Merge branch 'master' into newick

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "bio-types"
-version = "0.8.0-alpha.0"
+version = "0.9.1-alpha.0"
 authors = ["Johannes Köster <johannes.koester@tu-dortmund.de>"]
 description = "A collection of common biomedical types for use in rust-bio and rust-htslib."
 homepage = "https://rust-bio.github.io"

src/lib.rs

@@ -18,6 +18,5 @@ pub mod genome;
 #[cfg(feature = "phylogeny")]
 pub mod phylogeny;
 pub mod sequence;
-pub mod sequencing;
 pub mod strand;
 pub mod variant;

src/sequence.rs

@@ -1,3 +1,12 @@
+// Copyright 2021 Johannes Köster.
+// Licensed under the MIT license (http://opensource.org/licenses/MIT)
+// This file may not be copied, modified, or distributed
+// except according to those terms.
+
+#[cfg(feature = "serde")]
+use serde::{Deserialize, Serialize};
+use strum_macros::{AsRefStr, Display};
+
 /// A DNA base
 pub type Base = u8;
 /// An amino acid
@@ -10,5 +19,33 @@ pub trait SequenceRead {
     fn base(&self, i: usize) -> u8;
     fn base_qual(&self, i: usize) -> u8;
     fn len(&self) -> usize;
-    fn is_empty() -> bool;
+    fn is_empty(&self) -> bool;
+}
+
+/// Representation of sequence read pair orientation
+/// (e.g. F1R2 means that the forward read comes first on the reference contig,
+/// followed by the reverse read, on the same contig).
+///
+/// This enum can be pretty-printed into a readable string repesentation:
+///
+/// ```rust
+/// use bio_types::sequence::SequenceReadPairOrientation;
+///
+/// // format into string
+/// println!("{}", SequenceReadPairOrientation::F1R2);
+/// // obtain string via `AsRef<&'static str>`
+/// assert_eq!(SequenceReadPairOrientation::R1F2.as_ref(), "R1F2");
+/// ```
+#[derive(Debug, Clone, Copy, PartialEq, Eq, AsRefStr, Display)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+pub enum SequenceReadPairOrientation {
+    F1R2,
+    F2R1,
+    R1F2,
+    R2F1,
+    F1F2,
+    R1R2,
+    F2F1,
+    R2R1,
+    None,
 }