implement sequence-read trait

Cargo.toml

@@ -39,7 +39,7 @@ regex = "1.0"
 multimap = "0.4"
 fxhash = "0.2"
 statrs = "0.9.0"
-bio-types = ">=0.4"
+bio-types = ">=0.5.1"
 fnv = "1.0"
 strum = "0.13"
 strum_macros = "0.13"

src/io/fastq.rs

@@ -20,6 +20,8 @@ use std::io;
 use std::io::prelude::*;
 use std::path::Path;
 
+use bio_types::sequence::SequenceRead;
+
 use crate::utils::TextSlice;
 
 /// Trait for FASTQ readers.
@@ -234,6 +236,24 @@ impl fmt::Display for Record {
     }
 }
 
+impl SequenceRead for Record {
+    fn name(&self) -> &[u8] {
+        self.id.as_bytes()
+    }
+
+    fn base(&self, i: usize) -> u8 {
+        self.seq.as_bytes()[i]
+    }
+
+    fn base_qual(&self, i: usize) -> u8 {
+        self.qual.as_bytes()[i]
+    }
+
+    fn len(&self) -> usize {
+        self.seq().len()
+    }
+}
+
 /// An iterator over the records of a FastQ file.
 #[derive(Debug)]
 pub struct Records<R: io::Read> {