add --max-qual; minor updates; closes [#25]

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "nanoq"
-version = "0.8.4"
+version = "0.8.5"
 authors = ["esteinig <eike.steinig@unimelb.edu.au>", "ljmcoin <lachlan.coin@unimelb.edu.au>"]
 description = "Minimal but speedy quality control and summaries of nanopore reads"
 documentation = "https://github.com/esteinig/nanoq"

README.md

@@ -2,14 +2,14 @@
 
 [![build](https://github.com/esteinig/nanoq/actions/workflows/rust-ci.yaml/badge.svg?branch=master)](https://github.com/esteinig/nanoq/actions/workflows/rust-ci.yaml)
 [![codecov](https://codecov.io/gh/esteinig/nanoq/branch/master/graph/badge.svg?token=1X04YD8YOE)](https://codecov.io/gh/esteinig/nanoq)
-![](https://img.shields.io/badge/version-0.8.4-black.svg)
+![](https://img.shields.io/badge/version-0.8.5-black.svg)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02991/status.svg)](https://doi.org/10.21105/joss.02991)
 
 Ultra-fast quality control and summary reports for nanopore reads
 
 ## Overview
 
-**`v0.8.4`**
+**`v0.8.5`**
 
 - [Purpose](#purpose)
 - [Install](#install)
@@ -72,15 +72,15 @@ cargo install nanoq
 Explicit version (for some reason defaults to old version)
 
 ```
-conda install -c conda-forge -c bioconda nanoq=0.8.4
+conda install -c conda-forge -c bioconda nanoq=0.8.5
 ```
 
 #### `Binaries`
 
 Precompiled binaries for Linux and MacOS are attached to the latest release.
 
 ```
-VERSION=0.8.4
+VERSION=0.8.5
 RELEASE=nanoq-${VERSION}-x86_64-unknown-linux-musl.tar.gz
 
 wget https://github.com/esteinig/nanoq/releases/download/${VERSION}/${RELEASE}
@@ -144,26 +144,27 @@ done
 ### Parameters
 
 ```
-nanoq 0.8.4
+nanoq 0.8.5
 
 Read filters and summary reports for nanopore data
 
 USAGE:
     nanoq [FLAGS] [OPTIONS]
 
 FLAGS:
-    -f, --fast       Fast mode, do not consider quality values
+    -f, --fast       Ignore quality values if present
     -h, --help       Prints help information
-    -s, --stats      Statistics only, reads to /dev/null
+    -s, --stats      Summary statistics report
     -V, --version    Prints version information
-    -v, --verbose    Pretty print output statistics
+    -v, --verbose    Verbose output statistics [multiple up to -vvv]
 
 OPTIONS:
     -c, --compress-level <1-9>     Compression level to use if compressing output [default: 6]
     -i, --input <input>            Fast{a,q}.{gz,xz,bz}, stdin if not present
     -m, --max-len <INT>            Maximum read length filter (bp) [default: 0]
+    -w, --max-qual <FLOAT>         Maximum average read quality filter (Q) [default: 0]
     -l, --min-len <INT>            Minimum read length filter (bp) [default: 0]
-    -m, --min-qual <FLOAT>         Minimum average read quality filter (Q) [default: 0]
+    -q, --min-qual <FLOAT>         Minimum average read quality filter (Q) [default: 0]
     -o, --output <output>          Output filepath, stdout if not present
     -O, --output-type <u|b|g|l>    u: uncompressed; b: Bzip2; g: Gzip; l: Lzma
     -t, --top <INT>                Number of top reads in verbose summary [default: 5]

src/cli.rs

@@ -26,7 +26,11 @@ pub struct Cli {
     #[structopt(short = "q", long, value_name = "FLOAT", default_value = "0")]
     pub min_qual: f32,
 
-    /// Pretty print output statistics.  
+    /// Maximum average read quality filter (Q).
+    #[structopt(short = "w", long, value_name = "FLOAT", default_value = "0")]
+    pub max_qual: f32,
+
+    /// Verbose output statistics [multiple up to -vvv]  
     #[structopt(
         short,
         long,
@@ -38,7 +42,7 @@ pub struct Cli {
     #[structopt(short, long, value_name = "INT", default_value = "5")]
     pub top: usize,
 
-    /// Statistics only, reads to /dev/null.
+    /// Summary statistics report
     #[structopt(short, long)]
     pub stats: bool,
 
