feat: add option -r for subcli length

chore: remove changle log in README
- change log style (logger.rs)
- add categories in Cargo.toml

Cargo.toml

@@ -1,11 +1,12 @@
 [package]
 name = "fqkit"
-version = "0.4.3"
+version = "0.4.4"
 edition = "2021"
 authors = ["sharkLoc <[email protected]>"]
 rust-version = "1.77.2"
 homepage = "https://github.com/sharkLoc/fqkit"
 repository = "https://github.com/sharkLoc/fqkit"
+categories = ["Bioinformatics"]
 description = "fqkit: a simple and cross-platform program for fastq file manipulation"
 keywords = ["fastq", "reads","bio", "hts", "barcode"]
 readme = "README.md"

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: 0.4.3
+Version: 0.4.4
 
 Authors: sharkLoc <[email protected]>
 Source code: https://github.com/sharkLoc/fqkit.git
@@ -110,63 +110,4 @@ Global FLAGS:
 Use "fqkit help [command]" for more information about a command
 ```
 
-## change log
-<details>
-<summary>timeline</summary>
-
-2023.11.03:
- - update to version 0.2.12
- - add subcommand trim
- - update cmd help information
-
-2023.11.08:
- - update to version 0.2.13
- - add subcommand reverse
-
-2023.11.10:
- - update to version 0.2.14
- - add subcommand view
- - rebuilt some command interface
-
-2023.11.29:
- - update to version 0.2.15
- - recode func in stats subcommand
-
-2023.12.04
- - update to version 0.2.16
- - add subcommand size
-
-2023.12.05
- - update to version 0.2.17
- - update code for subcommand size and search
- - add subcommand fq2sam
- - add log information options verbosity
-
-2023.12.09
- - update to version 0.2.18
- - add subcommand sort, range, check and mask
- - update to version 0.2.19
- - add subcommand shuffle
-
-2023.12.10
- - update to version 0.3.0
- - add glob option --compress-level for gzip output file
-
-2023.12.11
-- update to version 0.3.1
-- add subcommand grep and fqscore
-
-2023.12.11
-- update to version 0.3.2
-- add subcommand slide
-
-2023.12.19
-- update to version 0.3.5
-- add subcommand filter
-
-2024.03.27
-- remove subcommand join
-
-</details>
-
 #### ** any bugs please report issues **💖

src/cli/length.rs

@@ -7,6 +7,7 @@ use std::time::Instant;
 
 pub fn fq_length(
     file: Option<&String>,
+    rev: bool,
     out: Option<&String>,
     compression_level: u32,
 ) -> Result<(), Error> {
@@ -29,7 +30,11 @@ pub fn fq_length(
     }
 
     let mut sort_len: Vec<(&usize, &usize)> = reads_len.iter().collect();
-    sort_len.sort_by_key(|x| x.0);
+    if rev {
+        sort_len.sort_by(|x,y|y.0.cmp(x.0));
+    } else {
+        sort_len.sort_by_key(|x| x.0);
+    }
 
     fo.write_all("lenth\tcount\n".as_bytes())?;
     for (k, v) in sort_len.iter() {

src/command.rs

@@ -4,7 +4,7 @@ use clap::{value_parser, Parser};
 #[command(
     name = "FqKit",
     author = "sharkLoc",
-    version = "0.4.3",
+    version = "0.4.4",
     about = "A simple and cross-platform program for fastq file manipulation",
     long_about = None,
     next_line_help = false,
@@ -674,6 +674,9 @@ pub enum Subcli {
     length {
         /// input fastq file, or read from stdin
         input: Option<String>,
+        /// output reversed result
+        #[arg(short = 'r', long = "reverse", help_heading = Some("FLAGS"))]
+        reverse: bool,
         /// 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>,

src/logger.rs

@@ -52,7 +52,7 @@ pub fn logger<P: AsRef<Path>>(
         }
         writeln!(
             buf,
-            "[{} {} - {}] {}",
+            "{} {} - {} {}",
             Local::now().format("%Y-%m-%dT%H:%M:%S"),
             style.value(record.level()),
             buf.style()

src/main.rs

@@ -433,8 +433,8 @@ fn main() -> Result<(), Error> {
                 arg.compression_level,
             )?;
         }
-        Subcli::length { input, out } => {
-            fq_length(input.as_ref(), out.as_ref(), arg.compression_level)?;
+        Subcli::length { input, reverse, out } => {
+            fq_length(input.as_ref(), reverse, out.as_ref(), arg.compression_level)?;
         }
         Subcli::view { input, out } => {
             view_fq(input.as_ref(), out.as_ref(), arg.compression_level)?;