version 0.3

Cargo.toml

@@ -1,10 +1,23 @@
 [package]
-name = "yarcd"
+name = "yacrd"
 version = "0.3.0"
 authors = ["Pierre Marijon <[email protected]>"]
 
+exclude = ["image/*", "validation/*", "tests/*"]
+
+description = "Using all-against-all read mapping, yacrd performs: computation of pile-up coverage for each read and detection of chimeras"
+#documentation = "https://github.com/natir/yacrd"
+homepage = "https://github.com/natir/yacrd"
+repository = "https://github.com/natir/yacrd"
+readme = "Readme.md"
+license = "MIT"
+keywords = ["bioinformatics", "chimera", "long-read"]
+
+[badges]
+travis-ci = { repository = "natir/yacrd", branch = "master" }
+
 [dependencies]
-bio          = "*"
+bio          = "0.21"
 csv          = "1"
 xz2          = "0.1"
 clap         = "2.31.2"
@@ -14,3 +27,7 @@ flate2       = "1.0"
 rust-lzma    = "0.2"
 lazy_static  = "1.0"
 serde_derive = "1.0"
+
+[[bin]]
+name = "yacrd"
+path = "src/main.rs"

Readme.md

@@ -1,5 +1,7 @@
 # Yet Another Chimeric Read Detector for long reads
 
+[![Build Status](https://travis-ci.org/natir/yacrd.svg?branch=master)](https://travis-ci.org/natir/yacrd)
+
 ![yacrd pipeline presentation](image/pipeline.svg)
 
 Using all-against-all read mapping, yacrd performs:
@@ -21,7 +23,7 @@ DAStrim (from the [DASCRUBBER suite](https://github.com/thegenemyers/DASCRUBBER)
 
 ## Input
 
-Any set of long reads (PacBio, Nanopore, anything that can be given to [https://github.com/lh3/minimap2](minimap2) ).
+Any set of long reads (PacBio, Nanopore, anything that can be given to [minimap2](https://github.com/lh3/minimap2) ).
 yacrd takes the resulting PAF (Pairwise Alignement Format) from minimap2 or MHAP file from some other long reads overlapper as input.
 
 ## Requirements
@@ -30,9 +32,17 @@ yacrd takes the resulting PAF (Pairwise Alignement Format) from minimap2 or MHAP
 
 ## Instalation
 
+### With cargo
+
+If you have a rust environment setup you can run :
+
+```
+cargo install yacrd
+```
+
 ### With conda
 
-yacrd are avaible in [bioconda channel](https://bioconda.github.io/)
+yacrd is avaible in [bioconda channel](https://bioconda.github.io/)
 
 if bioconda channel is setup you can run :
 
