replace flatten with map_while(Result::ok) on iter

Author: sharkLoc

Cargo.lock

@@ -1,6 +1,6 @@
 [package]
 name = "fqkit"
-version = "0.4.9"
+version = "0.4.10"
 edition = "2021"
 authors = ["sharkLoc <mmtinfo@163.com>"]
 rust-version = "1.77.2"

Cargo.toml

@@ -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: 0.4.9
+Version: 0.4.10
 
 Authors: sharkLoc <mmtinfo@163.com>
 Source code: https://github.com/sharkLoc/fqkit.git

README.md

@@ -15,7 +15,7 @@ fn barcode_list(file: &String, rev_comp: bool) -> Result<HashMap<String, String>
     info!("reading from barcode list file: {}", file);
 
     if rev_comp {
-        for line in fp.lines().map_while(std::io::Result::ok) {
+        for line in fp.lines().map_while(Result::ok) {
             let item = line.split('\t').collect::<Vec<&str>>(); // barcode => sample
             let bar: String = item[0]
                 .chars()
@@ -42,7 +42,7 @@ fn barcode_list(file: &String, rev_comp: bool) -> Result<HashMap<String, String>
             error_flag = "";
         }
     } else {
-        for line in fp.lines().map_while(std::io::Result::ok) {
+        for line in fp.lines().map_while(Result::ok) {
             let item = line.split('\t').collect::<Vec<&str>>();
             let bar: String = item[0]
                 .chars()

src/cli/barcode.rs

@@ -22,7 +22,7 @@ pub fn check_fastq(
 
     if save {
         let mut out_writer = file_writer(out, compression_level).map(fastq::Writer::new)?;
-        for rec in fp_reader.records().flatten() {
+        for rec in fp_reader.records().map_while(Result::ok) {
             total += 1;
             match rec.check() {
                 Ok(_) => {
@@ -37,7 +37,7 @@ pub fn check_fastq(
         }
         out_writer.flush()?;
     } else {
-        for rec in fp_reader.records().flatten() {
+        for rec in fp_reader.records().map_while(Result::ok) {
             total += 1;
             match rec.check() {
                 Ok(_) => {

src/cli/check.rs

@@ -46,8 +46,8 @@ pub fn concat_fqstq_lane(
         let fq_reader2 = file_reader(Some(pe.1)).map(fastq::Reader::new)?;
         for (rec1, rec2) in fq_reader1
             .records()
-            .flatten()
-            .zip(fq_reader2.records().flatten())
+            .map_while(Result::ok)
+            .zip(fq_reader2.records().map_while(Result::ok))
         {
             out_writer1.write_record(&rec1)?;
             out_writer2.write_record(&rec2)?;

src/cli/concat.rs

@@ -26,7 +26,7 @@ pub fn cut_adapter(
 
     let mut seqs = HashMap::new();
     let iters = seqfile_reader.records();
-    for rec in iters.flatten() {
+    for rec in iters.map_while(Result::ok) {
         //while let Some(each) = iters.next() {
         //let rec = each?;
         if seqs.contains_key(rec.id()) {

src/cli/cutadapter.rs

@@ -48,7 +48,7 @@ pub fn filter_fastq(
         for (rec1, rec2) in fq_reader1
             .records()
             .flatten()
-            .zip(fq_reader2.records().flatten())
+            .zip(fq_reader2.records().map_while(Result::ok))
         {
             if rec1.seq().iter().filter(|v| v == &&b'N').count() > nbase
                 || rec2.seq().iter().filter(|v| v == &&b'N').count() > nbase
@@ -117,8 +117,8 @@ pub fn filter_fastq(
             let pe_vec: Vec<_> = fq_iter1
                 .by_ref()
                 .take(chunk)
-                .flatten()
-                .zip(fq_iter2.by_ref().take(chunk).flatten())
+                .map_while(Result::ok)
+                .zip(fq_iter2.by_ref().take(chunk).map_while(Result::ok))
                 .collect();
             if pe_vec.is_empty() {
                 break;

src/cli/filter.rs

@@ -33,7 +33,7 @@ pub fn flatten_fq(
     let fields = get_flag(flag);
     let mut out_writer = file_writer(out, compression_level)?;
 
-    for rec in fq_reader.records().flatten() {
+    for rec in fq_reader.records().map_while(Result::ok) {
         let read = [rec.id().as_bytes(), rec.seq(), "+".as_bytes(), rec.qual()];
         let res = fields.iter().map(|idx| read[*idx]).collect::<Vec<&[u8]>>();
 

src/cli/flatten.rs

@@ -23,7 +23,7 @@ pub fn fq2fa(
 
     let mut fo = fasta::Writer::new(file_writer(out, compression_level)?);
     if remove {
-        for rec in fq_reader.records().flatten() {
+        for rec in fq_reader.records().map_while(Result::ok) {
             num += 1;
             fo.write(rec.id(), None, rec.seq())?;
         }