From 9d0ec3310aa79d9459662d3c03748945eee0fdef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@tu-dortmund.de>
Date: Thu, 25 Apr 2019 15:34:56 +0200
Subject: [PATCH] implement sequence-read trait

---
 Cargo.toml      |  2 +-
 src/io/fastq.rs | 20 ++++++++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/Cargo.toml b/Cargo.toml
index b13aac93fe..09ead39de9 100644
--- a/Cargo.toml
+++ b/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"
diff --git a/src/io/fastq.rs b/src/io/fastq.rs
index b867aeca8a..37502570c4 100644
--- a/src/io/fastq.rs
+++ b/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> {