cli/commands/quantify: Filter low mapping quality records

Author: zaeleus

atlas-cli/src/cli/quantify.rs

@@ -1,6 +1,7 @@
 use std::path::PathBuf;
 
 use clap::Parser;
+use noodles::sam::alignment::record::MappingQuality;
 
 #[derive(Parser)]
 pub struct Args {
@@ -16,6 +17,16 @@ pub struct Args {
     #[arg(long)]
     pub annotations: PathBuf,
 
+    /// Record mapping quality threshold.
+    #[arg(long, value_parser = parse_mapping_quality, default_value = "10")]
+    pub min_mapping_quality: MappingQuality,
+
     /// Source input (BAM).
     pub src: PathBuf,
 }
+
+fn parse_mapping_quality(s: &str) -> Result<MappingQuality, &'static str> {
+    s.parse::<u8>()
+        .map_err(|_| "invalid input")
+        .and_then(|n| MappingQuality::new(n).ok_or("missing mapping quality"))
+}

atlas-cli/src/commands/quantify.rs

@@ -73,7 +73,8 @@ pub fn quantify(args: quantify::Args) -> Result<(), QuantifyError> {
         "detected library layout"
     );
 
-    let filter = Filter;
+    let min_mapping_quality = args.min_mapping_quality;
+    let filter = Filter::new(min_mapping_quality);
 
     let mut reader = bam::io::reader::Builder.build_from_path(src)?;
     reader.read_header()?;

atlas-cli/src/commands/quantify/filter.rs

@@ -1,19 +1,33 @@
 use std::io;
 
-use noodles::bam;
+use noodles::{bam, sam::alignment::record::MappingQuality};
 
 use super::count::Event;
 
-pub(super) struct Filter;
+pub(super) struct Filter {
+    min_mapping_quality: MappingQuality,
+}
 
 impl Filter {
+    pub(super) fn new(min_mapping_quality: MappingQuality) -> Self {
+        Self {
+            min_mapping_quality,
+        }
+    }
+
     pub(super) fn filter(&self, record: &bam::Record) -> io::Result<Option<Event<'_>>> {
         let flags = record.flags();
 
         if flags.is_unmapped() {
             return Ok(Some(Event::Unmapped));
         }
 
+        if let Some(mapping_quality) = record.mapping_quality() {
+            if mapping_quality < self.min_mapping_quality {
+                return Ok(Some(Event::LowQuality));
+            }
+        }
+
         Ok(None)
     }
 }