@@ -58,7 +68,7 @@ cargo install
 2)
 
 ```
-yacrd 0.3 Mew
+yacrd 0.3 Ninetales
 Pierre Marijon <[email protected]>
 Yet Another Chimeric Read Detector
 
@@ -81,7 +91,7 @@ OPTIONS:
             Mapping input file in PAF or MHAP format (with .paf or .mhap extension), use - for read standard input (no
             compression allowed, paf format by default) [default: -]
     -o, --output <output>
-            Path where yacrd report are write, use - for write in standard output same compression as input or use
+            Path where yacrd report are writen, use - for write in standard output same compression as input or use
             --compression-out [default: -]
     -f, --filter <filter>...
             File containing reads that will be filtered (fasta|fastq|mhap|paf), new file are create like
@@ -91,7 +101,7 @@ OPTIONS:
             Overlap depth threshold below which a gap should be created [default: 0]
 
     -n, --not-covered-threshold <not-covered-threshold>
-            Coverage depth threshold above which a read are mark as not covered [default: 0.80]
+            Coverage depth threshold above which a read are marked as not covered [default: 0.80]
 
         --filtered-suffix <filtered-suffix>
             Change the suffix of file generate by filter option [default: _filtered]

src/main.rs

@@ -50,7 +50,7 @@ use std::collections::HashSet;
 
 fn main() {
     let matches = App::new("yacrd")
-        .version("0.3 Mew")
+        .version("0.3 Ninetales")
         .author("Pierre Marijon <[email protected]>")
         .about("Yet Another Chimeric Read Detector")
         .usage("yacrd [-i|--input] <input> [-o|--output] <output> [-f|--filter] <file1, file2, …> 
@@ -75,7 +75,7 @@ fn main() {
              .display_order(2)
              .takes_value(true)
              .default_value("-")
-             .help("Path where yacrd report are write, use - for write in standard output same compression as input or use --compression-out")
+             .help("Path where yacrd report are writen, use - for write in standard output same compression as input or use --compression-out")
              )
         .arg(Arg::with_name("filter")
              .short("f")
@@ -107,7 +107,7 @@ fn main() {
              .takes_value(true)
              .default_value("0.80")
              .long("not-covered-threshold")
-             .help("Coverage depth threshold above which a read are mark as not covered")
+             .help("Coverage depth threshold above which a read are marked as not covered")
              )
         .arg(Arg::with_name("filtered-suffix")
              .display_order(7)

tests/not_run.rs

@@ -22,7 +22,7 @@ SOFTWARE.
 
 use std::process::Command;
 
-static HELP_MESSAGE: &'static str = "yacrd 0.3 Mew
+static HELP_MESSAGE: &'static str = "yacrd 0.3 Ninetales
 Pierre Marijon <[email protected]>
 Yet Another Chimeric Read Detector
 
@@ -45,7 +45,7 @@ OPTIONS:
             Mapping input file in PAF or MHAP format (with .paf or .mhap extension), use - for read standard input (no
             compression allowed, paf format by default) [default: -]
     -o, --output <output>
-            Path where yacrd report are write, use - for write in standard output same compression as input or use
+            Path where yacrd report are writen, use - for write in standard output same compression as input or use
             --compression-out [default: -]
     -f, --filter <filter>...
             File containing reads that will be filtered (fasta|fastq|mhap|paf), new file are create like
@@ -55,7 +55,7 @@ OPTIONS:
             Overlap depth threshold below which a gap should be created [default: 0]
 
     -n, --not-covered-threshold <not-covered-threshold>
-            Coverage depth threshold above which a read are mark as not covered [default: 0.80]
+            Coverage depth threshold above which a read are marked as not covered [default: 0.80]
 
         --filtered-suffix <filtered-suffix>
             Change the suffix of file generate by filter option [default: _filtered]
@@ -72,18 +72,18 @@ mod not_run {
 
     #[test]
     fn version() {
-        let output = Command::new("./target/debug/yarcd")
+        let output = Command::new("./target/debug/yacrd")
             .arg("-V")
             .output()
             .expect("Could not run yacrd");
 
-        assert_eq!(output.stdout, b"yacrd 0.3 Mew\n");
+        assert_eq!(output.stdout, b"yacrd 0.3 Ninetales\n");
         println!("{:?}", output);
     }
 
     #[test]
     fn help() {
-        let output = Command::new("./target/debug/yarcd")
+        let output = Command::new("./target/debug/yacrd")
             .arg("-h")
             .output()
             .expect("Could not run yacrd");
@@ -93,7 +93,7 @@ mod not_run {
 
     #[test]
     fn no_argument() {
-        let output = Command::new("./target/debug/yarcd")
+        let output = Command::new("./target/debug/yacrd")
             .output()
             .expect("Could not run yacrd");
 

tests/realistic_scenario.rs

@@ -35,7 +35,7 @@ mod realistic_scenario {
 
     #[test]
     fn default() {
-        let child = Command::new("./target/debug/yarcd")
+        let child = Command::new("./target/debug/yacrd")
             .stdin(Stdio::from(fs::File::open("tests/data/test.paf").unwrap()))
             .stdout(Stdio::piped())
             .spawn()
@@ -49,7 +49,7 @@ mod realistic_scenario {
 
     #[test]
     fn file_mhap_gz_out_same_paf_default_default() {
-        let child = Command::new("./target/debug/yarcd")
+        let child = Command::new("./target/debug/yacrd")
             .arg("-i")
             .arg("tests/data/test.mhap.gz")
             .arg("-F")
@@ -81,7 +81,7 @@ Chimeric	1	10000	2000,0,2000;1000,4500,5500;2000,8000,10000
 ";
         let good: HashSet<&str> = expected.split("\n").collect();
 
-        Command::new("./target/debug/yarcd")
+        Command::new("./target/debug/yacrd")
             .arg("-i")
             .arg("-")
             .arg("-o")
@@ -92,7 +92,7 @@ Chimeric	1	10000	2000,0,2000;1000,4500,5500;2000,8000,10000
                 fs::File::open("tests/data/test_cov_1.paf").unwrap(),
             ))
             .stdout(Stdio::piped())
-            .spawn()
+            .output()
             .expect("Could ot run yacrd");
 
         assert_eq!(
@@ -113,7 +113,7 @@ Not_covered	3	10000	5500,4500,10000
 ";
         let good: HashSet<&str> = expected.split("\n").collect();
 
-        let child = Command::new("./target/debug/yarcd")
+        let child = Command::new("./target/debug/yacrd")
             .arg("-i")
             .arg("tests/data/test.paf.bz2")
             .arg("-o")
@@ -169,7 +169,7 @@ Chimeric	1	10000	2000,0,2000;1000,4500,5500;2000,8000,10000
 
         let good: HashSet<&str> = expected.split("\n").collect();
 
-        Command::new("./target/debug/yarcd")
+        Command::new("./target/debug/yacrd")
             .arg("-i")
             .arg("tests/data/test_cov_1.mhap.xz")
             .arg("-o")
@@ -184,7 +184,7 @@ Chimeric	1	10000	2000,0,2000;1000,4500,5500;2000,8000,10000
             .arg("tests/data/test.fasta")
             .stdin(Stdio::piped())
             .stdout(Stdio::piped())
-            .spawn()
+            .output()
             .expect("Could not run yacrd");
 
         {