@@ -195,6 +199,17 @@ mod tests {
         assert_eq!(actual, expected)
     }
 
+    #[test]
+    fn invalid_max_qual() {
+        let passed_args = vec!["nanoq", "-w", "test"];
+        let args: Result<Cli, clap::Error> = Cli::from_iter_safe(passed_args);
+
+        let actual = args.unwrap_err().kind;
+        let expected = clap::ErrorKind::ValueValidation;
+
+        assert_eq!(actual, expected)
+    }
+
     #[test]
     fn invalid_to_value() {
         let passed_args = vec!["nanoq", "-t", "test"];

src/main.rs

@@ -23,7 +23,7 @@ fn main() -> Result<()> {
             .filter_length(cli.min_len, cli.max_len)
             .context("unable to process reads")?,
         false => needle_cast
-            .filter(cli.min_len, cli.max_len, cli.min_qual)
+            .filter(cli.min_len, cli.max_len, cli.min_qual, cli.max_qual)
             .context("unable to process reads")?,
     };
 

src/needlecast.rs

@@ -96,6 +96,7 @@ impl NeedleCast {
         min_length: u32,
         max_length: u32,
         min_quality: f32,
+        max_quality: f32,
     ) -> Result<(Vec<u32>, Vec<f32>), ParseError> {
         let mut read_lengths: Vec<u32> = vec![];
         let mut read_qualities: Vec<f32> = vec![];
@@ -105,6 +106,9 @@ impl NeedleCast {
         } else {
             max_length
         };
+
+        let max_quality = if max_quality == 0. { 93. } else { max_quality };
+
         while let Some(record) = self.reader.next() {
             let rec = record.expect("failed to parse record");
             let seqlen = rec.num_bases() as u32; // NANOQ READ LENGTH LIMIT: ~ 4.2 x 10e9
@@ -113,7 +117,11 @@ impl NeedleCast {
                 let mean_error_prob = mean_error_probability(qual);
                 let mean_quality: f32 = -10f32 * mean_error_prob.log(10.0);
                 // FASTQ
-                if seqlen >= min_length && seqlen <= max_length && mean_quality >= min_quality {
+                if seqlen >= min_length
+                    && seqlen <= max_length
+                    && mean_quality >= min_quality
+                    && mean_quality <= max_quality
+                {
                     read_lengths.push(seqlen);
                     read_qualities.push(mean_quality);
                     rec.write(&mut self.writer, None)
@@ -241,7 +249,7 @@ mod tests {
 
         let cli = Cli::from_iter(&["nanoq", "-i", "tests/cases/test_ok.fq", "-o", "/dev/null"]);
         let mut caster = NeedleCast::new(&cli);
-        let (read_lengths, read_quals) = caster.filter(0, 0, 0.0).unwrap();
+        let (read_lengths, read_quals) = caster.filter(0, 0, 0.0, 0.0).unwrap();
 
         assert_eq!(read_lengths, vec![4]);
         assert_eq!(read_quals, vec![40.0]);
@@ -265,7 +273,7 @@ mod tests {
 
         let cli = Cli::from_iter(&["nanoq", "-i", "tests/cases/test_ok.fa", "-o", "/dev/null"]);
         let mut caster = NeedleCast::new(&cli);
-        let (read_lengths, read_quals) = caster.filter(0, 0, 0.0).unwrap();
+        let (read_lengths, read_quals) = caster.filter(0, 0, 0.0, 0.0).unwrap();
 
         assert_eq!(read_lengths, vec![4]);
         assert_eq!(read_quals, vec![]);
@@ -290,7 +298,7 @@ mod tests {
 
         let cli = Cli::from_iter(&["nanoq", "-i", "tests/cases/test_bad1.fa", "-o", "/dev/null"]);
         let mut caster = NeedleCast::new(&cli);
-        caster.filter(0, 0, 0.0).unwrap();
+        caster.filter(0, 0, 0.0, 0.0).unwrap();
     }
 
     #[test]
@@ -300,7 +308,7 @@ mod tests {
 
         let cli = Cli::from_iter(&["nanoq", "-i", "tests/cases/test_bad1.fq", "-o", "/dev/null"]);
         let mut caster = NeedleCast::new(&cli);
-        caster.filter(0, 0, 0.0).unwrap();
+        caster.filter(0, 0, 0.0, 0.0).unwrap();
     }
 
     #[test]
@@ -310,7 +318,7 @@ mod tests {
 
         let cli = Cli::from_iter(&["nanoq", "-i", "tests/cases/test_bad2.fq", "-o", "/dev/null"]);
         let mut caster = NeedleCast::new(&cli);
-        caster.filter(0, 0, 0.0).unwrap();
+        caster.filter(0, 0, 0.0, 0.0).unwrap();
     }
 
     #[test]

tests/app.rs

@@ -30,7 +30,7 @@ fn output_file_in_nonexistant_dir() -> Result<(), Box<dyn std::error::Error>> {
 }
 
 #[test]
-fn valid_inputs_raises_no_errors() -> Result<(), Box<dyn std::error::Error>> {
+fn valid_inputs_raise_no_errors() -> Result<(), Box<dyn std::error::Error>> {
     let mut cmd = Command::cargo_bin(env!("CARGO_PKG_NAME"))?;
     cmd.args(vec![
         "-i",