V0.5.1 correct bug in split module

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "yacrd"
-version = "0.5.1-alpha"
+version = "0.5.1"
 authors = ["Pierre Marijon <[email protected]>"]
 
 exclude = ["image/*", "validation/*", "tests/*"]

Readme.md

@@ -58,7 +58,7 @@ conda install yacrd
 ```
 git clone https://github.com/natir/yacrd.git
 cd yacrd
-git checkout v0.5.0
+git checkout v0.5.1
 
 cargo build
 cargo test

src/chimera.rs

@@ -23,9 +23,9 @@ SOFTWARE.
 /* local use */
 
 /* crates use */
-use serde_json;
 use serde::ser::SerializeStruct;
-
+use serde_json;
+
 /* standard use */
 use std;
 use std::cmp::Ordering;

src/main.rs

@@ -61,7 +61,7 @@ use std::collections::HashMap;
 
 fn main() {
     let matches = App::new("yacrd")
-        .version("0.5 Omanyte")
+        .version("0.5.1 Omanyte")
         .author("Pierre Marijon <[email protected]>")
         .about("Yet Another Chimeric Read Detector")
         .subcommand(SubCommand::with_name("chimeric")
@@ -252,8 +252,10 @@ fn main() {
             chimeric_matches.is_present("compression-out"),
             chimeric_matches.value_of("compression-out").unwrap_or("no"),
         );
-        let mut output: Box<std::io::Write> =
-            file::get_output(chimeric_matches.value_of("output").unwrap(), out_compression);
+        let mut output: Box<std::io::Write> = file::get_output(
+            chimeric_matches.value_of("output").unwrap(),
+            out_compression,
+        );
 
         let filters: Vec<_> = match chimeric_matches.is_present("filter") {
             true => chimeric_matches.values_of("filter").unwrap().collect(),
@@ -288,7 +290,14 @@ fn main() {
             .parse::<f64>()
             .unwrap();
 
-        overlap::find(inputs, formats, chim_thres, ncov_thres, &mut remove_reads, false);
+        overlap::find(
+            inputs,
+            formats,
+            chim_thres,
+            ncov_thres,
+            &mut remove_reads,
+            false,
+        );
 
         chimera::write(
             &mut output,
@@ -307,24 +316,28 @@ fn main() {
         for filename in splits {
             split::run(&remove_reads, filename, split_suffix);
         }
-    }
-    else if let Some(scrubbing_matches) = matches.subcommand_matches("scrubbing") {
-        println!("{:?}", scrubbing_matches);
-        let (mapping, map_compression) = file::get_input(scrubbing_matches.value_of("mapping").unwrap());
-        let mut format = utils::get_mapping_format(scrubbing_matches.value_of("mapping").unwrap()).unwrap();
+    } else if let Some(scrubbing_matches) = matches.subcommand_matches("scrubbing") {
+        let (mapping, map_compression) =
+            file::get_input(scrubbing_matches.value_of("mapping").unwrap());
+        let mut format =
+            utils::get_mapping_format(scrubbing_matches.value_of("mapping").unwrap()).unwrap();
 
         let mut raw_path = scrubbing_matches.value_of("sequence").unwrap();
         let mut scrubbed_path = scrubbing_matches.value_of("scrubbed").unwrap();
-        
+
         let out_compression = file::choose_compression(
             map_compression,
             scrubbing_matches.is_present("compression-out"),
-            scrubbing_matches.value_of("compression-out").unwrap_or("no"),
+            scrubbing_matches
+                .value_of("compression-out")
+                .unwrap_or("no"),
+        );
+
+        let mut report: Box<std::io::Write> = file::get_output(
+            scrubbing_matches.value_of("report").unwrap(),
+            out_compression,
         );
 
-        let mut report: Box<std::io::Write> =
-            file::get_output(scrubbing_matches.value_of("report").unwrap(), out_compression);
-
         let chim_thres = scrubbing_matches
             .value_of("chimeric-threshold")
             .unwrap()
@@ -337,8 +350,15 @@ fn main() {
             .unwrap();
 
