fix kmer count method

src/cli/kmer.rs

@@ -1,18 +1,17 @@
+use crate::utils::*;
 use anyhow::Error;
 use bio::io::fastq;
 use log::*;
-use std::{collections::HashMap, time::Instant};
-use crate::utils::*;
 use nthash::nthash;
-
+use std::{collections::HashMap, time::Instant};
 
 pub fn kmer_count(
     input: Option<&String>,
     kmer_len: usize,
     header: bool,
     output: Option<&String>,
     compression_level: u32,
-) -> Result<(),Error> {
+) -> Result<(), Error> {
     let start = Instant::now();
     let reader = file_reader(input).map(fastq::Reader::new)?;
     if let Some(file) = input {
@@ -23,21 +22,17 @@ pub fn kmer_count(
 
     let mut writer = file_writer(output, compression_level)?;
     let mut kmers = HashMap::new();
-    let (mut sidx, mut eidx) = (0,kmer_len);
+    let (mut sidx, mut eidx) = (0, kmer_len);
 
     for rec in reader.records().flatten() {
         let khash = nthash(rec.seq(), kmer_len);
 
-        let end = rec.seq().len() - kmer_len + 1;
-        while eidx <= end {
+        while eidx <= rec.seq().len() {
             let kseq = &rec.seq()[sidx..eidx];
             let khash_this = nthash(kseq, kmer_len)[0];
-            for k in khash.iter() {
-                if khash_this.eq(k) {
-                    *kmers.entry(kseq.to_owned()).or_insert(0_u64) += 1;
-                }
+            if khash.contains(&khash_this) {
+                *kmers.entry(kseq.to_owned()).or_insert(0_u64) += 1;
             }
-
             sidx += 1;
             eidx += 1;
         }
@@ -46,11 +41,11 @@ pub fn kmer_count(
     if header {
         writer.write_all("kmer\tcount\n".as_bytes())?;
     }
-    for (k,v) in kmers {
+    for (k, v) in kmers {
         writer.write_all(k.as_slice())?;
-        writer.write_all(format!("\t{}\n",v).as_bytes())?;
+        writer.write_all(format!("\t{}\n", v).as_bytes())?;
     }
     writer.flush()?;
     info!("time elapsed is: {:?}", start.elapsed());
     Ok(())
-}
+}

src/cli/mod.rs

@@ -9,6 +9,7 @@ pub mod fq2sam;
 pub mod fqscore;
 pub mod gcplot;
 pub mod grep;
+pub mod kmer;
 pub mod length;
 pub mod mask;
 pub mod merge;
@@ -31,4 +32,3 @@ pub mod tail;
 pub mod top;
 pub mod trimfq;
 pub mod view;
-pub mod kmer;

src/command.rs

@@ -292,7 +292,12 @@ pub enum Subcli {
         /// input fastq file, or read from stdin
         input: Option<String>,
         /// set kmer size
-        #[arg(short = 'k', long = "kmer-size", default_value_t = 21, value_name = "INT")]
+        #[arg(
+            short = 'k',
+            long = "kmer-size",
+            default_value_t = 21,
+            value_name = "INT"
+        )]
         size: usize,
         /// add header info in output file
         #[arg(short = 'H', long, help_heading = Some("FLAGS"))]

src/main.rs

@@ -10,9 +10,10 @@ use command::*;
 mod cli;
 use cli::{
     barcode::*, check::*, concat::*, cutadapter::cut_adapter, filter::*, flatten::*, fq2fa::*,
-    fq2sam::*, fqscore::*, gcplot::*, grep::*, length::*, mask::*, merge::*, plot::*, range::*,
-    remove::*, rename::*, reverse::*, search::*, select::*, shuffle::*, size::*, slide::*, sort::*,
-    split::*, split2::*, stats::*, subfq::*, tail::*, top::*, trimfq::*, view::*, kmer::*,
+    fq2sam::*, fqscore::*, gcplot::*, grep::*, kmer::*, length::*, mask::*, merge::*, plot::*,
+    range::*, remove::*, rename::*, reverse::*, search::*, select::*, shuffle::*, size::*,
+    slide::*, sort::*, split::*, split2::*, stats::*, subfq::*, tail::*, top::*, trimfq::*,
+    view::*,
 };
 
 fn main() -> Result<(), Error> {
@@ -470,8 +471,19 @@ fn main() -> Result<(), Error> {
         Subcli::view { input, out } => {
             view_fq(input.as_ref(), out.as_ref(), arg.compression_level)?;
         }
-        Subcli::kmer { input, size, header, out } => {
-            kmer_count(input.as_ref(), size, header, out.as_ref(), arg.compression_level)?;
+        Subcli::kmer {
+            input,
+            size,
+            header,
+            out,
+        } => {
+            kmer_count(
+                input.as_ref(),
+                size,
+                header,
+                out.as_ref(),
+                arg.compression_level,
+            )?;
         }
     }