMap, time::Instant};
+use std::collections::HashMap;
 
 pub fn kmer_count(
     input: Option<&String>,
@@ -13,7 +13,6 @@ pub fn kmer_count(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<(), Error> {
-    let start = Instant::now();
     let reader = file_reader(input).map(fastq::Reader::new)?;
     if let Some(file) = input {
         info!("reading from file: {}", file);
@@ -48,6 +47,5 @@ pub fn kmer_count(
         writer.write_all(format!("\t{}\n", v).as_bytes())?;
     }
     writer.flush()?;
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }

src/cli/length.rs

@@ -3,7 +3,6 @@ use anyhow::{Error, Ok};
 use bio::io::fastq;
 use log::*;
 use std::collections::HashMap;
-use std::time::Instant;
 
 pub fn fq_length(
     file: Option<&String>,
@@ -12,7 +11,6 @@ pub fn fq_length(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<(), Error> {
-    let start = Instant::now();
 
     let mut reads_len = HashMap::new();
     let mut total = 0usize;
@@ -43,7 +41,6 @@ pub fn fq_length(
     }
     fo.flush()?;
     info!("total scan reads number: {}", total);
-    info!("time elapsed is: {:?}", start.elapsed());
 
     Ok(())
 }

src/cli/mask.rs

@@ -2,7 +2,6 @@ use crate::utils::*;
 use anyhow::{Ok, Result};
 use bio::io::{fastq, fastq::Record};
 use log::*;
-use std::time::Instant;
 
 pub fn mask_fastq(
     file: Option<&String>,
@@ -13,7 +12,6 @@ pub fn mask_fastq(
     compression_level: u32,
     stdout_type: char,
 ) -> Result<()> {
-    let start = Instant::now();
 
     let (mut mask_base, mut mask_read) = (0, 0);
     let fp_reader = file_reader(file).map(fastq::Reader::new)?;
@@ -50,6 +48,5 @@ pub fn mask_fastq(
     fp_writer.flush()?;
 
     info!("total mask {} bases from {} reads", mask_base, mask_read);
-    info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
 }