         let mut remove_reads: chimera::BadReadMap = HashMap::new();
-
-        overlap::find(vec![mapping], vec![format], chim_thres, ncov_thres, &mut remove_reads, true);
+
+        overlap::find(
+            vec![mapping],
+            vec![format],
+            chim_thres,
+            ncov_thres,
+            &mut remove_reads,
+            true,
+        );
         split::run(&remove_reads, raw_path, "_splited");
 
         chimera::write(
@@ -347,9 +367,8 @@ fn main() {
             scrubbing_matches.is_present("json-output"),
         );
 
-
         let tmp_name = postdetection::generate_out_name(raw_path, "_splited");
-        
+
         std::fs::rename(tmp_name, scrubbed_path).unwrap();
     }
 }

src/overlap.rs

@@ -62,7 +62,7 @@ pub fn find<R: std::io::Read>(
     chim_thres: u64,
     ncov_thres: f64,
     remove_reads: &mut chimera::BadReadMap,
-    report_all: bool
+    report_all: bool,
 ) {
     let mut read2mapping: HashMap<chimera::NameLen, Vec<chimera::Interval>> = HashMap::new();
 
@@ -287,7 +287,7 @@ mod test {
             0,
             0.8,
             &mut remove_reads,
-            false
+            false,
         );
 
         chimera::write(&mut writer, &remove_reads, false);
@@ -302,7 +302,7 @@ mod test {
             0,
             0.8,
             &mut remove_reads,
-            false
+            false,
         );
 
         chimera::write(&mut writer, &remove_reads, false);
@@ -323,7 +323,7 @@ mod test {
             0,
             0.8,
             &mut remove_reads,
-            false
+            false,
         );
 
         chimera::write(&mut writer, &remove_reads, false);
@@ -344,7 +344,7 @@ mod test {
             1,
             0.8,
             &mut remove_reads,
-            false
+            false,
         );
 
         chimera::write(&mut writer, &remove_reads, false);
@@ -370,7 +370,7 @@ mod test {
             0,
             0.8,
             &mut remove_reads,
-            false
+            false,
         );
 
         chimera::write(&mut writer, &remove_reads, true);
@@ -397,7 +397,7 @@ mod test {
             0,
             0.8,
             &mut remove_reads,
-            false
+            false,
         );
 
         chimera::write(&mut writer, &remove_reads, false);
@@ -423,7 +423,7 @@ mod test {
             0,
             0.8,
             &mut remove_reads,
-            false
+            false,
         );
 
         chimera::write(&mut writer, &remove_reads, false);
@@ -447,7 +447,7 @@ mod test {
             0,
             0.8,
             &mut remove_reads,
-            false
+            false,
         );
 
         chimera::write(&mut writer, &remove_reads, false);
@@ -518,7 +518,7 @@ mod test {
     #[test]
     fn find_chimera_report_all() {
         let result = "NotBad\t3\t10000\t7500,2500,10000\nChimeric\t4\t6000\t1000,2500,3500\nChimeric\t1\t10000\t2000,0,2000;1000,4500,5500;2000,8000,10000\nNotBad\t2\t10000\t7500,0,7500\n".to_string();
-        
+
         let good: HashSet<&str> = result.split("\n").collect();
         let mut remove_reads: chimera::BadReadMap = HashMap::new();
         let mut writer: Vec<u8> = Vec::new();
@@ -529,7 +529,7 @@ mod test {
             1,
             0.8,
             &mut remove_reads,
-            true
+            true,
         );
 
         chimera::write(&mut writer, &remove_reads, false);

src/postdetection/fasta.rs

@@ -125,16 +125,26 @@ impl PostDetectionOperationFasta for Split {
         }
 
         let mut position = vec![0];
+        let mut passed_pos = std::collections::HashSet::new();
         for inter in gaps.iter() {
-            position.push(inter.begin);
-            position.push(inter.end);
+            if !passed_pos.contains(&inter.begin) {
+                position.push(inter.begin);
+                passed_pos.insert(inter.begin);
+            }
