add read pair orientation (#25)

* add read pair orientation

* fixes

* fix serde derive

* add missing use

* fmt

Author: johanneskoester

Cargo.lock

@@ -18,3 +18,4 @@ quick-error = "1.2"
 regex = "1.0"
 lazy_static = "1.1"
 derive-new = "0.5"
+strum_macros = "0.20"

Cargo.toml

@@ -13,5 +13,6 @@ pub mod alignment;
 pub mod annot;
 pub mod genome;
 pub mod sequence;
+pub mod sequencing;
 pub mod strand;
 pub mod variant;

src/lib.rs

@@ -0,0 +1,8 @@
+// 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.
+
+//! This module provides types useful for investigating sequencing data.
+
+pub mod read_pair_orientation;

src/sequencing/mod.rs

@@ -0,0 +1,39 @@
+// 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.
+
+//! This module provides a representation for read pair orientation, which is
+//! a readout of read mapping.
+
+#[cfg(feature = "serde")]
+use serde::{Deserialize, Serialize};
+use strum_macros::{AsRefStr, Display};
+
+/// Representation of 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::sequencing::read_pair_orientation::ReadPairOrientation;
+///
+/// // format into string
+/// println!("{}", ReadPairOrientation::F1R2);
+/// // obtain string via `AsRef<&'static str>`
+/// assert_eq!(ReadPairOrientation::R1F2.as_ref(), "R1F2");
+/// ```
+#[derive(Debug, Clone, Copy, PartialEq, Eq, AsRefStr, Display)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+pub enum ReadPairOrientation {
+    F1R2,
+    F2R1,
+    R1F2,
+    R2F1,
+    F1F2,
+    R1R2,
+    F2F1,
+    R2R1,
+    None,
+}