+            if !passed_pos.contains(&inter.end) {
+                position.push(inter.end);
+                passed_pos.insert(inter.end);
+            }
         }
-        position.push(record.seq().len() as u64);
 
+        if position.len() % 2 == 1 {
+            position.push(record.seq().len() as u64);
+        }
+
         if position.len() == 2 && position[0] == 0 && position[1] as usize == record.seq().len() {
             return vec![record.clone()];
         }
-        
+
         for (a, b) in position.chunks(2).map(|x| (x[0], x[1])) {
             if a == b {
                 continue; // empty interval
@@ -208,7 +218,8 @@ mod test {
                             int_type: chimera::IntervalType::Sure,
                         },
                     ],
-                ));
+                ),
+            );
             m.insert(
                 "2".to_string(),
                 (
@@ -226,19 +237,16 @@ mod test {
                             int_type: chimera::IntervalType::Sure,
                         },
                     ],
-                ));
+                ),
+            );
             m.insert(
                 "3".to_string(),
-                (
-                    chimera::BadReadType::NotBad,
-                    6000,
-                    vec![],
-                ),
+                (chimera::BadReadType::NotBad, 6000, vec![]),
             );
             m
         };
     }
-    
+
     const FASTA_FILE: &'static [u8] = b">1
 ACTG
 >2
@@ -363,7 +371,6 @@ ACTG
         assert_eq!(out, FASTA_FILE_SPLITED_ALL);
     }
 
-
     const SHORT_FASTA_FILE: &'static [u8] = b">1
 ACTGGGGGGACTG
 >2
@@ -395,6 +402,9 @@ ACTG
                 }
             }
         }
+
+        println!("{}", String::from_utf8_lossy(&out));
+        println!("{}", String::from_utf8_lossy(SHORT_FASTA_FILE_SPLIT));
         assert_eq!(out, SHORT_FASTA_FILE_SPLIT);
     }
 }

src/postdetection/fastq.rs

@@ -125,12 +125,26 @@ impl PostDetectionOperationFastq for Split {
         }
 
         let mut position = vec![0];
+        let mut passed_pos = std::collections::HashSet::new();
         for inter in gaps.iter() {
-            position.push(inter.begin);
-            position.push(inter.end);
+            if !passed_pos.contains(&inter.begin) {
+                position.push(inter.begin);
+                passed_pos.insert(inter.begin);
+            }
+            if !passed_pos.contains(&inter.end) {
+                position.push(inter.end);
+                passed_pos.insert(inter.end);
+            }
         }
-        position.push(record.seq().len() as u64);
 
+        if position.len() % 2 == 1 {
+            position.push(record.seq().len() as u64);
+        }
+
+        if position.len() == 2 && position[0] == 0 && position[1] as usize == record.seq().len() {
+            return vec![record.clone()];
+        }
+
         for (a, b) in position.chunks(2).map(|x| (x[0], x[1])) {
             if a == b {
                 continue; // empty interval

src/postdetection/mod.rs

@@ -29,7 +29,7 @@ pub mod paf;
 use std::path::Path;
 
 pub fn in_read(begin: usize, end: usize, length: usize) -> bool {
-    return begin < length || end < length;
+    return begin <= length && end <= length;
 }
 
 pub fn generate_out_name(filename: &str, suffix: &str) -> String {

tests/not_run.rs

@@ -22,7 +22,7 @@ SOFTWARE.
 
 use std::process::Command;
 
-static HELP_MESSAGE: &'static str = "yacrd 0.5 Omanyte
+static HELP_MESSAGE: &'static str = "yacrd 0.5.1 Omanyte
 Pierre Marijon <[email protected]>
 Yet Another Chimeric Read Detector
 
@@ -51,7 +51,7 @@ mod not_run {
             .output()
             .expect("Could not run yacrd");
 
-        assert_eq!(output.stdout, b"yacrd 0.5 Omanyte\n");
+        assert_eq!(output.stdout, b"yacrd 0.5.1 Omanyte\n");
         println!("{:?}", output);
     }